from:"Eric Deutsch"

RE: [spctools-discuss] How to assess quality of assembly of unmapped reads ?

2024-02-05 Thread 'Eric Deutsch' via spctools-discuss

Hi, it sounds like you question is related to DNA sequencing, not
proteomics. The TPP tools are designed for mass spectrometry proteomics,
not for DNA/RNA sequencing. Let me know if I’ve misunderstood.

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Tuan Anh Nguyen Van
*Sent:* Sunday, January 28, 2024 10:32 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] How to assess quality of assembly of unmapped
reads ?

Hello everyone,

I am going to construct the rice pangenome based on an iterative assembly
approach.

Based on this approach, I am planning to use paired-end read sequencing
data. I will map the paired-end reads to the reference genome and extract
the unmapped reads. Then, I will perform the de novo assembly for extracted
unmapped reads into novo contigs.

When I finish assembling unmapped reads, I am going to check the
contamination and redundant contigs in my assembled sequence and remove
these contaminated sequences before I add these novo contigs into the
pangenome. I plan to use FCS-GX to detect the contamination.

The newly assembled sequenced will be added to the current reference genome
to generate the entire pangenome.

But I am not clear, *how to assess the quality of the assembly of unmapped
reads ?*

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RE: [spctools-discuss] Feature request for LIBRA

2023-10-06 Thread 'Eric Deutsch' via spctools-discuss

Hi Debojyoti, we will see if we see if we can add that feature to Libra,
but you’re probably best off exporting the data from Libra to MSstatsTMT,
which you cite below, itself. It has many nice features in addition to
normalization, and so a good workflow would be to compute the raw TMT
values with Libra and then export to MSstatsTMT and do all your
normalization and comparisons there.

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Debojyoti Pal
*Sent:* Monday, October 2, 2023 9:57 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Feature request for LIBRA

Dear TPP team

I would like to point out that one of the most important aspects of
iTRAQ/TMT quantification is proper normalization. Many studies have
demonstrated the crucial importance of global spectrum level normalization
i.e. normalization of the whole data by the respective total intensity of
each channel (Huang et al., 2020, Mol Cell Proteomics 19(10), 1706–1723).
Unfortunately, this very simple normalization is missing in LIBRA.

I would request the TPP team to please incorporate this feature in the
LIBRA tool, so that intensity of each channel can be normalized with
respect to the total intensity of each channel. For example, if total
intensity of channel A is 10 and channel B is 12, then each reading
in channel B should be multiplied by 10/12.

Please incorporate this feature into the tool. It will dramatically
increase the accuracy of quantification when we compare it to validation
methods. Multiple studies have already pointed this out.

Regards

Debojyoti

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RE: [spctools-discuss] Optimal hardware for TPP server?

2023-10-05 Thread 'Eric Deutsch' via spctools-discuss

Hi Will, thanks for the question. There no easy answer. An SSD is good
because there’s a lot of disk I/O processing data. Comet itself is pretty
thrifty with memory, so you won’t need lots of memory for Comet. The
Prophets can use a lot of memory if you process huge experiments at once,
although they can often be broken up into pieces. Many of our cluster nodes
have only 96 GB of RAM and do fine for most datasets. I would probably
spend more on cores than on RAM. The machine you list there with 64 cores
and 128 GB is a good choice. If you can spend more than that, I think I
would increase the core count over more than 128 GB. A GPU won’t help for
Comet and the Prophets, so I would save money and go without the GPU.

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Will Comstock
*Sent:* Wednesday, October 4, 2023 10:57 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Optimal hardware for TPP server?

Hi all,

Kind of a naive tech question, but my lab is going to purchase a Linux
server to run the TPP and we're trying to decide on a hardware
configuration that would let us run Comet, PeptideProphet, PTM Prophet,
XPRESS, Libra, and a few other modules at robust speeds.

We currently run the TPP locally on a Windows PC with 64 cores (AMD
Threadripper 3990X) and 128gb of RAM running on an SSD. Would a stronger
CPU or more RAM (or even a GPU) give us any significant boost in search
speeds if we're running a Docker image of the TPP on a Linux server?

Thank you!

-Will

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RE: [spctools-discuss] Re: Next proteomics informatics course?

2023-06-27 Thread 'Eric Deutsch' via spctools-discuss

Hi everyone thanks, for the enthusiasm! We did discuss the options for this
internally and then neglected to follow up. We are thinking a 3-day
intensive course, covering all the major tools. I have set up a when2meet
poll here:

https://www.when2meet.com/?20466072-PAwWw

Please add your name (ignore the password) and then click and drag dates
that you would find suitable to attend the course. (the times are not
really relevant, just select the whole hour).

It is not binding, but helps us try to find a time that fits with most of
the people who are keen on attending the course.

It’s super easy, so please do it by the end of the week, and then we’ll try
to announce the dates rapidly if there’s enough interest. Please forward
this message to anyone you think would be interested in it!

Thanks!

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Reza Assalkhou
*Sent:* Tuesday, June 27, 2023 8:10 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Re: Next proteomics informatics course?

It will be great with a proteomics informatics course!

On Tuesday, June 27, 2023 at 5:57:48 PM UTC-7 Jimmy Eng wrote:

Any plans to offer another TPP course? A user emailed me about the course
so I came here to see if there was any info on a future course and saw this
post w/o a reply yet.

On Monday, June 12, 2023 at 9:52:33 AM UTC-7 suzmcde...@gmail.com wrote:

Hi there-is there a plan to run the proteomics informatics course again in
Seattle? I attended a few years ago, but it would be great for some new lab
members to attend too. Thanks!

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RE: [spctools-discuss] SSL problem

2023-03-27 Thread 'Eric Deutsch' via spctools-discuss

Hi Felipe, we just updated our servers to https with SSL since that seems
to be the standard now, and I think this is problem related to that.

Would you try to see if this URL works:

https://tppms.systemsbiology.net/tools/ptm/Ferries2017.zip

thanks,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *felipe velasquez
*Sent:* Monday, March 27, 2023 8:47 AM
*To:* spctools-discuss@googlegroups.com
*Subject:* [spctools-discuss] SSL problem

I am trying to perform the tutorial for PTMs, but when I use the URL for
'fetchDataset', Petunia sends me an error message:

The message is about a SSL connection... but I don´t Know how to solve it

I need Help

Thanks

Felipe Ignacio Velásquez Salinas

Bioquímico

Doctor en Microbiología

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Re: [spctools-discuss] MSFragger param

2023-02-21 Thread 'Eric Deutsch' via spctools-discuss

ah, I see, okay, sure, I put one here:

http://www.tppms.org/tmp/msfragger.params



On Tue, Feb 21, 2023 at 9:42 PM Priti Panchal 
wrote:

> Sir
> I need to upload the file at the "MSFragger search" step in TPP. I tried
> using the link sent above but could not get one. It would be a great help
> if you could share the text file of the parameter.
> Thank you
> Priti
> PhD Scholar
> Animal Biotechnology Centre, NDRI
> Karnal
>
>
> On Wed, Feb 22, 2023 at 10:05 AM 'Eric Deutsch' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> MSFragger itself can generate one for you, just run something like:
>>
>>
>>
>> /usr/bin/java -jar msfragger-3.2.one-jar.jar --config closed
>>
>> mv closed_fragger.params msfragger.params
>>
>>
>>
>>
>>
>>
>>
>> *From:* spctools-discuss@googlegroups.com <
>> spctools-discuss@googlegroups.com> *On Behalf Of *Priti Panchal
>> *Sent:* Tuesday, February 21, 2023 8:32 PM
>> *To:* spctools-discuss@googlegroups.com
>> *Subject:* [spctools-discuss] MSFragger param
>>
>>
>>
>> Hello all
>>
>> I need to run my file through the MSFragger pipeline in TPP. Can anyone
>> share an MSFragger param file with me?
>>
>> Thanks and Regards
>>
>> Priti
>>
>> PhD Scholar
>>
>> Animal Biotechnology Centre, NDRI
>>
>> Karnal
>>
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>> <https://groups.google.com/d/msgid/spctools-discuss/CANdSM59O81qiZHaU-L0_qQYzLr3O5Hi-bFCkMu_sH2Y6eWb%2B1Q%40mail.gmail.com?utm_medium=email_source=footer>
>> .
>>
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>> .
>>
>

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RE: [spctools-discuss] MSFragger param

2023-02-21 Thread 'Eric Deutsch' via spctools-discuss

MSFragger itself can generate one for you, just run something like:



/usr/bin/java -jar msfragger-3.2.one-jar.jar --config closed

mv closed_fragger.params msfragger.params







*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Priti Panchal
*Sent:* Tuesday, February 21, 2023 8:32 PM
*To:* spctools-discuss@googlegroups.com
*Subject:* [spctools-discuss] MSFragger param



Hello all

I need to run my file through the MSFragger pipeline in TPP. Can anyone
share an MSFragger param file with me?

Thanks and Regards

Priti

PhD Scholar

Animal Biotechnology Centre, NDRI

Karnal

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.

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RE: [spctools-discuss] TMT pro-16plex Libra Condition file

2022-09-27 Thread 'Eric Deutsch' via spctools-discuss

Upgrading to TPP 6.1.0 is definitely recommended, however, as there are
many additional benefits to upgrading than just more TMT channels:

http://tools.proteomecenter.org/wiki/index.php?title=TPP:6.1.0_Release_Notes

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Aarthie Senathirajah
*Sent:* Tuesday, September 27, 2022 8:31 AM
*To:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] TMT pro-16plex Libra Condition file

Thank you Yasir!

On Tue, 27 Sept 2022 at 11:29, Yasir Ahmed wrote:

Hi Aarthie,

You would need a more recent version of the TPP to output a 16-plex
condition file from the GUI. I've attached one here for you, but make sure
the parameter settings match your run setup.

Cheers,

Yasir

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On Sep 27, 2022, at 11:06 AM, Aarthie Senathirajah <
animallover@gmail.com> wrote:

I was wondering if anyone had an example of a condition file for for TMT
16-plex sets, there isn't an option on the TPP GUI it just goes up to 11
plex. Any help would be appreciated.

Thank you,

Aarthie

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RE: [spctools-discuss] Install without reboot?

2022-09-08 Thread 'Eric Deutsch' via spctools-discuss

Hi Will, excellent, thanks for posting the final tested solution!

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Will Comstock
*Sent:* Thursday, September 8, 2022 12:38 PM
*To:* spctools-discuss
*Subject:* Re: [spctools-discuss] Install without reboot?

Hi Eric,

Your advice worked! For the record, I did the following:

1. Installed the TPP v6.1 on the PCs running Windows 10
2. Entered directory C:/TPP/bin
3. Ran "tpptray.bat"
4. Clicked the TPP in the Windows tray and clicked "Start TPP web server"
5. Opened Petunia successfully

I appreciate your prompt help with this,

-Will

On Thursday, September 8, 2022 at 2:32:17 PM UTC-4 Eric Deutsch wrote:

Hi Will, I think the answer is yes, although I’d need to test on a fresh
computer for the exact protocol. I think you can launch the TPP Tray app
and then use that to start Apache and then you’re good to go. Is this for
Windows computers?

Eric

*From:* spctools...@googlegroups.com *On
Behalf Of *Will Comstock
*Sent:* Thursday, September 8, 2022 7:44 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Install without reboot?

I'm teaching a small mass spec course and I have a TPP demonstration
planned for the students, but unfortunately the institute computers wipe
upon restart. Is there any way for the students to install the TPP and
access the Petunia interface without having to reboot the computers? Can
the TPP be installed on and run from a USB drive instead of the computer
itself?

Thanks,

-Will Comstock

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RE: [spctools-discuss] Install without reboot?

2022-09-08 Thread 'Eric Deutsch' via spctools-discuss

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Will Comstock
*Sent:* Thursday, September 8, 2022 7:44 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Install without reboot?

Thanks,

-Will Comstock

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RE: [spctools-discuss] Comet parameters

2022-07-26 Thread Eric Deutsch

I’m not certain I understand your question. If you’re looking for a
template X!Tandem params file, there should be one in your installation in
the data/params folder. There should be a tandem_params.xml? In the same
folder as the template comet.params? Do you have that?



Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Anju Nagpal
*Sent:* Monday, July 25, 2022 10:33 PM
*To:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Comet parameters



Can i get the parameter list for Tandem search?

With regards
Anju Nagpal
PhD Scholar
Animal Biotechnology Centre
National Dairy Research Institute, Karnal




On Tue, 26 Jul 2022, 11:01 am 'Eric Deutsch' via spctools-discuss, <
spctools-discuss@googlegroups.com> wrote:

Correct, if you did not use iodoacetamide, then change it to 0.0





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Anju Nagpal
*Sent:* Monday, July 25, 2022 9:35 PM
*To:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Comet parameters



What if my experiment does not include any alkylation step?

Do I need to change it to 0?



On Mon, Jul 25, 2022 at 8:26 PM 'Eric Deutsch' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

Since Cys is almost always alkylated with iodoacetamide in most experiments:



http://www.unimod.org/modifications_view.php?editid1=4





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Anju Nagpal
*Sent:* Monday, July 25, 2022 1:59 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Comet parameters



Hi,

Why is a default value of 57.021464 is added for cysteine in comet
parameter?

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RE: [spctools-discuss] Comet parameters

2022-07-25 Thread 'Eric Deutsch' via spctools-discuss

Correct, if you did not use iodoacetamide, then change it to 0.0





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Anju Nagpal
*Sent:* Monday, July 25, 2022 9:35 PM
*To:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Comet parameters



What if my experiment does not include any alkylation step?

Do I need to change it to 0?



On Mon, Jul 25, 2022 at 8:26 PM 'Eric Deutsch' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

Since Cys is almost always alkylated with iodoacetamide in most experiments:



http://www.unimod.org/modifications_view.php?editid1=4





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Anju Nagpal
*Sent:* Monday, July 25, 2022 1:59 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Comet parameters



Hi,

Why is a default value of 57.021464 is added for cysteine in comet
parameter?

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RE: [spctools-discuss] Comet parameters

2022-07-25 Thread 'Eric Deutsch' via spctools-discuss

Since Cys is almost always alkylated with iodoacetamide in most experiments:



http://www.unimod.org/modifications_view.php?editid1=4





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Anju Nagpal
*Sent:* Monday, July 25, 2022 1:59 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Comet parameters



Hi,

Why is a default value of 57.021464 is added for cysteine in comet
parameter?

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RE: [spctools-discuss] Re: TPP 6.1.0 Release is now available

2022-06-07 Thread Eric Deutsch

Hi Malcolm, thank you for the corrections, the page is now updated. Let me
know if you find any other problems.



http://tools.proteomecenter.org/wiki/index.php?title=TPP_6.1.0:_Installing_on_Ubuntu_20.04_LTS



Thanks!

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Malcolm Cook
*Sent:* Tuesday, June 7, 2022 7:50 PM
*To:* spctools-discuss 
*Subject:* Re: [spctools-discuss] Re: TPP 6.1.0 Release is now available



Hi David,



Indeed, the svn link I took from these instructions

is
incorrect (and probably should be amended), while the link you advise (and
appearing above in the announcement) is correct.



BTW - I would offer to amend them myself but am unable to see if I am
allowed to have an account on the wiki - seemingly not.



FWIW - I do now find that downloading and expanding the tarball is many
times faster then using svn, so I will prefer it going forward.

Thanks,



~Malcolm



On Tuesday, June 7, 2022 at 5:53:04 PM UTC-5 David Shteynberg wrote:

Hi Malcolm,



Thanks for your interest in the TPP.

I think your url has a mistake in it.  Please try the following command:



svn checkout http://svn.code.sf.net/p/sashimi/code/tags/release_6-1-0




Cheers,

-David



On Tue, Jun 7, 2022 at 3:44 PM Malcolm Cook  wrote:

Hi,



I am checking out again from the release_6.1.0 since my `make all` is
problematic, I want to start over, and `make clean` seems perhaps
incomplete in its cleaning.



Alas I encounter this error whose workaround I can not guess:



svn checkout http://svn.code.sf.net/p/sashimi/code/tags/release_6.1.0
svn: E17: URL 'http://svn.code.sf.net/p/sashimi/code/tags/release_6.1.0'
doesn't exist



On Tuesday, June 7, 2022 at 12:37:31 AM UTC-5 Luis wrote:

Hi Malcolm,

Thank you for the congrats, and for catching that in our build notes; we
will correct it soon.  In the "Pulling from Sourceforge" section, just
follow the commented-out command instead of the last one:

#svn checkout http://svn.code.sf.net/p/sashimi/code/tags/release_6.1.0
<- this one; remove the leading pound sign

svn checkout 
http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline
  < not this one



As of tonight, though, the trunk code is still virtually identical to what
is tagged as release_6.1.0, so it should work fine.



Let us know if you run into any other issues.



Thank you for using TPP!

--Luis





On Mon, Jun 6, 2022 at 10:04 PM malcook  wrote:

Congrats on the new release.



You will probably want to modify these instructions
which
still advise to download from trunk.



I just followed  them.



Should I still expect this to work satisfactorily?



Thanks

On Friday, June 3, 2022 at 3:23:19 AM UTC-5 Luis wrote:

Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.1.0
"Parhelion"

We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP)
software, release 6.1.0.  The software is available for Windows as well as
Linux from all the usual locations (please see the section below, "Getting
the TPP Software").  Most users are recommended to use the Windows
installer, which installs and configures TPP and other required software,
such as a web server.  For advanced users who need to customize TPP, or for
those who run on Linux or OS X, the source code can be downloaded.


*Release Notes *
Release notes on the most important new features, changes, and known issues
are available at:

http://tools.proteomecenter.org/wiki/index.php?title=TPP:6.1.0_Release_Notes


*Getting the TPP Software*

Download the TPP version 6.1.0 native windows installer from the Sashimi
SourceForge project file release page:

 https://sourceforge.net/projects/sashimi/files/Trans-Proteomic Pipeline
(TPP)/TPP v6.1 (Parhelion) rev 0/


Everyone is encouraged to read and contribute to our wiki, at
  http://tools.proteomecenter.org/wiki/

For guides to installing and using our software, please see our wiki:
  http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP

For downloading the source code, please go to the following link:
  http://sourceforge.net/projects/sashimi/files/  and find the 6.1.0 source
code .zip package
or, check out the code directly from svn:
  svn export svn://svn.code.sf.net/p/sashimi/code/tags/release_6-1-0

For building from source, please refer to the README and INSTALL files in
src/ directory of TPP as well as the wiki.


*Acknowledgements*
The TPP Team: David, Luis, Mike, Eric, Jimmy, plus all other developers who
contributed to this release from ISB.  Thanks to developers and users from
the TPP's user community who also provided feedback and code contributions.

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RE: [spctools-discuss] Error 256 Convert raw to mzML

2022-04-06 Thread 'Eric Deutsch' via spctools-discuss

Hi, the problem is that the version of msconvert that you are using does
not know how to recognize your model of the Eclipse instrument. You could
specify the ignoreUnknownInstrumentError flag to ignore that problem. A
better solution is to download the latest ProteoWizard toolkit and use that
version of msconvert (you could also copy it to the TPP bin folder to
replace your version of TPP’s older version.)

We hope to release TPP 6.1 in a few weeks and this will include an updated
version of msconvert that will not have this problem.

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Jingyi Hu
*Sent:* Friday, April 1, 2022 7:47 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Error 256 Convert raw to mzML

Dear all,

I'm sorry to bother you. I was trying to convert my .raw file to .mzML file
using guest account and I encountered an error.

It showed like followings:

unable to parse instrument model; please report this error to the
ProteoWizard developers with this information: model(Orbitrap Eclipse)
name(Orbitrap Eclipse); if want to convert the file anyway, use the
ignoreUnknownInstrumentError flag

What should I do to fix the problem?

Thank you so much and all the best!

Jingyi Hu

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RE: [spctools-discuss] Error in converting .raw file to .mzml file

2022-04-06 Thread 'Eric Deutsch' via spctools-discuss

We hope to release TPP 6.1 in a few weeks and this will include an updated
version of msconvert that will not have this problem.

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Jingyi Hu
*Sent:* Friday, April 1, 2022 7:56 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Error in converting .raw file to .mzml file

Dear all,

I'm sorry to bother you. I was trying to convert my .raw file to .mzML file
and there reported a return code 256. It showed the followings:

What should I do to fix it?

Thank you and all the best!

Jingyi Hu

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RE: [spctools-discuss] Set number of cores/threads/RAM in SpectraST?

2021-12-03 Thread Eric Deutsch

Hi Philip, while I am not completely certain, I don’t think SpectraST has
any options for multi-threaded execution in the library import/conversion
steps. I recall Henry saying in the past that these operations tend to be
I/O bound mostly so multi-threading wouldn’t help very much? Maybe that was
true when disks were slower than today. Since you have so much RAM, you
might consider setting up a RAM disk:

https://en.wikipedia.org/wiki/List_of_RAM_drive_software

to see if that speeds things up considerably? Maybe not for the reading so
much as the writing? Read from an SSD and write to the RAM disk?

That may not help a lot, but it’s the only thing I can think of at the
moment. Maybe Henry has other ideas?

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Philip Gerth
*Sent:* Thursday, December 2, 2021 7:09 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Set number of cores/threads/RAM in SpectraST?

Good evening,

I am using SpectraST for creating a spectral library out of a 71 GB
msp.file, which lead to a very long remapping step. Like 4 days for 10 %
progress. The PC I am using has an available 350 GB RAM, but it only runs
with a fraction of the possible power ~ 10 GB. It also only uses 2 of 9
available cores.

I have seen that there are options for Comet and X!Tandem to increase the
processing speed, like “spectrum,threads, so My question is, are there any
ways to do the same for SpectraST? Or is there a specific limit for the
performance level for SpectraST?

Thank you in advance

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RE: [spctools-discuss] Re: Max input file size limit for comet search?

2021-09-17 Thread Eric Deutsch

I’m thinking that a very large mzXML file with “UDMSE” in it might be DIA
data, and thus Comet is not the right tool? Could this be MS^e data instead
of DDA data?

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Jason Winget
*Sent:* Friday, September 17, 2021 10:02 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Re: Max input file size limit for comet
search?

Hi Steven, what do your comet parameters look like?

I'm not sure if this is the problem, but for files with many scans it is
good to set the `spectrum_batch_size` parameter to something reasonable,
like 1. The instructions are found in the "fragment ions" comments
section of the default parameters file.

On Friday, September 17, 2021 at 1:58:10 AM UTC-4 steven...@gmail.com wrote:

Hi,

I'm a fairly new user to TPP and this sort of analysis in general and had a
question about input file sizes during Comet Search.

I have downloaded some MS data from a publication via an online database
in .mzXML format (the .raw files weren't provided) and have been trying to
run a peptide database search using the Comet software with the default
param settings. However I consistently get the message "Warning - no
spectra searched" and no output file is created (screenshot attached). The
mzXML file itself is actually quite large (~26GB) and I was wondering if
the size of the input file itself might be the issue? In the case where the
input files would be quite large, is there a potential workaround?

Apololgies if I've left out any critical information here

Thanks in advance,

Steven

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RE: [spctools-discuss] tpp2mzid help - 'no peptide evidence found ...'

2021-06-21 Thread Eric Deutsch

I have not yet created a container for 6 but I should. I could try to do
that soon if there is demand to use it/test it.



Thanks,

Eric





*From:* 'Alastair Skeffington' via spctools-discuss <
spctools-discuss@googlegroups.com>
*Sent:* Monday, June 21, 2021 8:59 AM
*To:* spctools-discuss 
*Subject:* Re: [spctools-discuss] tpp2mzid help - 'no peptide evidence
found ...'



Hi Mike,



Thanks for getting back to me so quickly. Here's the database:
https://we.tl/t-wZsZ3uSq1r



Is version 6 available as a container? I've never managed to install TPP
properly on a linux machine ...



Alastair

On Monday, 21 June 2021 at 17:50:24 UTC+2 mhoo...@systemsbiology.org wrote:

Hi Alastair,

There is a much newer version of tpp2mzid in our current release candidates
of TPP version 6. I’m hoping that the error messages have been resolved in
this new version. However, I also need the fasta search database file to
run the conversion with the newer tpp2mzid. Could you also provide a link
to that file and I will finish my tests and let you know the result?

Thanks,

Mike



*From:* 'Alastair Skeffington' via spctools-discuss <
spctools...@googlegroups.com>
*Sent:* Monday, June 21, 2021 6:45 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] tpp2mzid help - 'no peptide evidence found
...'



I'm at the end of a multi-year odyssey of a project, and I just need to
submit data to PRIDE.



Unfortunately, when I run tpp2mzid for some prot.xml files, I get an error
such as this:



Warning (A), no peptide evidence found for (mod): EENAFVQKIAE from
Br20418.t2



This only happens for some prot.xml files, but I'm not sure why. The
pep.xml files from which the prot.xml are derived convert fine.



I've put an example here: https://we.tl/t-Z9qNNjDC0k



I was running TPP via the docker
container: digitalproteomes/tpp:version-5.2.0.1



Here is the stdout in full:

Reading: HCLC_EhN.prot.xml

Reading: /data/HCLC_EhN_ipro.pep.xml

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

17648 psms read.

Warning (A), no peptide evidence found for (mod): EENAFVQKIAE from
Br20418.t2



Help would be very much appreciated!

Thanks,

Alastair

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RE: [spctools-discuss] Re: Exporting StPeter´s ng to mzid

2021-05-10 Thread Eric Deutsch

I should add that mzQuantML is almost universally unsupported and is not
recommended.

mzTab is the PSI format recommended for quant data:

https://pubmed.ncbi.nlm.nih.gov/24980485/

FYI, there is an effort underway to design an improved mzTab 2.0, but it is
a long ways off.

Eric

*From:* Eric Deutsch
*Sent:* Monday, May 10, 2021 2:42 PM
*To:* spctools-discuss@googlegroups.com
*Cc:* Eric Deutsch
*Subject:* RE: [spctools-discuss] Re: Exporting StPeter´s ng to mzid

Hi Valdemir, the tpp2mzid is indeed the preferred and recommended tool, not
idconvert.

I think the problem quite simply is that mzIdentML is not capable of
handling quant data. mzIdentML is designed only for identifications.
mzQuantML and mzTab are designed for quant data. So, no tool can or should
put quant data in mzIdentML.

https://pubmed.ncbi.nlm.nih.gov/22375074/

https://pubmed.ncbi.nlm.nih.gov/23599424/

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *mele...@gmail.com
*Sent:* Monday, May 10, 2021 2:30 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Re: Exporting StPeter´s ng to mzid

Thanks for your suggestion Jason,

StPeter´s quantifiers have been written in ProtXML but apparently are not
included in mzid.

Unfortunately, idconvert is returning Error writing analysis 1:
[Config::outputFilename] no spectraData elements (I´ll report this error...)

I´ve tried two Proteowizad versions including the latest one.

Does anyone know a way to incorporate them in mzid?

Thanks

Valdemir

Em sábado, 8 de maio de 2021 às 12:57:58 UTC-3, jwi...@gmail.com escreveu:

StPeter writes the quantification results back to the ProtXML. Have you
tried using idconvert from Proteowizard to convert the ProtXML to mzID?
http://proteowizard.sourceforge.net/tools/idconvert.html

On Friday, May 7, 2021 at 8:03:11 PM UTC-4 mele...@gmail.com wrote:

Hello,

How can I include StPeter´s quantifier (ng) during conversion from
prot.xml to mzid?

Is there some tpp2mizd parameter?

Thanks

Valdemir

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RE: [spctools-discuss] Re: Exporting StPeter´s ng to mzid

2021-05-10 Thread Eric Deutsch

Hi Valdemir, the tpp2mzid is indeed the preferred and recommended tool, not
idconvert.

https://pubmed.ncbi.nlm.nih.gov/22375074/

https://pubmed.ncbi.nlm.nih.gov/23599424/

Regards,

Eric

Thanks for your suggestion Jason,

StPeter´s quantifiers have been written in ProtXML but apparently are not
included in mzid.

Unfortunately, idconvert is returning Error writing analysis 1:
[Config::outputFilename] no spectraData elements (I´ll report this error...)

I´ve tried two Proteowizad versions including the latest one.

Does anyone know a way to incorporate them in mzid?

Thanks

Valdemir

Em sábado, 8 de maio de 2021 às 12:57:58 UTC-3, jwi...@gmail.com escreveu:

On Friday, May 7, 2021 at 8:03:11 PM UTC-4 mele...@gmail.com wrote:

Hello,

How can I include StPeter´s quantifier (ng) during conversion from
prot.xml to mzid?

Is there some tpp2mizd parameter?

Thanks

Valdemir

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RE: [spctools-discuss] Re: convert Splib

2021-04-13 Thread Eric Deutsch

You can convert the sptxt format to msp with:

rename mylibrary.sptxt mylibrary.msp

sptxt and msp are effectively the same thing. There is no specification on
exactly what msp is and it has evolved a little over time, and sptxt is
essentially the same as one of the variations.

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Wenguang
*Sent:* Tuesday, April 13, 2021 1:30 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Re: convert Splib

Hi Ben,

I think you can convert a spectral library in the format of sptxt into msp.
However, you may need to write your own simple script to perform this
text-based conversion.

Best regards,

Wenguang

On Friday, February 12, 2021 at 6:09:37 PM UTC+1 benoit@gmail.com wrote:

Hello,

I was wondering if it was possible to either generate spectral libraries in
another format than Splib or maybe to convert the produced splib into
another format such as msp.

I couldn't find anything about that.

Thanks a lot,

Ben

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RE: [spctools-discuss] Endogenous peptide identification

2020-12-10 Thread 'Eric Deutsch' via spctools-discuss

Hi Sud, I think you can just use this parameter with Comet:

search_enzyme_number = 0 # choose from list at end of this
params file

where 0 is defined at the bottom of the comet.params:

[COMET_ENZYME_INFO]

0. Cut_everywhere 0 - -

1. Trypsin1 KR P

This tends to be a very computationally expensive search, so limiting your
sequence database to a modest size would be beneficial.

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *sudarshan kumar
*Sent:* Thursday, December 10, 2020 2:11 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Endogenous peptide identification

Dear members,

I am new to this group. Can anyone help me get a standard refined search
parameters either in comet or tandem or in any other search engine to
identify endogenous peptides.

1. These peptides have not been cleaved by any enzyme

2. Modification are typically not as those which happen during trypsin
digestion.

3. Is FDR <1% in decoy search good in this case?

Please reply if you have any clues.

Reg,

sud

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RE: [spctools-discuss] maximum fasta file size

2020-10-21 Thread 'Eric Deutsch' via spctools-discuss

Hi Aziz, I can’t give an estimate because it depends on so many things. How
many spectra? Fully tryptic, semi-trypic? How many PTMs? Are you using
Comet? How many cores/threads does your machine have/did you let Comet use?
Etc. If you use Comet, you can usually look at the output to see its
progress. You should see something like:

Search start: 09/29/2020, 10:35:28 AM

- Load spectra: 15009

- Search progress: 29%

- Post analysis: done

- Load spectra: 15009

- Search progress: 54%

Etc.

To get a sense of how quickly progress is being made.

Also, check the RAM usage on your machine to make sure the computer isn’t
swapping due to low memory conditions.

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *AZIZ ALNAKLI
*Sent:* Wednesday, October 21, 2020 8:45 PM
*To:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] maximum fasta file size

Thanks Eric for your reply.

The database I am having is in a single file that is over 10 GB in size. It
has been almost 24 hrs since I got the job run, and it is still running.

Do you have a suggestion on the timeframe of jobs dealing with such huge
files?

Thanks. Regards.

On Thu, Oct 22, 2020 at 3:46 AM 'Eric Deutsch' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

Hi Aziz, there is no specific maximum size. In general, the larger your
database, the greater the memory requirements and CPU time needed for the
software tools and the lower your sensitivity, although it depends on the
degree of redundancy in your database. Hundreds of MB and hundreds of
thousands of protein sequences is routine.

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *AZIZ ALNAKLI
*Sent:* Tuesday, October 20, 2020 9:15 PM
*To:* spctools-discuss@googlegroups.com
*Subject:* [spctools-discuss] maximum fasta file size

what is the maximum fasta file size that TPP can handle?

Anyone knows?

Thank you all.

*Aziz Alnakli*

Master of Research Candidate (Bioinformatics Research Group)

*Faculty of Science and Engineering** | * Level 1 Room 120, F7B Building
(4 Wally's Walk)
Macquarie University, NSW 2109, Australia

*M:* + 61 424375954* | **aziz.alna...@students.mq.edu.au
*

[image: Image removed by sender. Macquarie University] <http://mq.edu.au/>

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*Aziz Alnakli*

Master of Research Candidate (Bioinformatics Research Group)

*Faculty of Science and Engineering** | * Level 1 Room 120, F7B Building
(4 Wally's Walk)
Macquarie University, NSW 2109, Australia

*M:* + 61 424375954* | **aziz.alna...@students.mq.edu.au
*

[image: Image removed by sender. Macquarie University] <http://mq.edu.au/>

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RE: [spctools-discuss] maximum fasta file size

2020-10-21 Thread 'Eric Deutsch' via spctools-discuss

what is the maximum fasta file size that TPP can handle?

Anyone knows?

Thank you all.

*Aziz Alnakli*

Master of Research Candidate (Bioinformatics Research Group)

*Faculty of Science and Engineering** | * Level 1 Room 120, F7B Building
(4 Wally's Walk)
Macquarie University, NSW 2109, Australia

*M:* + 61 424375954* | **aziz.alna...@students.mq.edu.au
*

[image: Image removed by sender. Macquarie University]

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RE: [spctools-discuss] SpectraST LibraryBuilding Decoys

2020-10-19 Thread 'Eric Deutsch' via spctools-discuss

Hi Juergen, this sounds like a sensible idea, but as far as I’m aware, this
functionality does not yet exist.

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Juergen Bartel
*Sent:* Monday, October 19, 2020 3:50 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] SpectraST LibraryBuilding Decoys

Dear all,

I am using spectraST frequently to build spectral libraries and also the
corresponding decoy libraries. Usually these libraries are build by
randomly shuffling sequences or adding amino acids to the peptide sequence.
Thus, during the downstream processing of search results with peptide or
protein prophet decoys can not be mapped to the correct protein, when using
a forward/reverse fasta file.

I was not worried about this before but, since recently started to use the
philosopher pipeline for FDR filtering on protein level, I am not sure
whether those decoy peptides will transfer correctly to the protein level?

I know that I can use the option to include unmapped peptides in the
prophets but I don't know how those peptides would be distributed to the
correct proteins? I guess the easiest way to ensure correct mapping would
be an option to export a fasta file together with the decoy generation
which includes the concatenated modified peptide sequences for each
protein. Does anyone know if such an option present in spectraST?

Best regards,

Juergen

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RE: [spctools-discuss] Re: TPP 5.2.0 installation error CentOS 7.8

2020-10-12 Thread 'Eric Deutsch' via spctools-discuss

You can get a recipe for using TPP with Docker here:

http://tools.proteomecenter.org/wiki/index.php?title=Running_the_TPP_docker_image

(or just Google for: tpp docker)

Although our main recipe for installing TPP 5.2 on Linux is for Ubuntu:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS

if someone has a recipe for CentOS, send it along to us and we’ll post it
on the wiki.

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Law
*Sent:* Sunday, October 11, 2020 7:08 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Re: TPP 5.2.0 installation error CentOS 7.8

Hi, Wenhao. Gald to know that you have solved the problem. I have met the
same error while installing the 5.2.0 TPP. So I deleted the compiled and
source file and tried everything again. Somehow it worked, the only change
was that I used chmod 777 before make all to make sure the
installation program could get access to INSTALL_DIR and TPP_DATADIR.

By the way, I wonder which docker content you used? Planning to use
docker on another cluster, installing the dependency on CentOS is really
tiring.

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RE: [spctools-discuss] Re: SpectraST: Missing modifications in decoy free library import in ProteomeDiscoverer

2020-07-10 Thread 'Eric Deutsch' via spctools-discuss

I have never tried this (importing from MS2) myself. So it works for a
spectrum with no M[147], but it fails for a spectrum with M[147]?





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *RS
*Sent:* Wednesday, July 8, 2020 9:34 AM
*To:* spctools-discuss 
*Subject:* Re: [spctools-discuss] Re: SpectraST: Missing modifications in
decoy free library import in ProteomeDiscoverer



I was trying to debug the problem using a single MS2 format Spectra. Here's
the Pastebin link  <https://pastebin.com/3Ju2C4r8>
However, I'm getting an error message while trying to build the spectrst
format library:

*C:\TPP\bin>spectrast.exe -cNSingleSpectraMet SingleSpectraMet.MS2*

*SpectraST started at Wed Jul 08 12:20:28 2020.*

*Total Run Time = 2 seconds.*

*SpectraST finished at Wed Jul 08 12:20:30 2020 with 1 error(s):*

*CREATE: Libraries to be imported have illegal formats. Exiting.*


Any help?

Thanks

On Wednesday, July 8, 2020 at 2:19:24 AM UTC-4 Eric Deutsch wrote:

I’ve never tried to import into PD, so I can’t help there. Presumably the
ADD DECOY doesn’t change things like M[147], so I also do not understand
why PD would recognize M[147] in a library with decoys but not in a library
without?





*From:* spctools...@googlegroups.com  *On
Behalf Of *RS
*Sent:* Tuesday, July 7, 2020 10:36 AM
*To:* spctools-discuss 
*Subject:* Re: [spctools-discuss] Re: SpectraST: Missing modifications in
decoy free library import in ProteomeDiscoverer



Thanks Eric,
Please let me know if you have any  remedies for the rest of the problems

On Tuesday, July 7, 2020 at 1:29:08 PM UTC-4 Eric Deutsch wrote:

Yes, M[147] is the TPP notation for oxidized methionine. The total mass of
oxidized methionine rounds to 147 Da.





*From:* spctools...@googlegroups.com  *On
Behalf Of *RS
*Sent:* Tuesday, July 7, 2020 9:38 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Re: SpectraST: Missing modifications in decoy
free library import in ProteomeDiscoverer



and I wonder why  Methionine oxidation  (*15.995* Da)   is replaced by M
[147], is that an internal code to represent that modification or something
got messed up?

On Tuesday, July 7, 2020 at 12:27:41 PM UTC-4 RS wrote:

Hello All,

I'm trying to create a spectral library from Proteome Discoverer (PD
)result files to re-import into PD  as PD accepts* sptxt* format libraries.

My workflow was as follows:

ProteomeDiscoverer 2.3 *msf * format search result files were converted to
a * blib* file. The filtered *blib* file was converted to *sp2 *format. The*
sp2* format file was finally converted to *sptxt *format library by
SpectraST.

While importing the sptxt format  file (without adding any decoy) I've seen
the amino acid modifications used  like Methionine oxidation and Cysteine
carbamidomethylation were not recognized by PD

However if I ADD DECOY to the library, followed by its import to PD , the
modifications show up in PD (see attached pics)

This is how the header info. of one such modified amino acid peptide
appears in the decoy-free library:

Name: M[147]ATALPPR/2

LibID: 329

MW: 873.4731

PrecursorMZ: 436.7366

Status: Normal

FullName: X.M[147]ATALPPR.X/2 (CID)

Comment: AvePrecursorMz=437.0325 BinaryFileOffset=10637539
FracUnassigned=0.90,4/5;0.89,17/20;0.66,1314/1631
Fullname=X.M[147]ATALPPR.X/2 Prob=1. ScanNum=2539.2539 Spec=Raw

NumPeaks: 1631

Can somebody let me know how to incorporate these modifications so that
they can be imported by ProteomeDiscoverer
Image links:

Decoy library <https://i.imgur.com/Yiz6QLt.png>


NO-Decoy library <https://i.imgur.com/1lLKlwt.png>


Thanks





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RE: [spctools-discuss] Re: SpectraST: Missing modifications in decoy free library import in ProteomeDiscoverer

2020-07-08 Thread 'Eric Deutsch' via spctools-discuss

I’ve never tried to import into PD, so I can’t help there. Presumably the
ADD DECOY doesn’t change things like M[147], so I also do not understand
why PD would recognize M[147] in a library with decoys but not in a library
without?





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *RS
*Sent:* Tuesday, July 7, 2020 10:36 AM
*To:* spctools-discuss 
*Subject:* Re: [spctools-discuss] Re: SpectraST: Missing modifications in
decoy free library import in ProteomeDiscoverer



Thanks Eric,
Please let me know if you have any  remedies for the rest of the problems

On Tuesday, July 7, 2020 at 1:29:08 PM UTC-4 Eric Deutsch wrote:

Yes, M[147] is the TPP notation for oxidized methionine. The total mass of
oxidized methionine rounds to 147 Da.





*From:* spctools...@googlegroups.com  *On
Behalf Of *RS
*Sent:* Tuesday, July 7, 2020 9:38 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Re: SpectraST: Missing modifications in decoy
free library import in ProteomeDiscoverer



and I wonder why  Methionine oxidation  (*15.995* Da)   is replaced by M
[147], is that an internal code to represent that modification or something
got messed up?

On Tuesday, July 7, 2020 at 12:27:41 PM UTC-4 RS wrote:

Hello All,

I'm trying to create a spectral library from Proteome Discoverer (PD
)result files to re-import into PD  as PD accepts* sptxt* format libraries.

My workflow was as follows:

ProteomeDiscoverer 2.3 *msf * format search result files were converted to
a * blib* file. The filtered *blib* file was converted to *sp2 *format. The*
sp2* format file was finally converted to *sptxt *format library by
SpectraST.

While importing the sptxt format  file (without adding any decoy) I've seen
the amino acid modifications used  like Methionine oxidation and Cysteine
carbamidomethylation were not recognized by PD

However if I ADD DECOY to the library, followed by its import to PD , the
modifications show up in PD (see attached pics)

This is how the header info. of one such modified amino acid peptide
appears in the decoy-free library:

Name: M[147]ATALPPR/2

LibID: 329

MW: 873.4731

PrecursorMZ: 436.7366

Status: Normal

FullName: X.M[147]ATALPPR.X/2 (CID)

Comment: AvePrecursorMz=437.0325 BinaryFileOffset=10637539
FracUnassigned=0.90,4/5;0.89,17/20;0.66,1314/1631
Fullname=X.M[147]ATALPPR.X/2 Prob=1. ScanNum=2539.2539 Spec=Raw

NumPeaks: 1631

Can somebody let me know how to incorporate these modifications so that
they can be imported by ProteomeDiscoverer
Image links:

Decoy library <https://i.imgur.com/Yiz6QLt.png>


NO-Decoy library <https://i.imgur.com/1lLKlwt.png>


Thanks





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RE: [spctools-discuss] Re: SpectraST: Missing modifications in decoy free library import in ProteomeDiscoverer

2020-07-07 Thread 'Eric Deutsch' via spctools-discuss

Yes, M[147] is the TPP notation for oxidized methionine. The total mass of
oxidized methionine rounds to 147 Da.





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *RS
*Sent:* Tuesday, July 7, 2020 9:38 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Re: SpectraST: Missing modifications in decoy
free library import in ProteomeDiscoverer



and I wonder why  Methionine oxidation  (*15.995* Da)   is replaced by M
[147], is that an internal code to represent that modification or something
got messed up?

On Tuesday, July 7, 2020 at 12:27:41 PM UTC-4 RS wrote:

Hello All,

I'm trying to create a spectral library from Proteome Discoverer (PD
)result files to re-import into PD  as PD accepts* sptxt* format libraries.

My workflow was as follows:

ProteomeDiscoverer 2.3 *msf * format search result files were converted to
a * blib* file. The filtered *blib* file was converted to *sp2 *format. The*
sp2* format file was finally converted to *sptxt *format library by
SpectraST.

While importing the sptxt format  file (without adding any decoy) I've seen
the amino acid modifications used  like Methionine oxidation and Cysteine
carbamidomethylation were not recognized by PD

However if I ADD DECOY to the library, followed by its import to PD , the
modifications show up in PD (see attached pics)

This is how the header info. of one such modified amino acid peptide
appears in the decoy-free library:

Name: M[147]ATALPPR/2

LibID: 329

MW: 873.4731

PrecursorMZ: 436.7366

Status: Normal

FullName: X.M[147]ATALPPR.X/2 (CID)

Comment: AvePrecursorMz=437.0325 BinaryFileOffset=10637539
FracUnassigned=0.90,4/5;0.89,17/20;0.66,1314/1631
Fullname=X.M[147]ATALPPR.X/2 Prob=1. ScanNum=2539.2539 Spec=Raw

NumPeaks: 1631

Can somebody let me know how to incorporate these modifications so that
they can be imported by ProteomeDiscoverer
Image links:

Decoy library 


NO-Decoy library 


Thanks





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RE: [spctools-discuss] Spectral library generation

2020-06-09 Thread 'Eric Deutsch' via spctools-discuss

Hi Srikanth, I suggest after your step “I have convert the results
individually to pepxml using Mascot2XML, Tandem2XML and Idconvert and then
apply peptideprophet on each file” (which is good), the next step is merge
the 3 PeptideProphet outputs into a single PepXML file with iProphet. Then
build your spectral library from that one file.

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Srinivas Srikanth
*Sent:* Monday, June 8, 2020 9:43 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Spectral library generation

Hi Phil,

I have a 15 hek files searched with Mascot, X!Tandem and MSGF+ separately.
I am trying to create a library using TPP pipeline and SpectraST.

I have convert the results individually to pepxml using Mascot2XML,
Tandem2XML and Idconvert and then apply peptideprophet on each file. My
question is about the next step,

Should I be merging individual search engine results using iprophet and to
make three combined files and then merge them again using iprophet?

Or I merge each run from three searches together using iprophet and then
merge the resulting 15 files together to apply ProteinProphet or Mayu ?

Srikanth

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RE: [spctools-discuss] Re: C:/TPP/bin/runsearch' is not recognized as an internal or external command

2020-06-09 Thread 'Eric Deutsch' via spctools-discuss

Sounds like an XY Problem here.

If it’s spectral clustering you want to do, and within the TPP, perhaps
consider SpectraST:

http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#Spectral_Archive_.28Unidentified_Spectral_Library.29_Building

You won’t need to fool around with DTA files and 8-track tapes.

Although the examples show mzXML files at the URL above, you should use
mzML files, of course.

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Phillip Wilmarth
*Sent:* Tuesday, June 9, 2020 8:44 AM
*To:* spctools-discuss
*Subject:* Re: [spctools-discuss] Re: C:/TPP/bin/runsearch' is not
recognized as an internal or external command

Hi Javan,

MSConvert can create MS2 format peak lists from RAW files. MS2 format is
kind of a file of concatenated DTA files. It is not too hard to convert
from one to the other. I have probably have a Python script somewhere that
makes MS2 files from folders of DTA files. I am not sure if I have one that
goes the other direction.

Cheers,

Phil

see: McDonald, W.H., Tabb, D.L., Sadygov, R.G., MacCoss, M.J., Venable, J.,
Graumann, J., Johnson, J.R., Cociorva, D. and Yates III, J.R., 2004. MS1,
MS2, and SQT—three unified, compact, and easily parsed file formats for the
storage of shotgun proteomic spectra and identifications. *Rapid
Communications in Mass Spectrometry*, *18*(18), pp.2162-2168.

On Tuesday, June 9, 2020 at 1:42:28 AM UTC-7, Javan Okendo wrote:

Thanks all for your help. I now understand why this can't work. The reason
I wanted to use SEQUEST was because the program I wanted to use only takes
.DTA file format for spectral clustering and I have looked around there is
not software which can give me these .DTA file formats.

On Tue, Jun 9, 2020 at 3:52 AM Phillip Wilmarth > wrote:

Hi Javan,

Many (many) years ago Thermo had a command line executable SEQUEST that
BioWorks called to run SEQUEST. Thermo put it inside hidden folders and
there were license key issues. You could not copy the EXE to another
machine and have it run. That scheme may have persisted for some of the
earliest Proteome Discoverer releases.

I do not think that there is still a SEQUEST.EXE associated with Proteome
Discoverer. Something made running SEQUEST from the command line break
(ancient memory cells are recalling something more...). Maybe it was a
transition to C# from C++ and command line parsing issues. I never could
get it to work. I gave up trying to run SEQUEST when Comet came out.

You can get a 60-day demo version of Proteome Discoverer from Thermo. I do
not know if you can create things like pepxml files from PD so that you
could post-process the SEQUEST searches with TPP. PD is internally all
SQLite3 relational database tables (something like 80 of them). It is
either not a very good design for the database tables or just really hard
to try and figure out (or both). You can snoop on the SQLite DB with
various tools, but a proper schema description would be helpful. Table
names and field names are not real transparent.

Cheers,

Phil

On Monday, June 8, 2020 at 3:51:50 PM UTC-7, Jimmy Eng wrote:

Javan,

You're not going to be able to run SEQUEST through the TPP unless you've
purchased the software from Thermo and have it installed on the same
computer that's running the TPP. It doesn't come with the TPP itself. And
support for the SEQUEST pipeline option should probably be removed from the
UI unless anyone can confirm that it actually still works.

On Monday, June 8, 2020 at 1:56:45 PM UTC-7, JAVAN OKENDO wrote:

I am getting the above mentioned error when running SEQUEST on TPP. I did
install the TPP correctly and when I try to run the program it gives an
error. See the screenshot with the error details

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[spctools-discuss] Trans-Proteomic Pipeline workshop at ASMS Tuesday 10am Central time

2020-06-01 Thread 'Eric Deutsch' via spctools-discuss

Hi everyone, we are hosting an ASMS workshop in the Tuesday 10am Central
timeslot tomorrow (8am Pacific, 11am Eastern). As far as we can tell, you
can only attend the workshop if you have already registered for ASMS. If
you are registered, go to your ASMS planner app (in a web browser or on
your phone), find the 10am Live Tuesday workshops, and we are:



Workshop Tues-06 Trans-Proteomic Pipeline: Recent Advances and Future
Directions



You can probably use this link:

https://eventpilot.us/web/planner.php?id=ASMS20

But you’ll need to log in with your ASMS credentials and presumably already
be registered for the conference. A hyperlink to join the webinar will
become available there when the event is about to start.



The agenda will be a discussion of these topics:

- Improved label-free quantitation with StPeter

- StPeter2Matrix for comparing many samples

- Export of TPP results to the mzIdentML format

- Spectrum-centric DIA analysis and quantitation with DISCO

- Kojak PeptideProphet support and de Bruijn decoys

- Using the Universal Spectrum Identifier in TPP



We hope to see to there!



Mike Hoopmann

David Shteynberg

Eric Deutsch

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RE: [spctools-discuss] SpectrasT can't recognize Protein N-term acetylation modification

2020-04-27 Thread 'Eric Deutsch' via spctools-discuss

Hi Ray, I suspect that SpectraST will recognize this notation:

n[42]MFLVNSFLK

N terminal modifications are shown after an n. Side-chain modifications are
shown after the residue.

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *RayS
*Sent:* Saturday, April 25, 2020 3:01 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] SpectrasT can't recognize Protein N-term
acetylation modification

I'm using SpectraST in TPP for building a splib format file from a
bibliospec MS2 format file. While converting it issues error message for
peptides with Protein N-term modifications

*"MS2 IMPORT: Peptide ID has unknown modification: "M[+42.01056]FLVNSFLK".
Skipped spectrum"*

I guess I can write this as user defined modification in a file and specify
the file name with *-M *option in the command line

*M[n]|+42.01056|Protein_N-term*

and the following command

*spectrast.exe -cNmyLib -M SpectraST_MyMod.txt myLib.ms2*

I guess the syntax I wrote is wrong because SpectraST still skips those
modifications.

Can anyone help me with the correct synatx and command please?

Thanks

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RE: [spctools-discuss] irt issue

2020-03-04 Thread 'Eric Deutsch' via spctools-discuss

Hi Srikanth, I can confirm that SpectraST supports mzML files. In fact we
always/only use mzML files.

As far as the iRT error, I am not familiar with this. I could only
speculate. Maybe Henry or David have ideas?

Thanks,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Srinivas Srikanth
*Sent:* Tuesday, March 3, 2020 4:40 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] irt issue

Hi,

I have a pepxml from iprophet combining results from Mascot/X!Tandem and
MSGF+. When I am trying to create a spectral library using Spectrast with
the following command:

spectrast -cNspeclib -cICID-QTOF -cP0.814339 -c_IRTirt.txt
-Lspectrastlog_hek.log mascot_xtandem_msgfp_combine.pep.xml

I get and error log which says RT inversion detected at iRT 68.168 for some
files and then it creates an empty splib file. Can you tell me what does
this error exactly mean?

ERROR PEPXML IMPORT: RT normalization by linear interpolation. Found 21
landmarks in MS run "170825_pc4_hek_2dcon_13". RT inversion detected at iRT
= 68.8618. No RT normalization performed.

Also, does spectrast support mzml or we always need mzXML?

Regards,

Srikanth

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[spctools-discuss] Upcoming Trans-Proteomic Pipeline (TPP) courses

2020-01-22 Thread 'Eric Deutsch' via spctools-discuss

Hi everyone, the next Trans-Proteomic Pipeline (TPP) course is coming up
soon. Please register if you’d like to get hands-on training on the TPP.
The next course is:



In Seattle, March 2-6, the week before the US HUPO annual conference (
https://www.ushupo.org/):

https://moritz.isbscience.org/courses/proteomics-informatics-course/march-2020-seattle/



The registration deadline is still a month away, but you are encouraged to
sign up soon!



The following course will be:



In Stockholm, Sweden October 12-16, the week before the 2020 HUPO World
Congress. Registration is not open yet, but mark your calendar if you’d
like to attend that course.



Let me know if you have questions!



Regards,

Eric





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Senior Research Scientist

Institute for Systems Biology

401 Terry Ave North

Seattle WA 98109

Email: edeut...@systemsbiology.org

ORCiD: -0001-8732-0928

Office: +1-206-732-1397

Fax: +1-206-732-1260

WWW: https://www.systemsbiology.org/eric-deutsch

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RE: [spctools-discuss] Interpretation of stats from pepXML viewer

2019-12-13 Thread 'Eric Deutsch' via spctools-discuss

Thanks for the clarification, Jimmy!



*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Jimmy Eng
*Sent:* Friday, December 13, 2019 8:27 AM
*To:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Interpretation of stats from pepXML viewer



Regarding inputs and output counts to Comet, as Eric mentioned, there are
search parameters which affect whether or not a spectrum will be searched
at all.  These are: activation_method, digest_mass_range,
max_precursor_charge, minimum_peaks, minimum_intensity, and
remove_precursor_peak (which can affect minimum_peaks).  A query spectrum
that happens to be out of bounds for any of these parameters will not be
analyzed (is effectively ignored) and will not show up in the output.  Any
spectra that passes these filters will have an output entry in Comet's
pepXML output file, even if there's no matching peptide output.  Such blank
outputs can happen in cases where the database or tolerances are so small
that no peptides are scored or the spectrum is so poor that the xcorr score
is less than or equal to zero.  This is why you see 1752 spectra in the
pepXML after Comet searches of both your databases as that's the number of
spectra that actually get analyzed and is a function of the input and not
the database being searched.



On Fri, Dec 13, 2019 at 2:29 AM 'Alastair Skeffington' via spctools-discuss
 wrote:

Hi,



Can someone explain what's happen here please:



Number of spectra in the .mgf file = 1856

Number of spectra after conversion to mzXML = 1856

Number of spectra in pepXML file after comet search: 1752



I then search against database A (DB-A) and database B (DB-B) and count the
number of spectra in the pepXML file as counts of "https://groups.google.com/d/msgid/spctools-discuss/09b3c5de-a9b9-46be-8b40-d502a5c17bf6%40googlegroups.com

.

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RE: [spctools-discuss] Interpretation of stats from pepXML viewer

2019-12-13 Thread 'Eric Deutsch' via spctools-discuss

Hi Alistair, thanks for posting your questions. Although it’s possible
something problematic is happening, I think the answers to your questions
are:

1) Most search engines including Comet have a minimum spectrum quality
threshold to even search the spectrum, e.g. minimum of 10 peaks. There are
settings in the comet.params. Also, if your database is very small (not
generally recommended) with very narrow tolerances, there may not be any
possible peptides that match the query spectrum precursor m/z within
tolerance. In both cases, there is no result from the search engine, and
therefore nothing in the pepXML

2) My best guess here is: the default behavior of PeptideProphet is to NOT
write out any spectra with probability < 0.05 to the output file so that it
is smaller and faster to explore. You can turn off this behavior with the
-p0 option to xinteract. This will pass through all PSMs.

*From:* 'Alastair Skeffington' via spctools-discuss <
spctools-discuss@googlegroups.com>
*Sent:* Friday, December 13, 2019 2:29 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Interpretation of stats from pepXML viewer

Hi,

Can someone explain what's happen here please:

Number of spectra in the .mgf file = 1856

Number of spectra after conversion to mzXML = 1856

Number of spectra in pepXML file after comet search: 1752

I then search against database A (DB-A) and database B (DB-B) and count the
number of spectra in the pepXML file as counts of "https://groups.google.com/d/msgid/spctools-discuss/09b3c5de-a9b9-46be-8b40-d502a5c17bf6%40googlegroups.com

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RE: [spctools-discuss] Perl library errors: Centos 7

2019-12-06 Thread 'Eric Deutsch' via spctools-discuss

Great! If you can send me your log of what CentOS yum commands you had to
run to install prequisites (which are different than the Ubuntu apt
commands), I can create a CentOS recipe that would help out some other
folks.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Shagun Gupta
*Sent:* Thursday, December 5, 2019 11:56 AM
*To:* spctools-discuss 
*Subject:* Re: [spctools-discuss] Perl library errors: Centos 7



Hi Eric



ls -al gives me:

total 36

drwx--. 17 tpp  tpp  4096 Nov 13 11:10 .

drwxr-xr-x.  8 root root  109 Nov 11 14:45 ..

-rw---.  1 tpp  tpp  2930 Nov 21 14:44 .bash_history

-rw-r--r--.  1 tpp  tpp18 Oct 30  2018 .bash_logout

-rw-r--r--.  1 tpp  tpp   193 Oct 30  2018 .bash_profile

-rw-r--r--.  1 tpp  tpp   231 Oct 30  2018 .bashrc

drwxr-xr-x.  2 tpp  tpp  4096 Nov 11 16:08 bin

drwxrwxr-x.  3 tpp  tpp26 Nov 11 14:43 .cache

drwxr-xr-x.  2 tpp  tpp  4096 Nov 11 16:08 cgi-bin

drwxr-xr-x.  2 tpp  tpp  4096 Nov 11 16:08 conf

drwxrwxr-x.  3 tpp  tpp26 Nov 11 14:43 .config

drwxrwxr-x.  6 tpp  tpp   123 Nov 16 14:07 .cpan

drwxr-xr-x.  6 tpp  tpp   204 Nov 11 16:08 html

drwxr-xr-x.  4 tpp  tpp42 Nov 11 16:08 lib

drwxr-xr-x. 12 tpp  tpp   189 Nov 11 16:08 lic

drwxr-xr-x.  2 tpp  tpp10 Nov 11 16:08 log

drwxr-xr-x.  4 tpp  tpp42 Nov 11 16:08 man

drwxr-xr-x.  2 tpp  tpp  4096 Nov 11 16:08 schema

drwxrwxr-x.  3 tpp  tpp85 Nov 11 14:46 .subversion

drwxrwxr-x.  3 tpp  tpp46 Nov 11 14:46 svn

drwxr-xr-x.  3 tpp  tpp27 Nov 11 16:08 users



ls -al lib gives me:

total 8

drwxr-xr-x.  4 tpp tpp   42 Nov 11 16:08 .

drwx--. 17 tpp tpp 4096 Nov 13 11:10 ..

drwxr-xr-x.  3 tpp tpp 4096 Nov 11 16:08 Mayu

drwxr-xr-x.  3 tpp tpp   69 Nov 11 16:08 perl



ls -al lib/perl gives me:

total 12

drwxr-xr-x. 3 tpp tpp   69 Nov 11 16:08 .

drwxr-xr-x. 4 tpp tpp   42 Nov 11 16:08 ..

drwxr-xr-x. 2 tpp tpp   38 Nov 11 16:08 TPP

-r--r--r--. 1 tpp tpp 4873 Nov 11 16:08 tpplib_perl.pm

-r--r--r--. 1 tpp tpp 1359 Nov 11 16:08 TPP.pm



export PERL5LIB=/home/tpp/lib/perl

echo $PERL5LIB



gives me:

/home/tpp/lib/perl



perl -v gives me:

This is perl 5, version 16, subversion 3 (v5.16.3) built for
x86_64-linux-thread-multi

(with 39 registered patches, see perl -V for more detail)



Copyright 1987-2012, Larry Wall



Perl may be copied only under the terms of either the Artistic License or
the

GNU General Public License, which may be found in the Perl 5 source kit.



Complete documentation for Perl, including FAQ lists, should be found on

this system using "man perl" or "perldoc perl".  If you have access to the

Internet, point your browser at http://www.perl.org/, the Perl Home Page.





cd bin

./test_tpi.pl



Now shows me that all the libraries have been installed!



Looks like I might have had an error typing the PERL5LIB pathway. Thanks a
lot!



-Shagun



On Tuesday, December 3, 2019 at 2:27:07 PM UTC-5, Eric Deutsch wrote:

Okay, well, assuming you’re still getting this error, I would need more
information to suggest a next course of action.  Can you send the output of
this:



cd /home/tpp

ls -al

ls -al lib

ls -al lib/perl

export PERL5LIB=/home/tpp/lib/perl

echo $PERL5LIB

perl -v

cd bin

./test_tpi.pl



?







*From:* spctools...@googlegroups.com  <
spctools...@googlegroups.com > *On Behalf Of *Shagun Gupta
*Sent:* Tuesday, December 3, 2019 9:54 AM
*To:* spctools-discuss >
*Subject:* Re: [spctools-discuss] Perl library errors: Centos 7



yes! Apart from some library changes (because of Centos) and path to the
directories, I didn't change anything and didn't have any issues with make
install!



On Monday, December 2, 2019 at 10:51:54 PM UTC-5, Eric Deutsch wrote:

So then you did:



cd /home/tpp/bin

export PERL5LIB=/home/tpp/lib/perl

./test_tpi.pl



?







*From:* spctools...@googlegroups.com  *On
Behalf Of *Shagun Gupta
*Sent:* Monday, December 2, 2019 6:47 PM
*To:* spctools-discuss 
*Subject:* Re: [spctools-discuss] Perl library errors: Centos 7



Hi Eric



I did do make install step. TPP was installed in /home/tpp and I changed
all the directory specs accordingly!





On Friday, November 22, 2019 at 3:25:50 PM UTC-5, Eric Deutsch wrote:

Hi Shagan, did you perform the `make install` step? Was TPP actually
installed in /usr/local/tpp? Or was it installed somewhere else?





*From:* spctools...@googlegroups.com  *On
Behalf Of *Shagun Gupta
*Sent:* Friday, November 22, 2019 11:33 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Perl library errors: Centos 7



Hi



I have been trying to install TPP (Sashimi) on a Centos 7 server. I don't
have any issues with make. However, on downloading perl libraries as
specified here:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS



and checking for installation of all with,

cd /usr/local/tpp/bin

export PERL5LIB=/usr/local/tpp/lib/perl

./test_tpi.pl

 I get the war

RE: [spctools-discuss] Perl library errors: Centos 7

2019-12-03 Thread 'Eric Deutsch' via spctools-discuss

Okay, well, assuming you’re still getting this error, I would need more
information to suggest a next course of action. Can you send the output of
this:

cd /home/tpp

ls -al

ls -al lib

ls -al lib/perl

export PERL5LIB=/home/tpp/lib/perl

echo $PERL5LIB

perl -v

cd bin

./test_tpi.pl

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Shagun Gupta
*Sent:* Tuesday, December 3, 2019 9:54 AM
*To:* spctools-discuss
*Subject:* Re: [spctools-discuss] Perl library errors: Centos 7

yes! Apart from some library changes (because of Centos) and path to the
directories, I didn't change anything and didn't have any issues with make
install!

On Monday, December 2, 2019 at 10:51:54 PM UTC-5, Eric Deutsch wrote:

So then you did:

cd /home/tpp/bin

export PERL5LIB=/home/tpp/lib/perl

./test_tpi.pl

*From:* spctools...@googlegroups.com <
spctools...@googlegroups.com > *On Behalf Of *Shagun Gupta
*Sent:* Monday, December 2, 2019 6:47 PM
*To:* spctools-discuss >
*Subject:* Re: [spctools-discuss] Perl library errors: Centos 7

Hi Eric

I did do make install step. TPP was installed in /home/tpp and I changed
all the directory specs accordingly!

On Friday, November 22, 2019 at 3:25:50 PM UTC-5, Eric Deutsch wrote:

Hi Shagan, did you perform the `make install` step? Was TPP actually
installed in /usr/local/tpp? Or was it installed somewhere else?

*From:* spctools...@googlegroups.com *On
Behalf Of *Shagun Gupta
*Sent:* Friday, November 22, 2019 11:33 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Perl library errors: Centos 7

I have been trying to install TPP (Sashimi) on a Centos 7 server. I don't
have any issues with make. However, on downloading perl libraries as
specified here:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS

and checking for installation of all with,

cd /usr/local/tpp/bin

export PERL5LIB=/usr/local/tpp/lib/perl

./test_tpi.pl

I get the warning that the following three libraries (TPP,
TPP::StatUtilities and tpplib_perl) are missing. I am not sure how to
download them since cpan can't find them by name and ".pm" files are in the
folder "/home/tpp/svn/trans_proteomic_pipeline/perl/lib".

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RE: [spctools-discuss] Perl library errors: Centos 7

2019-12-02 Thread 'Eric Deutsch' via spctools-discuss

So then you did:

cd /home/tpp/bin

export PERL5LIB=/home/tpp/lib/perl

./test_tpi.pl

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Shagun Gupta
*Sent:* Monday, December 2, 2019 6:47 PM
*To:* spctools-discuss
*Subject:* Re: [spctools-discuss] Perl library errors: Centos 7

Hi Eric

I did do make install step. TPP was installed in /home/tpp and I changed
all the directory specs accordingly!

On Friday, November 22, 2019 at 3:25:50 PM UTC-5, Eric Deutsch wrote:

Hi Shagan, did you perform the `make install` step? Was TPP actually
installed in /usr/local/tpp? Or was it installed somewhere else?

*From:* spctools...@googlegroups.com <
spctools...@googlegroups.com > *On Behalf Of *Shagun Gupta
*Sent:* Friday, November 22, 2019 11:33 AM
*To:* spctools-discuss >
*Subject:* [spctools-discuss] Perl library errors: Centos 7

I have been trying to install TPP (Sashimi) on a Centos 7 server. I don't
have any issues with make. However, on downloading perl libraries as
specified here:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS

and checking for installation of all with,

cd /usr/local/tpp/bin

export PERL5LIB=/usr/local/tpp/lib/perl

./test_tpi.pl

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RE: [spctools-discuss] Perl library errors: Centos 7

2019-11-22 Thread 'Eric Deutsch' via spctools-discuss

Hi Shagan, did you perform the `make install` step? Was TPP actually
installed in /usr/local/tpp? Or was it installed somewhere else?

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Shagun Gupta
*Sent:* Friday, November 22, 2019 11:33 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Perl library errors: Centos 7

I have been trying to install TPP (Sashimi) on a Centos 7 server. I don't
have any issues with make. However, on downloading perl libraries as
specified here:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS

and checking for installation of all with,

cd /usr/local/tpp/bin

export PERL5LIB=/usr/local/tpp/lib/perl

./test_tpi.pl

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RE: [spctools-discuss] Re: Question: mzML parsing issue SpectraST 5.0 (stand alone, Linux, MacOS)

2019-11-05 Thread 'Eric Deutsch' via spctools-discuss

Thanks for reporting, Oliver. We have not seen this issue ourselves.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *oliveralka
*Sent:* Tuesday, November 5, 2019 1:34 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Re: Question: mzML parsing issue SpectraST
5.0 (stand alone, Linux, MacOS)



As an update:

I was able to build TPP 5.0 and TPP 5.2 on Ubuntu 19.04.

Using SpectraST with the above mentioned complied version was successful
and everything parsed correctly.

We are not yet sure what is going on with our version, but we are looking
into it.



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RE: [spctools-discuss] Combination of consensus libraries and import in MRM format via spectraST

2019-09-24 Thread Eric Deutsch

Hi Kristina, I’m not fully following the steps and how they are related.
Can you describe what “original” is and where it came from (incl. SpectraST
version) and then provide the subsequent steps (actual commands) (including
renaming to msp?)



Thanks,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Kristina Plate
*Sent:* Tuesday, September 24, 2019 9:55 AM
*To:* spctools-discuss 
*Subject:* Re: [spctools-discuss] Combination of consensus libraries and
import in MRM format via spectraST



Hi Eric,



I'm sorry, if it's a little bit confusing. Theoretically I can rebuild the
spectral libraries but it will be difficult to get all pepxml files. So I
just want to know if it is risky to take this mixed approach.



It seems to be a thing of the mix up of older and newer spectrast version,
because if I built a spectral library myself fully with spectraST 5.0 there
are no m ion annotations no matter which import parameters I use. So, even
if these m ions are more plausible they don't occur if I built it from the
scratch.



Also it's interesiting that these changes only occur during import from
splib files, not from msp files. Further, libraries with m ion annotations
change "back" to the m ion free annotation if they are imported from msp
files.



*(1) original:*



Name: LILAGLVADGK/2

301.1492  347.0 y6^2/-0.530,y3-17/-0.985,y3-18/-0.001 48/44
0.0057|0.58

311.1680  414.6 ?50/44 0.0054|0.72

319.1597  1481.3y3/-0.002 71/44 0.0025|0.32

327.2017  2003.3?71/44 0.0048|0.30

341.2172  726.1 ?59/44 0.0060|0.42





*(2) after import (1) from splib file with -cM parameter:*



Name: LILAGLVADGK/2

301.1506  347.0 y3-18/0.000 48/44 0.0057|0.58

311.1680  414.6 ?50/44 0.0054|0.72

319.1612  1481.3y3/0.000 71/44 0.0025|0.32

327.2027  2003.3m2:5/0.000 71/44 0.0048|0.30

341.2183  726.1 m9:12/0.000 59/44 0.0060|0.42





*(3) after reimport (2) only from msp file (w or w/o -cM parameter):*



Name: LILAGLVADGK/2

301.6790  347.0 y6^2/0.000,y3-17/-0.456,y3-18/0.528  48/44 0.0057|0.58

311.1680  414.6 ?50/44 0.0054|0.72

319.1612  1481.3y3/0.000 71/44 0.0025|0.32

327.2027  2003.3?71/44 0.0048|0.30

341.2183  726.1 ?59/44 0.0060|0.42



All steps were done with the same version of spectraST. Especially the
first line: where the software gets the information about the other
alternative fragment types (the msp file was the only file in directory)?

I'm sorry if this is confusing but I just want to understand what is
happening during the processes.



Thank you very much for your patience!

Kind regards,

Kristina


Am Montag, 23. September 2019 17:48:10 UTC+2 schrieb Eric Deutsch:

Hi Kristina, I am not so sure about answers to your questions. It would be
ideal to use SpectraST 5.0 in all your processing if you can easily do
this, yes, but in some cases it would not matter much. In general, where
peak interpretation is involved, SpectraST 5.0 is better. But I don’t know
relative to what you’re doing exactly when peak re-interpretation happens.



Can you just rebuild all your libraries with SpectraST 5.0? That would be
safest.



Regards,

Eric







*From:* spctools...@googlegroups.com  <
spctools...@googlegroups.com > *On Behalf Of *Kristina Plate
*Sent:* Monday, September 23, 2019 4:22 AM
*To:* spctools-discuss >
*Subject:* Re: [spctools-discuss] Combination of consensus libraries and
import in MRM format via spectraST



Hi Eric,



thank you very much for your reply and the detailed and, yes, quite
reasonable explanation. Some of the spectral libraries I got for the
combination were built with SpectraST 4.0 and the remaining builds as well
as the combination and further import steps were done with SpectraST 5.0.
But there are two factors bothering me:



1. I thought too, that the "issue" is caused by different SpectraST
versions. But when I did the MRM import (spectraST 5.0) on the single
spectral libraries which were built with the older version (see above),
this phenomenon didn't occur.



2. Even if it's explainable by a smarter interpretation by SpectraST, does
that mean that I can use these changed spectra or is it questionable to use
spectral libraries of older software versions imported with a newer one?



Thank you and kind regards,

Kristina

Am Freitag, 20. September 2019 20:49:28 UTC+2 schrieb Eric Deutsch:

Hi Kristina, I’m not certain I fully understand your issue, but maybe I can
answer some questions:



Partial old:

Name: DIETIIQK/2 *(old entry, original library)*

308.1581  226.5 ?

309.0826  359.4 ?

325.6734  1596.8b6-35^2/0.000,b6-36^2/0.492

329.1945  141.2 a6^2/0.000

343.1920  668.4
b6^2/0.000,y3-45/-0.042,y6-45^2/-0.516,y6-46^2/-0.024



Partial new:

Name: DIETIIQK/2 *(new entry, combined library)*

308.1581  226.5 ?

309.0826  359.4 ?

326.1680  1596.8?

328.2231  141.2 m4:6/0.

RE: [spctools-discuss] Questions about spectral library generation different search engines and shared peptides

2019-09-23 Thread Eric Deutsch

Hi Nikita, perhaps someone has some better answers than I do, but here is
what I can say based on your description.

Regarding the cutoff, I wonder if in your combined analysis you are using a
peptide-level FDR of 1%, whereas in the single analyses you are using an
PSM-level FDR of 1%? A peptide-level FDR of 1% is more stringent than a
PSM-level FDR of 1% and this might account for the difference?

I am not aware of a mode to remove shared peptides from a library, although
this does sound like a useful feature. Maybe someone else knows?

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Nikita Boeren
*Sent:* Monday, September 23, 2019 4:16 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Questions about spectral library generation
different search engines and shared peptides

Dear TPP team and users,

I am a graduate student and I am trying to figure out a few things
regarding spectral library generation using TPP for SWATH analysis. My
questions do not involve direct issues with the use of TPP, but more about
the results.

My workflow is: Comet or X!Tandem search, PeptideProphet, iProphet, Mayu
(1% protein FDR), SpectraST and SpectraST2TSV.

I have used both Comet and X!Tandem search engines to create two libraries.
Also, I combined those two search outputs (via iProphet) to create another
library. In contrast of what I expected, my final list of proteins in my
combined library is less than using only Comet results (see Venn diagram).
How can this happen? The cut off probabilities corresponding to protein FDR
<1% for Comet (0.897393) and X!Tandem (0.872656) were as expected lower
than combined (0.966806).

Can anyone explain me why the combined library contains less proteins?

Also, I would like to ask you how to remove shared peptides from the
library without getting format issues in further workflows?

Thank you in advance.

Regards,

Nikita

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RE: [spctools-discuss] Combination of consensus libraries and import in MRM format via spectraST

2019-09-23 Thread Eric Deutsch

Hi Kristina, I am not so sure about answers to your questions. It would be
ideal to use SpectraST 5.0 in all your processing if you can easily do
this, yes, but in some cases it would not matter much. In general, where
peak interpretation is involved, SpectraST 5.0 is better. But I don’t know
relative to what you’re doing exactly when peak re-interpretation happens.



Can you just rebuild all your libraries with SpectraST 5.0? That would be
safest.



Regards,

Eric







*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Kristina Plate
*Sent:* Monday, September 23, 2019 4:22 AM
*To:* spctools-discuss 
*Subject:* Re: [spctools-discuss] Combination of consensus libraries and
import in MRM format via spectraST



Hi Eric,



thank you very much for your reply and the detailed and, yes, quite
reasonable explanation. Some of the spectral libraries I got for the
combination were built with SpectraST 4.0 and the remaining builds as well
as the combination and further import steps were done with SpectraST 5.0.
But there are two factors bothering me:



1. I thought too, that the "issue" is caused by different SpectraST
versions. But when I did the MRM import (spectraST 5.0) on the single
spectral libraries which were built with the older version (see above),
this phenomenon didn't occur.



2. Even if it's explainable by a smarter interpretation by SpectraST, does
that mean that I can use these changed spectra or is it questionable to use
spectral libraries of older software versions imported with a newer one?



Thank you and kind regards,

Kristina

Am Freitag, 20. September 2019 20:49:28 UTC+2 schrieb Eric Deutsch:

Hi Kristina, I’m not certain I fully understand your issue, but maybe I can
answer some questions:



Partial old:

Name: DIETIIQK/2 *(old entry, original library)*

308.1581  226.5 ?

309.0826  359.4 ?

325.6734  1596.8b6-35^2/0.000,b6-36^2/0.492

329.1945  141.2 a6^2/0.000

343.1920  668.4
b6^2/0.000,y3-45/-0.042,y6-45^2/-0.516,y6-46^2/-0.024



Partial new:

Name: DIETIIQK/2 *(new entry, combined library)*

308.1581  226.5 ?

309.0826  359.4 ?

326.1680  1596.8?

328.2231  141.2 m4:6/0.000

344.1816  668.4 m3:5/0.000



The first two peaks are fine. For the third entry, I am guessing that in
the original library this peak got shifted to exact m/z of the presumed
interpretation b6-35^2. But this is a highly unlikely interpretation. So in
the new entry, that peak retains its original m/z (i.e. not snapped to a
presumed interpretation) and a “?”. SpectraST seems to be smarter about not
assigning a silly interpretation.



For the next peak with intensity 141.2, the old library had an
interpretation of a6^2 and the m/z is snapped to that interpretation. But
a6^2 is a super unlikely interpretation, or maybe let’s call it impossible
and wrong. In the new library, this same peak has been interpreted as an
internal fragmentation ion and the m/z has been snapped to that. The m4:6
means that the peptide was fragmented in two places such that you get a
little ion that is TII and has a charge so you see it. Internal
fragmentation turns out to be fairly common and so m4:6 is far more
plausible an interpretation than a6^2. Same for m3:5 (ETI). Not necessarily
correct, but far more plausible than an a6^2 and a b6^2.



So I’m guessing that the first spectrum comes from a version where internal
fragmentation was not yet supported, and the second spectrum comes from a
newer version of SpectraST that knows about internal fragmentation and
interprets peaks better.



Does that seem like a reasonable explanation of what’s going on? Henry
might know more.



Regards,

Eric













*From:* spctools...@googlegroups.com  <
spctools...@googlegroups.com > *On Behalf Of *Kristina Plate
*Sent:* Friday, September 20, 2019 6:22 AM
*To:* spctools-discuss >
*Subject:* [spctools-discuss] Combination of consensus libraries and import
in MRM format via spectraST



Hello again,



as I described before (topic: *What happens during consensus building?*) I
have a problem with some messed up spectra in my spectral libraries.

I combined four spectral libraries and built consensus spectra. Afterwards
I reimported the combined consensus spectral library in MRM format and
converted it in an assay library. When I checked the SPTXT file I found
some *slightly changed spectra* and new *"ion types" m*. Please see my
example of an old, normal spectrum and the corresponding new one below:



Name: DIETIIQK/2 *(old entry, original library)*

LibID: 4160

MW: 960.5481

PrecursorMZ: 480.2740

Status: Normal

FullName: X.DIETIIQK.X/2 (CID-QTOF)

Comment: AvePrecursorMz=480.5611 BinaryFileOffset=23385298
FracUnassigned=0.09,1/5;0.23,11/20;0.06,7/31 MassDiff=-0.0014 Mods=0 NAA=8
NISTProtein=Id_02 NMC=0 NTT=1 Nreps=1/1 OrigMaxIntensity=11 Parent=480.274
Pep=Tryptic PrecursorIntensity=0 Prob=1. Protein=1/Id_02
RawSpectrum=file_02_04.69683.69683 RetentionTime=

RE: [spctools-discuss] Combination of consensus libraries and import in MRM format via spectraST

2019-09-20 Thread Eric Deutsch

Hi Kristina, I’m not certain I fully understand your issue, but maybe I can
answer some questions:



Partial old:

Name: DIETIIQK/2 *(old entry, original library)*

308.1581  226.5 ?

309.0826  359.4 ?

325.6734  1596.8b6-35^2/0.000,b6-36^2/0.492

329.1945  141.2 a6^2/0.000

343.1920  668.4
b6^2/0.000,y3-45/-0.042,y6-45^2/-0.516,y6-46^2/-0.024



Partial new:

Name: DIETIIQK/2 *(new entry, combined library)*

308.1581  226.5 ?

309.0826  359.4 ?

326.1680  1596.8?

328.2231  141.2 m4:6/0.000

344.1816  668.4 m3:5/0.000



The first two peaks are fine. For the third entry, I am guessing that in
the original library this peak got shifted to exact m/z of the presumed
interpretation b6-35^2. But this is a highly unlikely interpretation. So in
the new entry, that peak retains its original m/z (i.e. not snapped to a
presumed interpretation) and a “?”. SpectraST seems to be smarter about not
assigning a silly interpretation.



For the next peak with intensity 141.2, the old library had an
interpretation of a6^2 and the m/z is snapped to that interpretation. But
a6^2 is a super unlikely interpretation, or maybe let’s call it impossible
and wrong. In the new library, this same peak has been interpreted as an
internal fragmentation ion and the m/z has been snapped to that. The m4:6
means that the peptide was fragmented in two places such that you get a
little ion that is TII and has a charge so you see it. Internal
fragmentation turns out to be fairly common and so m4:6 is far more
plausible an interpretation than a6^2. Same for m3:5 (ETI). Not necessarily
correct, but far more plausible than an a6^2 and a b6^2.



So I’m guessing that the first spectrum comes from a version where internal
fragmentation was not yet supported, and the second spectrum comes from a
newer version of SpectraST that knows about internal fragmentation and
interprets peaks better.



Does that seem like a reasonable explanation of what’s going on? Henry
might know more.



Regards,

Eric













*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Kristina Plate
*Sent:* Friday, September 20, 2019 6:22 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Combination of consensus libraries and import
in MRM format via spectraST



Hello again,



as I described before (topic: *What happens during consensus building?*) I
have a problem with some messed up spectra in my spectral libraries.

I combined four spectral libraries and built consensus spectra. Afterwards
I reimported the combined consensus spectral library in MRM format and
converted it in an assay library. When I checked the SPTXT file I found
some *slightly changed spectra* and new *"ion types" m*. Please see my
example of an old, normal spectrum and the corresponding new one below:



Name: DIETIIQK/2 *(old entry, original library)*

LibID: 4160

MW: 960.5481

PrecursorMZ: 480.2740

Status: Normal

FullName: X.DIETIIQK.X/2 (CID-QTOF)

Comment: AvePrecursorMz=480.5611 BinaryFileOffset=23385298
FracUnassigned=0.09,1/5;0.23,11/20;0.06,7/31 MassDiff=-0.0014 Mods=0 NAA=8
NISTProtein=Id_02 NMC=0 NTT=1 Nreps=1/1 OrigMaxIntensity=11 Parent=480.274
Pep=Tryptic PrecursorIntensity=0 Prob=1. Protein=1/Id_02
RawSpectrum=file_02_04.69683.69683 RetentionTime=2745.2,2745.2,2745.2
Sample=1/sample_02,1,1 Se=1^C1:pb=1./0,fv=2.7040/0 Spec=CREATE
TotalIonCurrent=8.9e+003 iRT=33.4,33.4,33.4

NumPeaks: 31

308.1581  226.5 ?

309.0826  359.4 ?

325.6734  1596.8b6-35^2/0.000,b6-36^2/0.492

329.1945  141.2 a6^2/0.000

343.1920  668.4
b6^2/0.000,y3-45/-0.042,y6-45^2/-0.516,y6-46^2/-0.024

353.2183  967.7 y3-35/0.000

354.2183  480.9 y3-35i/0.000

355.2183  481.6 y3-35i/0.000

358.1609  442.5 b3/0.000,y6-17^2/0.456,y6-18^2/0.948

358.1970  96.7 ?

365.2030  293.0 ?

373.2367  296.2 ?

388.2554  1744.6y3/0.000,b7-36^2/-0.955

424.1714  315.8 b4-35/0.000,b4-36/0.984

442.1820  644.1 b4-17/0.000,b4-18/0.984

457.7633  546.4 p-45^2/0.000,p-46^2/0.492,y4-44/0.414

458.2791  109.5 p-44^2/0.000,b4/-0.929

471.7608  110.9 p-17^2/0.000,p-18^2/0.492

472.2608  111.1 p-17^2i/0.000

477.1321  111.6 ?

480.2740  336.0 p^2/0.000

484.3130  224.9 y4-17/0.000,y4-18/0.984

501.3395  523.5 y4/0.000

553.1674  240.4 ?

567.3501  487.3 y5-35/0.000

584.3766  247.1 y5-18/0.000

602.3872  2935.1y5/0.000

696.3927  205.5 y6-35/0.000,y6-36/0.984

714.4032  2211.4y6-17/0.000,y6-18/0.984

731.4298  1.0   y6/0.000

732.4298  414.9 y6i/0.000



Name: DIETIIQK/2 *(new entry, combined library)*

LibID: 4673

MW: 960.5481

PrecursorMZ: 480.2740

Status: Normal

FullName: X.DIETIIQK.X/2 (CID-QTOF)

Comment: AvePrecursorMz=480.5611 BinaryFileOffset=20613807
FracUnassigned=0.09,1/5;0.25,13/20;0.17,13/31 MassDiff=-0.0014 Mods=0 NAA=8
NISTProtein=Id_02 NMC=0 NTT=1 Nreps=1/1 OrigMaxIntensity=11 Parent=480.274
Pep=Tryptic PepContext=1/NTPR_DIHE PrecursorIntensity=0

RE: [spctools-discuss] problem to install TPP 5.2.0

2019-06-25 Thread Eric Deutsch

Hi Virginie, thank you for your interest in TPP.

That command assumes that the user account that you will be installing tpp
as is called “tpp” with group “tpp”.

You could either create a Linux user “tpp” and a group “tpp” first, or you
could replace that with the current user and group that you are installing
with. Probably the current account you’re running with is fine. To find out
the current username and group, try typing just:

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Virginie Imbault
*Sent:* Tuesday, June 25, 2019 1:01 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] problem to install TPP 5.2.0

Dear all,

I have a virtual machine with Ubuntu 18.04 LTS and I'm trying to install
TPP 5.2.0. So I follow the wiki "TPP 5.2.0: Installing on Ubuntu 18.04
LTS". But I have an error.

when I write:

sudo chown tpp.tpp /usr/local/tpp

chown: incorrect user: "tpp.tpp"

Can I help me?

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[spctools-discuss] Upcoming Trans-Proteomic Pipeline (TPP) courses

2019-06-11 Thread Eric Deutsch

Hi everyone, I just wanted to remind you all about upcoming Trans-Proteomic
Pipeline courses if you’d like to sign up to get hands-on training of the
TPP. The upcoming courses are:



In Southampton, UK June 28-30 before BSPR 2019 (seems full, but maybe wait
list is possible):

https://www.bspr.org/event/bspr-meeting-2019



In Seattle, July 10-12, the 3 days following the Cascadia Proteomics
Symposium <http://www.cascadiaproteomics.org/> we’ll have a course at ISB:

https://moritz.systemsbiology.org/courses/proteomics-informatics-course/july-2019-seattle/



In Adelaide, Australia September 9-13, the week before the 2019 HUPO World
Congress:

https://moritz.systemsbiology.org/courses/proteomics-informatics-course/september-2019-adelaide-australia/

(Note that HUPO abstracts are due this week!)



Let me know if you have questions!



Regards,

Eric





--

Eric W. Deutsch

Senior Research Scientist

Institute for Systems Biology

401 Terry Ave North

Seattle WA 98109

Email: edeut...@systemsbiology.org

ORCiD: -0001-8732-0928

Office: +1-206-732-1397

Fax: +1-206-732-1260

WWW: https://www.systemsbiology.org/eric-deutsch

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RE: [spctools-discuss] TPP 5.2 compile error Ubuntu 18.04

2019-05-17 Thread Eric Deutsch

Hi Alejandro, which checkout did you do? Was it this?



svn checkout -r 7909
http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline



Or a little different?



Thanks,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Alejandro
*Sent:* Friday, May 17, 2019 2:57 PM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] TPP 5.2 compile error Ubuntu 18.04



Hello all,



Im trying to install TPP 5.2 on a computer running Ubuntu 18.04. I'm
following the guide but so far I have been unsuccessful. I just changed the
username and kept the tpp group. The install location is as is in the
guide, and the /dat would be different. After running

make all

As per the guide I tried to run again (make all) but always throws the same
error.


I get the following error:;



*~/svn/trans_proteomic_pipeline$ make all*



g++  -g  -std=c++11 -Wno-deprecated -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE   -DTPPLIB
-I/home/laptop/svn/trans_proteomic_pipeline/src
-I/home/laptop/svn/trans_proteomic_pipeline/build/gnu-x86_64/include
-D__LINUX__ -fPIC -MMD -c -o
/home/laptop/svn/trans_proteomic_pipeline/build/gnu-x86_64/artifacts/Parsers/mzParser/saxmzmlhandler.o
/home/laptop/svn/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp

/home/laptop/svn/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp:571:58:
error: no ‘bool mzpSAXMzmlHandler::readHeaderFromOffset(f_off)’ member
function declared in class ‘mzpSAXMzmlHandler’

 bool mzpSAXMzmlHandler::readHeaderFromOffset(f_off offset){


^

/home/laptop/svn/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp:633:60:
error: no ‘bool mzpSAXMzmlHandler::readSpectrumFromOffset(f_off)’ member
function declared in class ‘mzpSAXMzmlHandler’

 bool mzpSAXMzmlHandler::readSpectrumFromOffset(f_off offset){


^

/home/laptop/svn/trans_proteomic_pipeline/src/Parsers/Makefile:87: recipe
for target
'/home/laptop/svn/trans_proteomic_pipeline/build/gnu-x86_64/artifacts/Parsers/mzParser/saxmzmlhandler.o'
failed

make: ***
[/home/laptop/svn/trans_proteomic_pipeline/build/gnu-x86_64/artifacts/Parsers/mzParser/saxmzmlhandler.o]
Error 1





The "^" sign is bellow the closing parenthesis on (f_off offset) and on my
terminal is highlighted in red



I really don't know how to troubleshoot this.



Any help would be appreciated.



Alejandro





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RE: [spctools-discuss] Re: Combining the DIA Umpire results by iProphet

2019-04-06 Thread Eric Deutsch

I think the SeeMS tool from ProteoWizard may be your best bet. If you have
TPP installed, it may already be installed with TPP. Or otherwise, it is
easy to download and install. Install all of ProteoWizard, and then from
the Start menu under the ProteoWizard folder will be SeeMS.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *ilya gertsman
*Sent:* Friday, April 5, 2019 1:42 PM
*To:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Re: Combining the DIA Umpire results by
iProphet



Does anyone know of a good tool for viewing mzXML files, enabling one to
look at total ion current, perform XIC's for m/z's of interest, and other
basic functions (maybe something like AB Sciex's PeakView for .wiff files,
but only generic ms files formats)?  I saw a tool listed for TPP called
mzXML viewer, but do not see how to access this through TPP.  Any
recommendations would be greatly appreciated!

Many thanks!
ilya



On Fri, Apr 5, 2019 at 10:26 AM Ankit Balhara 
wrote:

Hi David,



Thanks for your kind help. Actually I am estimating the FDR by using the
Mayu tool, after combining the iprophet results of all the three datasets
which I have, as this gives me single Posterior probability (PPs/IPs) that
I am using in the SpectraST command line so as to generate the spectral
library.

Yes, I got the point which you have highlighted, but can I use Mayu for
estimating the FDR at final stage and then filter the results below the
threshold PP of FDR less than 1%, instead of filtering the results at each
iProphet analyses?



Thanks

Ankit









On Fri, 5 Apr 2019 at 20:03, David Shteynberg <
david.shteynb...@systemsbiology.org> wrote:

Hello Ankit,



If you computer has the resources to handle all files then running one
iProphet job to combine the results will give you one analysis result with
FDR rates that apply to all the data.  If you do multiple iProphet runs
then you have to be more careful about how you combine the results because
your runs will overlap more in the correct result than the incorrect
results so simply taking all results together above an FDR threshold will
inflate your final FDR.  One easy way to do this is to divide the FDR by
the number of iProphet runs being combined.  For example if you split the
results into two iProphet analyses and you want the combined FDR to be less
than 1% you would filter each iProphet analyses at 0.5% FDR and then take
the total set.  Does that make sense?



Cheers,

-David



On Thu, Apr 4, 2019 at 8:57 AM Ankit Balhara 
wrote:

Thanks Felipe.



I have posted this issue in the issues section of DIA-Umpire issue tracker.



Ankit







On Thu, 4 Apr 2019 at 19:21, Felipe da Veiga Leprevost <
leprevos...@gmail.com> wrote:

Hi Ankit;



Please feel free to submit your DIA-Umpire questions and issues to our
DIA-Umpire issue tracker: https://github.com/Nesvilab/DIA-Umpire



Regards

On Wednesday, April 3, 2019 at 7:05:59 AM UTC-4, Ankit Balhara wrote:

Hi All,



I am analyzing the SWATH-MS data using the DIA-Umpire. And I have 3 data
files of same sample which lead to generation of 9 .mgf output files from
DIA-Umpire, which were converted into 9 mzXML and then subjected to Comet
and X! Tandem search, and subsequently to peptide prophet and hence total
files generated during this process are 18 pep.xml files.

My ultimate aim to build the assay library. So, I am confused how to
combine the results of these 18 peptideprophet files.



Should I combine the Comet search results of each data file separately and
X! Tandem results separately and then combine these outputs again using
iProphet? This should result in generation of 3 iprophet result files
corresponding to each data file, which can again combined into one file by
iProphet in final step?



Or there is another way out of this problem?



Thanks



Ankit

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RE: [spctools-discuss] Re: StPeter SIn displays all --n/a-- in protXML viewer (TPP v. 5.2.0)

2019-03-25 Thread Eric Deutsch

Hi Jason, I have no solution yet, but I have one more data point. It seemed
to work well when I used all the default TPPGUI settings. But then in
another run when I fiddled with several of the settings, I had a similar
result as you describe. So I think there is a bug in one of the settings
that needs to be found and fixed. I have not had time to follow up. It
would be interesting to see if it works for you with all default settings.
And then figure out which setting is causing the issue. I can’t look at it
today, but let me know if you find something a little more specific.



Thanks,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Jason Winget
*Sent:* Monday, March 25, 2019 10:02 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Re: StPeter SIn displays all --n/a-- in
protXML viewer (TPP v. 5.2.0)



I should probably add that I use the -d flag, so the attributes are dSIn
instead of SIn. I wonder if that's the issue and it has to do with how the
reader parses the  attributes...

On Monday, March 25, 2019 at 12:59:27 PM UTC-4, Jason Winget wrote:

Hi folks, I was running the tutorial for DISCO using the new TPP version
and decided to also look at the results with StPeter.

Everything seemed to run fine, and I can see the  blocks in
the resulting protXML file with values. When I view these with the Petunia
protXML viewer, however, all the results show "-- n/a --" in the StPeter
SIn column.

This is true before or after filtering the results and also when ordering
by descending StPeter_Quant. I also tried switching the quantification
display between text and graphical bars to no effect.

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RE: [spctools-discuss] Combining the data on two tissues in one library

2019-03-15 Thread Eric Deutsch

Hi Ankit, both strategies would likely work okay. I would prefer first
combining all your data with iProphet and then creating the library with
SpectraST. An issue to consider: if you combine several libraries that have
been processed or thresholded individually, the final FDR will be higher
for the combined dataset than the individual ones. This is because the
correct identifications will mostly be in common, but the false
identifications will be mostly different in the different experiments and
so they will accumulate. So combining everything first with iProphet will
give you a better understanding of your FDR.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Ankit Balhara
*Sent:* Thursday, March 14, 2019 11:47 PM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Combining the data on two tissues in one
library



Hi,



I have acquired the DDA and DIA data on various tissues, and trying to
build a spectral library by combining the DDA results of all tissues, that
can be used further for the DIA data analysis. I am trying two approaches-
one assay library generation with SpectraST and other using skyline to
build the library. Now, I confused, how should I proceed.



Should I combine the peptideprophet results of various tissues by using
iProphet?

Or, create assay libraries for each tissue separately using the SpectraST
and then import them separately in a common Skyline document?



I would be very grateful for your help.



Thanks in advance.

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RE: [spctools-discuss] mzXML - peak encoding/decoding

2019-02-05 Thread Eric Deutsch

Hi Jeff, thanks for sharing these tips on the list!



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *jeffreyavansan...@gmail.com
*Sent:* Monday, February 4, 2019 4:15 PM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] mzXML - peak encoding/decoding



Hello all,



I just wanted to share a little bit of knowledge that I figured out while
fighting with the mzXML format in Python scripts.



Specifically, I was interested in taking data we had processed through an
in-house pipeline that gave CSV files, and convert it back to an mzXML file
format for further analyses. This was mostly trivial, but the encoding of
the peak data was really tripping me up for quite some time. Finally, I was
able to figure out a really simple way to encode (and decode) these data.
You can find a really simple example at
https://gist.github.com/jvansan/a2f627eb19435ba3986ac45751557b5f



An even quicker description of encoding:



Given an Numpy array with m/z - intensity pairs



arr = np.array([[  203.053 ,  8901.],[  365.1051, 24050.],[
366.1083,  2312.]])



You need to convert this to a Big Endian 64-bit floating-point number



dt = np.dtype('>f8')

arr = arr.astype(dt)



You can then do the necessary zlib compression and base64 encoding to get
the serialized peak list string:



content = base64.b64encode(zlib.compress(arr))



No new questions here, just wanted to share in hope that anyone Googling
what I was will be able to find this.

Also apologies if this is considered spam here.



Cheers,

Jeff

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RE: [spctools-discuss] Problem during spectrast library generation

2019-01-29 Thread Eric Deutsch

Hi Ankit, I suppose the first question to ask is: how many iRT peptides are
in your iRT.txt file and how many of those have a corresponding entry in
the library?



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Ankit Balhara
*Sent:* Tuesday, January 29, 2019 1:22 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Problem during spectrast library generation



Hi,



I am trying to build the spectral library using the SpectraST. I have
analyzed the DDA data upto the Mayu FDR determination step, also got the
IPP/PP values corresponding to 1%FDR. After that I am using following
command, but got the error that "Too few landmarks with distinct iRTs to
perform RT normalization". Could anybody please help me out?



c:\TPP\bin>spectrast -cNSpecLib -cICID-QTOF -cf "Protein! ~ 'rev_'"
-cP0.891383 -c_IRTc:\TPP\data\iRT.txt -c_IRR
c:\TPP\data\params\interact.ipro.pep.xml

SpectraST started at Tue Jan 29 14:38:13 2019.

Processing
"c:\TPP\data\params\interact.ipro.pep.xml"...500...1000...1500...DONE!

Importing all spectra with P>=0.891383 ...INFO:  Reading file:
c:/TPP/data/HLM_27_DDA.mzXML

10%...20%...30%...40%...50%...60%...70%...80%...90%...DONE!



Library file (BINARY) "SpecLib.splib" created.

Library file (TEXT) "SpecLib.sptxt" created.

M/Z Index file "SpecLib.spidx" created.

Peptide Index file "SpecLib.pepidx" created.



Total number of spectra in library: 1661

Total number of distinct peptide ions in library: 1560

Total number of distinct stripped peptides in library: 1429



CHARGE+1: 0 ; +2: 1187 ; +3: 450 ; +4: 24 ; +5: 0 ; >+5: 0 ;
Unk: 0

TERMINI   Tryptic: 1654 ; Semi-tryptic: 7 ; Non-tryptic: 0

PROBABILITY   >0.: 1347 ; 0.999-0.: 147 ; 0.99-0.999: 89 ;
0.9-0.99: 76 ; <0.9: 2

NREPS 20+: 0 ; 10-19: 0 ; 4-9: 0 ; 2-3: 0 ; 1: 1661

MODIFICATIONS C,Carbamidomethyl: 288 ; C,Pyro-carbamidomethyl: 2

  M,Oxidation: 12

  Q,Gln->pyro-Glu: 4

  n,Acetyl: 5



Total Run Time = 24 seconds.

SpectraST finished at Tue Jan 29 14:38:37 2019 with 1 error(s):

PEPXML IMPORT: Too few landmarks with distinct iRTs to perform RT
normalization.



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RE: [spctools-discuss] Re: Running TPP/Petunia GUI with Docker

2018-12-09 Thread Eric Deutsch

Hi Robert, I think you just need to go here:

http://myhost:10401/tpp/cgi-bin/tpp_gui.pl



instead of here:

http://myhost:10401/



? Could that be it?



Thanks,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Robert Winkler
*Sent:* Thursday, December 6, 2018 10:28 PM
*To:* spctools-discuss@googlegroups.com
*Cc:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Re: Running TPP/Petunia GUI with Docker



Hi Eric,



The port 10401 works fine. However, there is no Petunia showing up. When
calling http://localhost:10401/ from the Firefox Browser the "Apache2
Ubuntu Default Page" appears. The host system is Fedora 29.



To me it seems like a problem in the Apache2 configuration.



This is a summary of what I did (I also tested other ports, mounted
directories etc.):



#docker system prune --all --force



#docker run -dit --user=root -p 10401:10401 -v
/home/robertwinkler/dataspace/nextcloud/DATA/:/data spctools/tpp apache2ctl
-DFOREGROUND

f1ad3670f4f7117db97c9cff8061a95df718c748e348660a0ca1c78818a0e848



# docker ps

CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES

f1ad3670f4f7 spctools/tpp "apache2ctl -DFORE..." 23 minutes ago Up 23
minutes 0.0.0.0:10401->10401/tcp quizzical_bhabha



# docker images

REPOSITORY TAG IMAGE ID CREATED SIZE

docker.io/spctools/tpp latest 73727a87cff0 8 days ago 2.86 GB



Best, Robert



On Dec 3 2018, at 6:29 pm, Eric Deutsch  wrote:

Hi Robert, when you get an error like this:







Bind for 0.0.0.0:10401
<https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/0?redirect=http%3A%2F%2F0.0.0.0%3A10401=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t>
failed: port is already allocated







That means that there is already an Apache service listening on the 10401
point on the Docker **host** machine. The first thing to consider is there
perhaps already another container running on 10401. Maybe you don’t need to
start another container because it’s already running. Based on the your
`docker ps` it looks like this is your issue. Maybe you don’t need to
launch another TPP? Or maybe you would want to shut down that older
container before launching a new one?







Or it’s possible that you already have TPP installed and running on the
machine that is the Docker host. If that’s the case, you’ll want to map to
a different port so that you can run both at the same time (which is fine),
like this:







sudo docker pull spctools/tpp



sudo docker run -dit --user=root -p 10402:10401 -v /tmp/tppdata:/data
spctools/tpp apache2ctl -DFOREGROUND







Here what I’ve done is bind the local port 10402 to the Apache web server
running in the container. You would then use a web browser to go to:







http://myhost:10402/tpp/cgi-bin/tpp_gui.pl







Regards,



Eric











*From:* spctools-discuss@googlegroups.com
<https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/1?redirect=mailto%3Aspctools-discuss%40googlegroups.com=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t>
https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/2?redirect=mailto%3Aspctools-discuss%40googlegroups.com=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t>>
*On Behalf Of *Robert

*Sent:* Saturday, December 1, 2018 12:22 AM

*To:* spctools-discuss https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/3?redirect=mailto%3Aspctools-discuss%40googlegroups.com=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t>
>

*Subject:* Re: [spctools-discuss] Re: Running TPP/Petunia GUI with Docker





Hi, I am getting



/usr/bin/docker-current: Error response from daemon: driver failed
programming external connectivity on endpoint adoring_engelbart
(33ba8ed4cceaa86424363b5a9f1635ebf4ebb641c47c24c714f2ee1fe8846663): Bind
for 0.0.0.0:10401
<https://link.getmailspring.com/link/1544163446.local-95947193-1da1-v1.5.3-420ce...@getmailspring.com/4?redirect=http%3A%2F%2F0.0.0.0%3A10401=c3BjdG9vbHMtZGlzY3Vzc0Bnb29nbGVncm91cHMuY29t>
failed: port is already allocated.



opening the http://localhost:10401/

shows the default Apache2 Ubuntu Page



docker ps

CONTAINER IDIMAGE   COMMAND
CREATED STATUS  PORTS  NAMES

799753202ce1ebf55696681a"apache2ctl -DFORE..."   11 hours
agoUp 11 hours 0.0.0.0:10401->10401/tcp   dazzling_mahavira





Am Donnerstag, 29. November 2018 01:32:55 UTC+1 schrieb Eric Deutsch:



Hi Robert, thanks for testing. Based on our testing, we now changed the
calling sequence for starting Petunia to this:





*docker run -dit --user=root -p 10401:10401 -v /tmp/tppdata:/data
spctools/tpp apache2ctl -DFOREGROUND*





as described in the refreshed tutorial:



http://tools.proteomecenter.org/wiki/index.php?title=Running_the_TPP_docker_image
&

RE: [spctools-discuss] Re: External Tools Export mzIdentML

2018-12-03 Thread Eric Deutsch

Hi George, I haven’t had a chance to test this more thoroughly yet, but I
wonder if it might be Shared Drives setting in Docker, like this?

[image: image]







*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *guoguodigi...@msn.com
*Sent:* Monday, December 3, 2018 2:26 PM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Re: External Tools Export mzIdentML



Thank you Eric

I can run tpp docker image properly on my user documents folder. But when I
creat the container with working dir attached to another folder (like
E:\tppdata), the software will not get full access privillage. Is there any
docker or windows options to fix the problem?

Cheers,

George

On Friday, 30 November 2018 08:36:38 UTC+13, guoguo...@msn.com wrote:

Dear all,



Congratulations on the new image release.

I have successfully set up the docker image of 5.2.0.



But I can't run the External Tools: Export mzIdentML properly. I have tried
pep.xml and pro.xml, both returned a "file not found" message. See attached.



Anyone can help?

Cheers,

George



[image: Picture1.png]

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RE: [spctools-discuss] Re: Running TPP/Petunia GUI with Docker

2018-12-03 Thread Eric Deutsch

Hi Robert, when you get an error like this:



Bind for 0.0.0.0:10401 failed: port is already allocated



That means that there is already an Apache service listening on the 10401
point on the Docker **host** machine. The first thing to consider is there
perhaps already another container running on 10401. Maybe you don’t need to
start another container because it’s already running. Based on the your
`docker ps` it looks like this is your issue. Maybe you don’t need to
launch another TPP? Or maybe you would want to shut down that older
container before launching a new one?



Or it’s possible that you already have TPP installed and running on the
machine that is the Docker host. If that’s the case, you’ll want to map to
a different port so that you can run both at the same time (which is fine),
like this:



sudo docker pull spctools/tpp

sudo docker run -dit --user=root -p 10402:10401 -v /tmp/tppdata:/data
spctools/tpp apache2ctl -DFOREGROUND



Here what I’ve done is bind the local port 10402 to the Apache web server
running in the container. You would then use a web browser to go to:



http://myhost:10402/tpp/cgi-bin/tpp_gui.pl



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Robert
*Sent:* Saturday, December 1, 2018 12:22 AM
*To:* spctools-discuss 
*Subject:* Re: [spctools-discuss] Re: Running TPP/Petunia GUI with Docker



Hi, I am getting



/usr/bin/docker-current: Error response from daemon: driver failed
programming external connectivity on endpoint adoring_engelbart
(33ba8ed4cceaa86424363b5a9f1635ebf4ebb641c47c24c714f2ee1fe8846663): Bind
for 0.0.0.0:10401 failed: port is already allocated.



opening the http://localhost:10401/

shows the default Apache2 Ubuntu Page



docker ps
CONTAINER IDIMAGE   COMMAND
CREATED STATUS  PORTS  NAMES
799753202ce1ebf55696681a"apache2ctl -DFORE..."   11 hours
agoUp 11 hours 0.0.0.0:10401->10401/tcp   dazzling_mahavira





Am Donnerstag, 29. November 2018 01:32:55 UTC+1 schrieb Eric Deutsch:

Hi Robert, thanks for testing. Based on our testing, we now changed the
calling sequence for starting Petunia to this:



*docker run -dit --user=root -p 10401:10401 -v /tmp/tppdata:/data
spctools/tpp apache2ctl -DFOREGROUND*



as described in the refreshed tutorial:

http://tools.proteomecenter.org/wiki/index.php?title=Running_the_TPP_docker_image



Let us know what you think of that!



Regarding your precautions question, it seems to depend on how Docker is
installed on your system. If you have to run `sudo docker` for each
command, then things are written as root. On one of our computers, the IT
guys have jailed the user docker runs as as UID 10, so that’s a little
different. So I’m not sure the best advice here. In the tutorial we suggest
do a `chmod 777` that seems to make things work out nicely. On Windows, it
should all be find if the user has admin privileges. But there still might
be problems if the user doesn’t have admin privileges? I’m uncertain. I
haven’t tested that yet.



Regards,

Eric







*From:* spctools...@googlegroups.com  <
spctools...@googlegroups.com > *On Behalf Of *Robert
*Sent:* Tuesday, November 27, 2018 3:17 AM
*To:* spctools-discuss >
*Subject:* Re: [spctools-discuss] Re: Running TPP/Petunia GUI with Docker




Sure, Eric! Could you please give me the recommended command line
parameters for running TPP Petunia on both systems (Linux and Windows 10)?
Any precautions concerning the ownership etc. of the host system?



Am Donnerstag, 22. November 2018 19:47:25 UTC+1 schrieb Eric Deutsch:

Hi Robert, great, thanks for the testing! Can you elaborate a little on
what the symptoms are here for the file access through the GUI? I think the
file access worked fine in my testing. Maybe one potential fix is setting
some more permissive privileges in the directory you’re mapping into the
--user root container?


Run TPP image

   - *Start TPP image:*
   docker run -dit --user=root -p 10401:10401 -v
   /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast_centroided/:/data
   spctools/tpp
   - *Open GUI* with Firefox at
   http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
   GUI and guest:guest login works!
   However: Problems with accessing the directory structure/ uploading
   files.





*From:* spctools...@googlegroups.com  *On
Behalf Of *Robert
*Sent:* Thursday, November 22, 2018 7:11 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Re: Running TPP/Petunia GUI with Docker



The complete Test on Linux 64 bit and Windows 10
TPP 5.2 Docker CLI on LinuxSystem and software

   - Docker version 1.13.1, build accfe55-unsupported
   - Docker image: docker.io/spctools/tpp ID ebf55696681a
   - running on Fedora 29, Intel® Core™ i7-7700HQ CPU @ 2.80GHz, 16 Gb RAM

Data

   - Reference *data set* from ProteomeXchange repository, identifier
   PXD001819 (Journal of Proteomics 132 (2016) 51–62

RE: [spctools-discuss] Re: Running TPP/Petunia GUI with Docker

2018-11-28 Thread Eric Deutsch

Hi Robert, thanks for testing. Based on our testing, we now changed the
calling sequence for starting Petunia to this:



*docker run -dit --user=root -p 10401:10401 -v /tmp/tppdata:/data
spctools/tpp apache2ctl -DFOREGROUND*



as described in the refreshed tutorial:

http://tools.proteomecenter.org/wiki/index.php?title=Running_the_TPP_docker_image



Let us know what you think of that!



Regarding your precautions question, it seems to depend on how Docker is
installed on your system. If you have to run `sudo docker` for each
command, then things are written as root. On one of our computers, the IT
guys have jailed the user docker runs as as UID 10, so that’s a little
different. So I’m not sure the best advice here. In the tutorial we suggest
do a `chmod 777` that seems to make things work out nicely. On Windows, it
should all be find if the user has admin privileges. But there still might
be problems if the user doesn’t have admin privileges? I’m uncertain. I
haven’t tested that yet.



Regards,

Eric







*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Robert
*Sent:* Tuesday, November 27, 2018 3:17 AM
*To:* spctools-discuss 
*Subject:* Re: [spctools-discuss] Re: Running TPP/Petunia GUI with Docker




Sure, Eric! Could you please give me the recommended command line
parameters for running TPP Petunia on both systems (Linux and Windows 10)?
Any precautions concerning the ownership etc. of the host system?



Am Donnerstag, 22. November 2018 19:47:25 UTC+1 schrieb Eric Deutsch:

Hi Robert, great, thanks for the testing! Can you elaborate a little on
what the symptoms are here for the file access through the GUI? I think the
file access worked fine in my testing. Maybe one potential fix is setting
some more permissive privileges in the directory you’re mapping into the
--user root container?


Run TPP image

   - *Start TPP image:*
   docker run -dit --user=root -p 10401:10401 -v
   /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast_centroided/:/data
   spctools/tpp
   - *Open GUI* with Firefox at
   http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
   GUI and guest:guest login works!
   However: Problems with accessing the directory structure/ uploading
   files.





*From:* spctools...@googlegroups.com  <
spctools...@googlegroups.com > *On Behalf Of *Robert
*Sent:* Thursday, November 22, 2018 7:11 AM
*To:* spctools-discuss >
*Subject:* [spctools-discuss] Re: Running TPP/Petunia GUI with Docker



The complete Test on Linux 64 bit and Windows 10

TPP 5.2 Docker CLI on LinuxSystem and software

   - Docker version 1.13.1, build accfe55-unsupported
   - Docker image: docker.io/spctools/tpp ID ebf55696681a
   - running on Fedora 29, Intel® Core™ i7-7700HQ CPU @ 2.80GHz, 16 Gb RAM

Data

   - Reference *data set* from ProteomeXchange repository, identifier
   PXD001819 (Journal of Proteomics 132 (2016) 51–62), Orbitrap Velos data of
   human standard proteins (UPS Sigma) spiked into yeast background.
   - *Conversion of raw data* to .mzML profile, then to .mfg centroid data
   using
   docker run -it --privileged=true -v
   /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast/mzML_profile/:/data
   chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert --mgf
   /data/*.mzML
   - *Target data base* ups_human_yeast.fasta, composed of : Uniprot *Homo
   sapiens* + Uniprot *Saccharomyces cervisiae* + Sigma UPS proteins
   sequences
   Size of .mgf files: ~700 Mb each, 27 files
   FASTA with 33,183 entries

Start Docker

# systemctl start docker
1. Command Line Interface (CLI)

   - *Start TPP docker image* with *mounted data directory*:
   docker run -it --privileged=true -v
   /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast_centroided/:/data
   spctools/tpp bash

Run comet PSM search

   - go to data directory data/mgf and *create comet parameters file*:
   comet -p
   change name to comet.params and edit
   database_name = ups_human_yeast.fasta
   decoy_search = 1
   - Start comet search:
   time comet *.mgf
   time real 28m45.053s, ~1min/sample, ~140 Mb/sample

Run PeptideProphet

   - in the directory of comet .pep.xml results run: for i in *.pep.xml; do
   PeptideProphetParser $i; done
   ~15 s/sample, ~80 Mb/sample

Run ProteinProphet

   - in the directory of PeptideProphet .pep.xml results run: for i in
   *.pep.xml; do ProteinProphet $i $i.prot.xml NOGROUPS; done
   ~3 s/sample, ~7 Mb/sample

2. Petunia GUI session (on Linux 64 bit)System and software

   - Docker version 1.13.1, build accfe55-unsupported
   - Docker image: docker.io/spctools/tpp ID ebf55696681a
   - running on Fedora 29, Intel® Core™ i7-7700HQ CPU @ 2.80GHz, 16 Gb RAM

Run TPP image

   - *Start TPP image:*
   docker run -dit --user=root -p 10401:10401 -v
   /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast_centroided/:/data
   spctools/tpp
   - *Open GUI* with Firefox at
   http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
   GUI and guest:guest login works!
   However:

RE: [spctools-discuss] root in TPP docker image 16899d782bad on Win 10?

2018-11-28 Thread Eric Deutsch

Hi Robert, no this was unintentional. But it is now fixed. Try another pull
and see if that works better. We changed things a little based on feedback.
See the updated tutorial for changes in calling sequence:



http://tools.proteomecenter.org/wiki/index.php?title=Running_the_TPP_docker_image







*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Robert
*Sent:* Tuesday, November 27, 2018 3:24 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] root in TPP docker image 16899d782bad on Win
10?



Hi, I just started the new TPP image 16899d782bad, running on Win 10.
Before, I was normal biodocker user, now I am root.
Is this intended?

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RE: [spctools-discuss] simple text editor for TPP 5.2 docker?

2018-11-26 Thread Eric Deutsch

Hi Robert, good idea, thanks! We have added vim and nano to the image.



docker pull spctools/tpp



Regards,

Eric









*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Robert
*Sent:* Wednesday, November 21, 2018 12:09 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] simple text editor for TPP 5.2 docker?



Hi, a simple text editor (e.g. vi(m) and/or nano) would make the life much
more convenient for running the TPP in a headless (well, referring to
'without graphical interface' ;-)) mode.
E.g. for editing comet.params, writing little scripts etc.
Best, Robert

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RE: [spctools-discuss] Re: Running TPP/Petunia GUI with Docker

2018-11-22 Thread Eric Deutsch

Hi Robert, great, thanks for the testing! Can you elaborate a little on
what the symptoms are here for the file access through the GUI? I think the
file access worked fine in my testing. Maybe one potential fix is setting
some more permissive privileges in the directory you’re mapping into the
--user root container?


Run TPP image

   - *Start TPP image:*
   docker run -dit --user=root -p 10401:10401 -v
   /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast_centroided/:/data
   spctools/tpp
   - *Open GUI* with Firefox at
   http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
   GUI and guest:guest login works!
   However: Problems with accessing the directory structure/ uploading
   files.





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Robert
*Sent:* Thursday, November 22, 2018 7:11 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Re: Running TPP/Petunia GUI with Docker



The complete Test on Linux 64 bit and Windows 10


TPP 5.2 Docker CLI on LinuxSystem and software

   - Docker version 1.13.1, build accfe55-unsupported
   - Docker image: docker.io/spctools/tpp ID ebf55696681a
   - running on Fedora 29, Intel® Core™ i7-7700HQ CPU @ 2.80GHz, 16 Gb RAM

Data

   - Reference *data set* from ProteomeXchange repository, identifier
   PXD001819 (Journal of Proteomics 132 (2016) 51–62), Orbitrap Velos data of
   human standard proteins (UPS Sigma) spiked into yeast background.
   - *Conversion of raw data* to .mzML profile, then to .mfg centroid data
   using
   docker run -it --privileged=true -v
   /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast/mzML_profile/:/data
   chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert --mgf
   /data/*.mzML
   - *Target data base* ups_human_yeast.fasta, composed of : Uniprot *Homo
   sapiens* + Uniprot *Saccharomyces cervisiae* + Sigma UPS proteins
   sequences
   Size of .mgf files: ~700 Mb each, 27 files
   FASTA with 33,183 entries

Start Docker

# systemctl start docker
1. Command Line Interface (CLI)

   - *Start TPP docker image* with *mounted data directory*:
   docker run -it --privileged=true -v
   /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast_centroided/:/data
   spctools/tpp bash

Run comet PSM search

   - go to data directory data/mgf and *create comet parameters file*:
   comet -p
   change name to comet.params and edit
   database_name = ups_human_yeast.fasta
   decoy_search = 1
   - Start comet search:
   time comet *.mgf
   time real 28m45.053s, ~1min/sample, ~140 Mb/sample

Run PeptideProphet

   - in the directory of comet .pep.xml results run: for i in *.pep.xml; do
   PeptideProphetParser $i; done
   ~15 s/sample, ~80 Mb/sample

Run ProteinProphet

   - in the directory of PeptideProphet .pep.xml results run: for i in
   *.pep.xml; do ProteinProphet $i $i.prot.xml NOGROUPS; done
   ~3 s/sample, ~7 Mb/sample

2. Petunia GUI session (on Linux 64 bit)System and software

   - Docker version 1.13.1, build accfe55-unsupported
   - Docker image: docker.io/spctools/tpp ID ebf55696681a
   - running on Fedora 29, Intel® Core™ i7-7700HQ CPU @ 2.80GHz, 16 Gb RAM

Run TPP image

   - *Start TPP image:*
   docker run -dit --user=root -p 10401:10401 -v
   /home/robertwinkler/dataspace/nextcloud/DATA/UPS48_yeast_centroided/:/data
   spctools/tpp
   - *Open GUI* with Firefox at
   http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
   GUI and guest:guest login works!
   However: Problems with accessing the directory structure/ uploading
   files.

TPP 5.2 Docker CLI on WindowsSystem and software

   - Docker version 18.06.1-ce, build e68fc7a
   - Docker image: docker.io/spctools/tpp ID ebf55696681a
   - running on OS Name Microsoft Windows 10 Enterprise, Processor Intel®
   Core™ i5-3470S CPU @ 2.90GHz, 2901 Mhz, 4 Core(s), 4 Logical Processor(s),
   8 Gb RAM

Data

   - *MS/MS data* from Waters Synapt DDA experiments, exported to .mgf (see
   below). 2 samples with ~400 Mb each.
   - *FASTA database* composed from EST database and Uniref50 plants,
   created by
   cat db_1.fasta db_2.fasta > uni50plantsplus.fasta, 3,557,556 entries.
   Data set not public yet (sorry).

Convert Waters Synapt data to mgf

·load msconvert image with vendor libraries: docker run -it -v
C:\TPP\data:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses bash

·dive into data directory and run with LockMass Filter:
wine msconvert --filt "lockmassRefiner mz=785.8426" --mgf *.raw

·exit image by exit.

·*Start TPP* docker session:
docker run -it -v C:\TPP\data:/data spctools/tpp bash
Comet PSM search

   - use comet.params from above, just change database_name =
   uni50plantsplus.fasta
   - with .mgf files, .fasta sequence database and comet.params in the same
   directory, run:
   time comet *.mgf Load spectra killed; change in comet.params:
spectrum_batch_size
   = 1000

Run PeptideProphet

   - in the directory of comet .pep.xml results run: for i in *.pep.xml; do
   PeptideProphetParser $i; done

Run

RE: [spctools-discuss] How to set number of cores/threads/RAM in TPP

2018-11-21 Thread Eric Deutsch

The parameter for X!Tandem is “spectrum, threads”. Set that to 8 or
whatever is appropriate for your machine.



The parameter for Comet is “num_threads”. The default is 0, which is to
detect how many CPUs you have and use them all. Or you can set it to a
number you like.



I don’t know the state of multithreading of other TPP tools as of 5.1. But
they’re a lot faster than the searching anyway.



Eric







*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Gunjan Pandey
*Sent:* Tuesday, November 20, 2018 4:40 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] How to set number of cores/threads/RAM in TPP



I am running  *TPP v5.1.0 Syzygy, Build 201711031215-7670
(Windows_NT-x86_64) * in Windows Server 2012 R2 Standard with two Xeon Gold
6140 processors and 1 TB of RAM.

However, X!Tandom is using only Two threads and 4 GB of RAM and painfully
slow. Same is true for many other scripts.



1. Could you please let me know where to look for these parameters for
X!Tandem, Comet, and other scripts?



2. Do we need to setup for individual scripts or for TPP as a whole?



3. If for TPP, in which file please?



Thank you.

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RE: [spctools-discuss] TPP 5.2 ProteinProphet WARNING: Trying to compute mass of non-residue:

2018-11-20 Thread Eric Deutsch

Hi Robert, I think this warning comes when the FASTA database has
unexpected characters in it. Is there anything unusual about the FASTA
database you’re using? Unusual spaces or something?



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Robert
*Sent:* Tuesday, November 20, 2018 5:50 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] TPP 5.2 ProteinProphet WARNING: Trying to
compute mass of non-residue:



Hi, I am testing the docker version of TPP 5.2 on Windows 10,
works fine so far, but in the ProteinProphet step appears a warning (I
stopped the script after several minutes of the warning message running).
WARNING: Trying to compute mass of non-residue:
WARNING: Trying to compute mass of non-residue:
WARNING: Trying to compute mass of non-residue:
WARNING: Trying to compute mass of non-residue:
WARNING: Trying to compute mass of non-residue:
Any idea how to track down the error (I suppose a strange symbol??)?
Best, Robert

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RE: [spctools-discuss] Linux version of TPP

2018-11-19 Thread Eric Deutsch

If I understand your question correctly, just add the TPP bin directory to
your PATH, so with bash:



export PATH=$HOME/tpp/bin:$PATH



now you can just do:



xinteract



Is that what you mean?



Regards,

Eric





*From:* Kamal Mandal 
*Sent:* Monday, November 19, 2018 10:38 AM
*To:* Eric Deutsch 
*Cc:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Linux version of TPP



Looks like its working. But I have to either add all the executable files
as global aliases or I have to use complete address all the time. Anyway,
its better than not having tpp at all.

Can you suggest any better to handle it?



-Kamal



On Mon, Nov 19, 2018 at 9:45 AM Eric Deutsch 
wrote:

Hi Kamal, you could try downloading and trying to run these binaries
compiled under CentOS 7.5:



cd ~

wget http://www.tppms.org/sw/TPP5.2RC4/tppUsrLocalTpp-CentOS7.5.tgz

tar -zxf tppUsrLocalTpp-CentOS7.5.tgz

(this will create a tpp/ directory with the TPP programs in it. Test it
with the following)

tpp/bin/comet -p

tpp/bin/xinteract



See if that works for you. The `comet` command will run and create a
comet.params.new file in the current working directory. The xinteract will
generate a usage statement.



Regards,

Eric







*From:* Kamal Mandal 
*Sent:* Monday, November 19, 2018 9:27 AM
*To:* Eric Deutsch 
*Cc:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Linux version of TPP



Hi Eric,

I heard the following reply from our system administrator. Can you please
go through it and suggest me some alternative.



"I would recommend not installing the static versions of libstdc++ and
glibc and fixing the "Trans-Proteomics Pipeline" to use the shared
versions.  If only because the shared versions are maintained by us, the
wynton administrators.  If the pipeline is statically linked, then it
should be recompiled/relinked everytime the system is updated.  There can
be a speed advantage with static linking, but without a benchmark showing a
big advantage, it's not worth the maintenance headache."



-Kamal



On Sun, Nov 18, 2018 at 10:50 PM Kamal Mandal  wrote:

Thanks a lot Eric. I will check that with the administrator and let you
know.



-Kamal



On Sun, Nov 18, 2018 at 10:46 PM Eric Deutsch 
wrote:

Hi Kamal, glad you got subversion working. Odd that  svn:// did not work
but http did, but that’s fine, they are equivalent for this purpose.



The error messages in your attachment look like what you would get this
these yums were not run:



sudo yum -y install libstdc++-static

sudo yum -y install glibc-static



You probably need all of the packages I listed in the previous message
downthread. Can you check to see if those were installed?



Thanks,

Eric







*From:* Kamal Mandal 
*Sent:* Saturday, November 17, 2018 11:31 PM
*To:* Eric Deutsch 
*Cc:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Linux version of TPP



Hi Eric,

I managed to get svn. Though I had to use "http://svn.code.sf.net
<http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline>"
instead of "svn://svn.code.sf.net
<http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline>". I
don't know if that makes any difference.

However, I am getting an error while compiling - "make all".

Please find the attached file containing the error message.

Please suggest the needful.



-Kamal



On Thu, Nov 15, 2018 at 11:28 PM Kamal Mandal  wrote:

Eric,

I would like to get the tarball of TPP. That might help. I can ask our
administrator to install these dependencies.

Regarding docker- I tried "docker --version", it said "command not found".



Thanks,



-Kamal



On Thu, Nov 15, 2018 at 11:19 PM Eric Deutsch 
wrote:

Hi Kamal, I can post a tarball of the latest code if you’d like to download
that and try compiling it. However, there are a substantial number of other
requirements. I just launched a fresh CentOS 7.5 node and tried to compile
TPP. I found the following dependencies needed to be installed before it
would work nicely:



sudo yum -y install subversion

sudo yum -y groupinstall 'Development Tools'

sudo yum -y install gnuplot

sudo yum -y install gd-devel

sudo yum -y install libzip-devel

sudo yum -y install bzip2-devel

sudo yum -y install libstdc++-static

sudo yum -y install glibc-static

sudo yum -y install perl-devel



If you have someone you can ask to install those, then you should be able
to build TPP. If you cannot ask anyone to install such things for you, then
this may be difficult.



Is there Docker available on your machine/cluster? That would make it
easier.



Regards,

Eric











*From:* Kamal Mandal 
*Sent:* Thursday, November 15, 2018 9:44 PM
*To:* spctools-discuss@googlegroups.com
*Cc:* edeut...@systemsbiology.org
*Subject:* Re: [spctools-discuss] Linux version of TPP



HI Eric,

Thanks a lot for your quick response. Actually I tried this way but didn'

RE: [spctools-discuss] Linux version of TPP

2018-11-19 Thread Eric Deutsch

Hi Kamal, you could try downloading and trying to run these binaries
compiled under CentOS 7.5:

cd ~

wget http://www.tppms.org/sw/TPP5.2RC4/tppUsrLocalTpp-CentOS7.5.tgz

tar -zxf tppUsrLocalTpp-CentOS7.5.tgz

(this will create a tpp/ directory with the TPP programs in it. Test it
with the following)

tpp/bin/comet -p

tpp/bin/xinteract

See if that works for you. The `comet` command will run and create a
comet.params.new file in the current working directory. The xinteract will
generate a usage statement.

Regards,

Eric

*From:* Kamal Mandal
*Sent:* Monday, November 19, 2018 9:27 AM
*To:* Eric Deutsch
*Cc:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Linux version of TPP

Hi Eric,

I heard the following reply from our system administrator. Can you please
go through it and suggest me some alternative.

"I would recommend not installing the static versions of libstdc++ and
glibc and fixing the "Trans-Proteomics Pipeline" to use the shared
versions. If only because the shared versions are maintained by us, the
wynton administrators. If the pipeline is statically linked, then it
should be recompiled/relinked everytime the system is updated. There can
be a speed advantage with static linking, but without a benchmark showing a
big advantage, it's not worth the maintenance headache."

-Kamal

On Sun, Nov 18, 2018 at 10:50 PM Kamal Mandal wrote:

Thanks a lot Eric. I will check that with the administrator and let you
know.

-Kamal

On Sun, Nov 18, 2018 at 10:46 PM Eric Deutsch
wrote:

Hi Kamal, glad you got subversion working. Odd that svn:// did not work
but http did, but that’s fine, they are equivalent for this purpose.

The error messages in your attachment look like what you would get this
these yums were not run:

sudo yum -y install libstdc++-static

sudo yum -y install glibc-static

You probably need all of the packages I listed in the previous message
downthread. Can you check to see if those were installed?

Thanks,

Eric

*From:* Kamal Mandal
*Sent:* Saturday, November 17, 2018 11:31 PM
*To:* Eric Deutsch
*Cc:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Linux version of TPP

Hi Eric,

I managed to get svn. Though I had to use "http://svn.code.sf.net
<http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline>"
instead of "svn://svn.code.sf.net
<http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline>". I
don't know if that makes any difference.

However, I am getting an error while compiling - "make all".

Please find the attached file containing the error message.

Please suggest the needful.

-Kamal

On Thu, Nov 15, 2018 at 11:28 PM Kamal Mandal wrote:

Eric,

I would like to get the tarball of TPP. That might help. I can ask our
administrator to install these dependencies.

Regarding docker- I tried "docker --version", it said "command not found".

Thanks,

-Kamal

On Thu, Nov 15, 2018 at 11:19 PM Eric Deutsch
wrote:

Hi Kamal, I can post a tarball of the latest code if you’d like to download
that and try compiling it. However, there are a substantial number of other
requirements. I just launched a fresh CentOS 7.5 node and tried to compile
TPP. I found the following dependencies needed to be installed before it
would work nicely:

sudo yum -y install subversion

sudo yum -y groupinstall 'Development Tools'

sudo yum -y install gnuplot

sudo yum -y install gd-devel

sudo yum -y install libzip-devel

sudo yum -y install bzip2-devel

sudo yum -y install libstdc++-static

sudo yum -y install glibc-static

sudo yum -y install perl-devel

If you have someone you can ask to install those, then you should be able
to build TPP. If you cannot ask anyone to install such things for you, then
this may be difficult.

Is there Docker available on your machine/cluster? That would make it
easier.

Regards,

Eric

*From:* Kamal Mandal
*Sent:* Thursday, November 15, 2018 9:44 PM
*To:* spctools-discuss@googlegroups.com
*Cc:* edeut...@systemsbiology.org
*Subject:* Re: [spctools-discuss] Linux version of TPP

HI Eric,

Thanks a lot for your quick response. Actually I tried this way but didn't
work. I am not very much expert in computation, but it looks like "svn"
command is not working in our cluster. I thought if I download the entire
package, that might help.

Can you suggest some way out of it? Here is the specification of our
cluster - "CentOS Linux 7 (Core)"

-Kamal

On Thu, Nov 15, 2018 at 9:07 PM Eric Deutsch
wrote:

Hi Kamal, I’m not certain what would be best, but suppose you just install
the TPP in your own area under your username. So, based on the instructions
here:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS

You could install TPP in a space off your home directory and then use it
that way

RE: [spctools-discuss] Linux version of TPP

2018-11-18 Thread Eric Deutsch

Hi Kamal, glad you got subversion working. Odd that svn:// did not work
but http did, but that’s fine, they are equivalent for this purpose.

The error messages in your attachment look like what you would get this
these yums were not run:

sudo yum -y install libstdc++-static

sudo yum -y install glibc-static

You probably need all of the packages I listed in the previous message
downthread. Can you check to see if those were installed?

Thanks,

Eric

*From:* Kamal Mandal
*Sent:* Saturday, November 17, 2018 11:31 PM
*To:* Eric Deutsch
*Cc:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Linux version of TPP

Hi Eric,

However, I am getting an error while compiling - "make all".

Please find the attached file containing the error message.

Please suggest the needful.

-Kamal

On Thu, Nov 15, 2018 at 11:28 PM Kamal Mandal wrote:

Eric,

I would like to get the tarball of TPP. That might help. I can ask our
administrator to install these dependencies.

Regarding docker- I tried "docker --version", it said "command not found".

Thanks,

-Kamal

On Thu, Nov 15, 2018 at 11:19 PM Eric Deutsch
wrote:

sudo yum -y install subversion

sudo yum -y groupinstall 'Development Tools'

sudo yum -y install gnuplot

sudo yum -y install gd-devel

sudo yum -y install libzip-devel

sudo yum -y install bzip2-devel

sudo yum -y install libstdc++-static

sudo yum -y install glibc-static

sudo yum -y install perl-devel

If you have someone you can ask to install those, then you should be able
to build TPP. If you cannot ask anyone to install such things for you, then
this may be difficult.

Is there Docker available on your machine/cluster? That would make it
easier.

Regards,

Eric

*From:* Kamal Mandal
*Sent:* Thursday, November 15, 2018 9:44 PM
*To:* spctools-discuss@googlegroups.com
*Cc:* edeut...@systemsbiology.org
*Subject:* Re: [spctools-discuss] Linux version of TPP

HI Eric,

Can you suggest some way out of it? Here is the specification of our
cluster - "CentOS Linux 7 (Core)"

-Kamal

On Thu, Nov 15, 2018 at 9:07 PM Eric Deutsch
wrote:

Hi Kamal, I’m not certain what would be best, but suppose you just install
the TPP in your own area under your username. So, based on the instructions
here:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS

You could install TPP in a space off your home directory and then use it
that way on the cluster. Maybe something like this:

Assume your home directory is /home/kmandal, you could try something like
this:

cd /home/kmandal

mkdir tpp svn data

cd svn

svn checkout svn://
svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline

echo "INSTALL_DIR = /users/kmandal/tpp" > site.mk

echo "TPP_DATADIR = /users/kmandal/data" >> site.mk

make all

make install

If that all works, then the TPP executables are all in
/users/kmandal/tpp/bin

The possible snag is that you still need to have the equivalents of these
requirements installed on your machine to compile it:

sudo apt --yes install subversion

sudo apt --yes install build-essential

sudo apt --yes install perl

sudo apt --yes install zlib1g-dev

sudo apt --yes install libghc-bzlib-dev

sudo apt --yes install gnuplot

sudo apt --yes install unzip

sudo apt --yes install expat

sudo apt --yes install libexpat1-dev

Maybe your machine has all these already, or maybe not. Do you have a sys
administrator that you can ask to install those components?

What version of Linux is your cluster running, do you know?

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Kamal Mandal
*Sent:* Thursday, November 15, 2018 7:02 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Linux version of TPP

Hello,

Can anybody help me with the link for downloading the linux version of TPP.

The available recipe of installation doesn't work for me since I cannot use
"sudo" in our cluster. I can install it only in my own

RE: [spctools-discuss] Linux version of TPP

2018-11-15 Thread Eric Deutsch

sudo yum -y install subversion

sudo yum -y groupinstall 'Development Tools'

sudo yum -y install gnuplot

sudo yum -y install gd-devel

sudo yum -y install libzip-devel

sudo yum -y install bzip2-devel

sudo yum -y install libstdc++-static

sudo yum -y install glibc-static

sudo yum -y install perl-devel

If you have someone you can ask to install those, then you should be able
to build TPP. If you cannot ask anyone to install such things for you, then
this may be difficult.

Is there Docker available on your machine/cluster? That would make it
easier.

Regards,

Eric

*From:* Kamal Mandal
*Sent:* Thursday, November 15, 2018 9:44 PM
*To:* spctools-discuss@googlegroups.com
*Cc:* edeut...@systemsbiology.org
*Subject:* Re: [spctools-discuss] Linux version of TPP

HI Eric,

Can you suggest some way out of it? Here is the specification of our
cluster - "CentOS Linux 7 (Core)"

-Kamal

On Thu, Nov 15, 2018 at 9:07 PM Eric Deutsch
wrote:

Hi Kamal, I’m not certain what would be best, but suppose you just install
the TPP in your own area under your username. So, based on the instructions
here:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS

You could install TPP in a space off your home directory and then use it
that way on the cluster. Maybe something like this:

Assume your home directory is /home/kmandal, you could try something like
this:

cd /home/kmandal

mkdir tpp svn data

cd svn

svn checkout svn://
svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline

echo "INSTALL_DIR = /users/kmandal/tpp" > site.mk

echo "TPP_DATADIR = /users/kmandal/data" >> site.mk

make all

make install

If that all works, then the TPP executables are all in
/users/kmandal/tpp/bin

The possible snag is that you still need to have the equivalents of these
requirements installed on your machine to compile it:

sudo apt --yes install subversion

sudo apt --yes install build-essential

sudo apt --yes install perl

sudo apt --yes install zlib1g-dev

sudo apt --yes install libghc-bzlib-dev

sudo apt --yes install gnuplot

sudo apt --yes install unzip

sudo apt --yes install expat

sudo apt --yes install libexpat1-dev

Maybe your machine has all these already, or maybe not. Do you have a sys
administrator that you can ask to install those components?

What version of Linux is your cluster running, do you know?

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Kamal Mandal
*Sent:* Thursday, November 15, 2018 7:02 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Linux version of TPP

Hello,

Can anybody help me with the link for downloading the linux version of TPP.

The available recipe of installation doesn't work for me since I cannot use
"sudo" in our cluster. I can install it only in my own space.

-Kamal

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Kamal Mandal, M.Tech

Research Scholar

National Institute of Immunology, New Delhi

Aruna Asaf Ali Marg

New Delhi - 110067

*India*

*Contact no. :- +91- 9560445356 *

RE: [spctools-discuss] Linux version of TPP

2018-11-15 Thread Eric Deutsch

Hi Kamal, I’m not certain what would be best, but suppose you just install
the TPP in your own area under your username. So, based on the instructions
here:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS

You could install TPP in a space off your home directory and then use it
that way on the cluster. Maybe something like this:

Assume your home directory is /home/kmandal, you could try something like
this:

cd /home/kmandal

mkdir tpp svn data

cd svn

svn checkout svn://
svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline

echo "INSTALL_DIR = /users/kmandal/tpp" > site.mk

echo "TPP_DATADIR = /users/kmandal/data" >> site.mk

make all

make install

If that all works, then the TPP executables are all in
/users/kmandal/tpp/bin

The possible snag is that you still need to have the equivalents of these
requirements installed on your machine to compile it:

sudo apt --yes install subversion

sudo apt --yes install build-essential

sudo apt --yes install perl

sudo apt --yes install zlib1g-dev

sudo apt --yes install libghc-bzlib-dev

sudo apt --yes install gnuplot

sudo apt --yes install unzip

sudo apt --yes install expat

sudo apt --yes install libexpat1-dev

Maybe your machine has all these already, or maybe not. Do you have a sys
administrator that you can ask to install those components?

What version of Linux is your cluster running, do you know?

Regards,

Eric

*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Kamal Mandal
*Sent:* Thursday, November 15, 2018 7:02 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Linux version of TPP

Hello,

Can anybody help me with the link for downloading the linux version of TPP.

The available recipe of installation doesn't work for me since I cannot use
"sudo" in our cluster. I can install it only in my own space.

-Kamal

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RE: [spctools-discuss] Running TPP/Petunia GUI with Docker

2018-11-14 Thread Eric Deutsch

Hi Daryl, give this a try and provide any feedback you have:



http://tools.proteomecenter.org/wiki/index.php?title=Running_the_TPP_docker_image



You can either run individual commands or launch the GUI and work from that.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Darryl Davis
*Sent:* Tuesday, October 23, 2018 3:30 AM
*To:* spctools-discuss 
*Subject:* Re: [spctools-discuss] Running TPP/Petunia GUI with Docker



Hi Eric,

I also would very much like to sign up as a tester.

Thanks,

DD

On Monday, October 22, 2018 at 1:23:00 PM UTC-4, Eric Deutsch wrote:

Hi Robert, there is a TPP Docker container available via BioContainers:

https://hub.docker.com/r/biocontainers/tpp/



However, I’m pretty sure that this does not contain the GUI layer, it is
just the tools. (correct me if I’m wrong!)



However, with the imminent release of TPP 5.2.0, we are planning on have
both a tools-only and a GUI-enabled Docker container.  If anyone is
interested in being a tester of the container(s), please let us know!



Regards,

Eric





*From:* spctools...@googlegroups.com  <
spctools...@googlegroups.com > *On Behalf Of *Robert
*Sent:* Monday, October 22, 2018 5:50 AM
*To:* spctools-discuss >
*Subject:* [spctools-discuss] Running TPP/Petunia GUI with Docker



Dear TPP friends,

has anyone tried (or even solved) to run the TPP/Petunia GUI from a Docker
container/image?

Best, Robert

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RE: [spctools-discuss] convert prot.xml to EXCEL with biocontainers/tpp

2018-11-14 Thread Eric Deutsch

Hi Robert, we just put up a new Docker image for beta testing, see these
notes:



http://tools.proteomecenter.org/wiki/index.php?title=Running_the_TPP_docker_image



Have a look at that, and try running what you’re trying to do in the latest
image and see if that works better. If not, would you post the command
you’re trying to run?



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Robert
*Sent:* Monday, November 5, 2018 10:41 PM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] convert prot.xml to EXCEL with
biocontainers/tpp



Hi, I just run the TPP docker Prophet scripts.

However, the EXCELxx option for exporting the protein results into a
tabular format seems not to work (in contrast, EXCELPEPS works).

I also tried perl propxml2html.pl, but it complains: pepxml2html.pl: cannot
open xsl file : No such file or directory.

Is there any (standard) way on how to get the prot.xml into a tabular text
format with the tpp docker image?

Best, Robetr



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RE: [spctools-discuss] Running TPP/Petunia GUI with Docker

2018-10-22 Thread Eric Deutsch

Hi Robert, there is a TPP Docker container available via BioContainers:

https://hub.docker.com/r/biocontainers/tpp/



However, I’m pretty sure that this does not contain the GUI layer, it is
just the tools. (correct me if I’m wrong!)



However, with the imminent release of TPP 5.2.0, we are planning on have
both a tools-only and a GUI-enabled Docker container.  If anyone is
interested in being a tester of the container(s), please let us know!



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Robert
*Sent:* Monday, October 22, 2018 5:50 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Running TPP/Petunia GUI with Docker



Dear TPP friends,

has anyone tried (or even solved) to run the TPP/Petunia GUI from a Docker
container/image?

Best, Robert

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[spctools-discuss] TPP course Orlando Sep 25-29

2018-08-23 Thread Eric Deutsch

Hi everyone, there’s still room in the Trans-Proteomic Pipeline course the
week before the HUPO World Congress in Orlando if you’d like to sign up and
get hands-on training of the TPP. Please see this site for more information
and registration details:



https://hupo2018.org/Program/Workshops-Pre-and-Post

https://hupo2018.org/Portals/0/FlyerTPPCourseOrlando2018-09_Final_Update2.pdf



Let me know if you have questions!



Regards,

Eric





--

Eric W. Deutsch

Senior Research Scientist

Institute for Systems Biology

401 Terry Ave North

Seattle WA 98109

Email: edeut...@systemsbiology.org

ORCiD: -0001-8732-0928

Office: +1-206-732-1397

Fax: +1-206-732-1260

WWW: https://www.systemsbiology.org/eric-deutsch

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RE: [spctools-discuss] Re: Stpeter comet vs Xtandem?

2018-06-06 Thread Eric Deutsch

Oops, sorry, that should have been Sep 24-28. Information and registration
page is not up yet, but will be soon. We will announce here when it is open.



Thanks,

Eric





*From:* Eric Deutsch 
*Sent:* Wednesday, June 6, 2018 7:11 AM
*To:* spctools-discuss@googlegroups.com
*Cc:* Eric Deutsch 
*Subject:* RE: [spctools-discuss] Re: Stpeter comet vs Xtandem?



The next course will be September 28-48 in Orlando, Florida. This is the
week before the World HUPO Congress (https://www.hupo2018.org/), also in
Orlando. So, if you will be attending HUPO this fall, it might be an ideal
opportunity to arrive early in Orlando and attend the course.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Panos Ioannidis
*Sent:* Tuesday, June 5, 2018 9:50 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Re: Stpeter comet vs Xtandem?



Hi Jason,



Thanks a lot for the information. I would very much like to attend one of
your courses, if you guys are having one in Europe. We plan on doing some
protein sequencing in our lab in the next few months, so I'm sure the
course will be worth it.



Thanks again for your time,

Panos

On Tuesday, 5 June 2018 19:08:20 UTC+3, Jason Winget wrote:

Hi Panos,
>From your questions it seems like you would get a lot of benefit from the
TPP 5-day course. I suggest keeping an eye on this group for announcements
of when one might be available that you can attend.



Here are some brief answers in the meantime. Each search engine is
attempting to assign as many spectra to peptides as possible, however each
takes its own approach to solving this problem. Therefore some engines
perform better in certain circumstances, while others might prevail in
alternate circumstances. The speed of the search engine is not correlated
with the quality of its output. There are a number of good papers on mass
spec search engines that you can easily explore via pubmed or google
scholar.



Generally analysts will just use a single search engine because it's the
common one used in their lab. An example of this would be the Andromeda
search engine built into the popular MaxQuant software, or Mascot which has
a long history in the field. The TPP is agnostic and allows the analyst to
use the search engine of their choice, although it comes with some bundled
in for convenience. I would suggest trying a few on your data to get an
empirical idea of which perform the best for your platform.



Combining results from multiple search engines does generally boost total
peptide-spectrum matches, but I wouldn't say it's a common practice. The
trade off in computational time may not be worth the gains.



Again, I strongly suggest you attend the TPP course or chat with some of
the team at a conference booth, because I am leaving out a lot of nuance
here.

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RE: [spctools-discuss] Re: Stpeter comet vs Xtandem?

2018-06-06 Thread Eric Deutsch

The next course will be September 28-48 in Orlando, Florida. This is the
week before the World HUPO Congress (https://www.hupo2018.org/), also in
Orlando. So, if you will be attending HUPO this fall, it might be an ideal
opportunity to arrive early in Orlando and attend the course.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Panos Ioannidis
*Sent:* Tuesday, June 5, 2018 9:50 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Re: Stpeter comet vs Xtandem?



Hi Jason,



Thanks a lot for the information. I would very much like to attend one of
your courses, if you guys are having one in Europe. We plan on doing some
protein sequencing in our lab in the next few months, so I'm sure the
course will be worth it.



Thanks again for your time,

Panos

On Tuesday, 5 June 2018 19:08:20 UTC+3, Jason Winget wrote:

Hi Panos,
>From your questions it seems like you would get a lot of benefit from the
TPP 5-day course. I suggest keeping an eye on this group for announcements
of when one might be available that you can attend.



Here are some brief answers in the meantime. Each search engine is
attempting to assign as many spectra to peptides as possible, however each
takes its own approach to solving this problem. Therefore some engines
perform better in certain circumstances, while others might prevail in
alternate circumstances. The speed of the search engine is not correlated
with the quality of its output. There are a number of good papers on mass
spec search engines that you can easily explore via pubmed or google
scholar.



Generally analysts will just use a single search engine because it's the
common one used in their lab. An example of this would be the Andromeda
search engine built into the popular MaxQuant software, or Mascot which has
a long history in the field. The TPP is agnostic and allows the analyst to
use the search engine of their choice, although it comes with some bundled
in for convenience. I would suggest trying a few on your data to get an
empirical idea of which perform the best for your platform.



Combining results from multiple search engines does generally boost total
peptide-spectrum matches, but I wouldn't say it's a common practice. The
trade off in computational time may not be worth the gains.



Again, I strongly suggest you attend the TPP course or chat with some of
the team at a conference booth, because I am leaving out a lot of nuance
here.

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RE: [spctools-discuss] Duplicate peptides in consensus spectral library with different protein identifications

2018-05-03 Thread Eric Deutsch

Hi Sami, there are two kinds of SpectraST libraries, raw libraries and
consensus libraries. Raw libraries may have many replicates and that’s
fine. Consensus libraries will not have replicates. Replicates are
converted into a consensus by SpectraST when suitable flags are set. Note
that the same peptide with two different charge states are NOT replicates.
Those are different, because both the precursor and the product ion
spectrum are different.



Regarding different protein mappings, I believe that SpectraST has an
option to remap the peptides in a library against a new FASTA file. I
forget the option but you should be able to find it in the docs, I can’t
view them at the moment. Let me know if you can’t find it and I’ll look.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com 
*On Behalf Of *Sami Pietilä
*Sent:* Thursday, May 3, 2018 6:00 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Duplicate peptides in consensus spectral
library with different protein identifications



Hi all!

I am using spectrast from TPP 5.1 to generate a consensus spectral library.
I noticed that the resulting library can contain the same peptide
(identical sequence) multiple times. The charge stage might vary between
the entries as well as the protein annotation (also originating sample can
be different).

Somehow it looks like a single peptide sequence can have different protein
annotation in a library depending on what is the originating sample. Is
this by design? I am wondering how to deal with this situation when
analyzing the resulting data.

Thanks

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RE: [spctools-discuss] TPP build issues on an Ubuntu 17 system

2018-02-20 Thread Eric Deutsch

Hi, is it really "idcovert" as you quoted? Or is the error about "idconvert"
?



*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *
ku...@healthtechnologyinnovations.com
*Sent:* Sunday, February 18, 2018 12:32 PM
*To:* spctools-discuss <spctools-discuss@googlegroups.com>
*Subject:* Re: [spctools-discuss] TPP build issues on an Ubuntu 17 system



Thanks, Eric.  I made some progress (but not enough!).  Here is what I did:



cd  build/gnu-x86-64/artifacts directory



$ aclocal

$ automake

$ make



This helped resolve the libtools issue. Went back to the release directory
and tried to make all.

Surprisingly, the make went on for over 30 minutes (I assume progress) but
stopped due to "idcovert".  It could not find it.

I found a directory with source code for idconvert, msconvert etc. but the
Makefile in that directory does not make the binaries.  Do you know where I
could find them?

Thanks



On Tuesday, February 13, 2018 at 3:02:42 PM UTC-8, Eric Deutsch wrote:

Hi, we haven’t tried to install it on Ubuntu 17, only the 16.04 LTS, with
the recipe you found. So I can’t really help much at this point. I googled
a little and found this:



https://stackoverflow.com/questions/3096989/libtool-version-mismatch-error



Does this help maybe? If you do figure it out, please post the diffs from
the instructions from 16 to 17.



Thanks,

Eric





*From:* spctools...@googlegroups.com  [mailto:
spctools...@googlegroups.com ] *On Behalf Of *
ku...@healthtechnologyinnovations.com 
*Sent:* Monday, February 12, 2018 5:08 PM
*To:* spctools-discuss <spctools...@googlegroups.com >
*Subject:* [spctools-discuss] TPP build issues on an Ubuntu 17 system



Ladies and gents:



I am trying to generate TPP from source. Here is what I did:



I have an Ubuntu 17 machine (Intel Xenon + Nvidia system).

Followed the instructions posted at
http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.1.0:_Installing_on_Ubuntu_16.04_LTS
:

1) Installed the prerequisite packages, with no errors

2) Created the suitable place to install

3) Pulled the 5.1.0 source code

4) Created the site.mk (as per the instructions)



When trying to make libgd, I started running into issues:

First, I got this:



WARNING: 'automake-1.14' is missing on your system.

 You should only need it if you modified 'Makefile.am' or

 'configure.ac' or m4 files included by 'configure.ac'.

 The 'automake' program is part of the GNU Automake package:

 <http://www.gnu.org/software/automake>

 It also requires GNU Autoconf, GNU m4 and Perl in order to run:

 <http://www.gnu.org/software/autoconf>

 <http://www.gnu.org/software/m4/>

 <http://www.perl.org/>

Makefile:337: recipe for target 'Makefile.in' failed

make: *** [Makefile.in] Error 1

I resolved it using this:

cd build/gnu-x86_64/artifacts/libpng-1.5.19

$ aclocal

$ automake

$ make

I have automake-1.15 and the above steps helped me go past that issue.



Now I am at this compile issue, which seems to be very difficult to
resolve.





touch config.h.in

cd . && /bin/bash ./config.status config.h

config.status: creating config.h

/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H
-I.  -DPNG_CONFIGURE_LIBPNG   -g -O2 -MT libpng15_la-png.lo -MD -MP -MF
.deps/libpng15_la-png.Tpo -c -o libpng15_la-png.lo `test -f 'png.c' || echo
'./'`png.c

libtool: Version mismatch error.  This is libtool 2.4.2, but the

libtool: definition of this LT_INIT comes from libtool 2.4.6.

libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2

libtool: and run autoconf again.

Makefile:797: recipe for target 'libpng15_la-png.lo' failed

make[1]: *** [libpng15_la-png.lo] Error 63

make[1]: Leaving directory
'/local/svn/release_5-1-0/build/gnu-x86_64/artifacts/libpng-1.5.19'

extern/Makefile:893: recipe for target
'/local/svn/release_5-1-0/build/gnu-x86_64/lib/libpng.a' failed

make: *** [/local/svn/release_5-1-0/build/gnu-x86_64/lib/libpng.a] Error 2



Googling libtool issues, I am not getting anywhere.

Any help would greatly be appreciated: Has anyone tried building in Ubuntu
17?



Thanks

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RE: [spctools-discuss] TPP build issues on an Ubuntu 17 system

2018-02-13 Thread Eric Deutsch

Hi, we haven’t tried to install it on Ubuntu 17, only the 16.04 LTS, with
the recipe you found. So I can’t really help much at this point. I googled
a little and found this:

https://stackoverflow.com/questions/3096989/libtool-version-mismatch-error

Does this help maybe? If you do figure it out, please post the diffs from
the instructions from 16 to 17.

Thanks,

Eric

*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *
ku...@healthtechnologyinnovations.com
*Sent:* Monday, February 12, 2018 5:08 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] TPP build issues on an Ubuntu 17 system

Ladies and gents:

I am trying to generate TPP from source. Here is what I did:

I have an Ubuntu 17 machine (Intel Xenon + Nvidia system).

Followed the instructions posted at
http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.1.0:_Installing_on_Ubuntu_16.04_LTS
:

1) Installed the prerequisite packages, with no errors

2) Created the suitable place to install

3) Pulled the 5.1.0 source code

4) Created the site.mk (as per the instructions)

When trying to make libgd, I started running into issues:

First, I got this:

WARNING: 'automake-1.14' is missing on your system.

You should only need it if you modified 'Makefile.am' or

'configure.ac' or m4 files included by 'configure.ac'.

The 'automake' program is part of the GNU Automake package:

It also requires GNU Autoconf, GNU m4 and Perl in order to run:

Makefile:337: recipe for target 'Makefile.in' failed

make: *** [Makefile.in] Error 1

I resolved it using this:

cd build/gnu-x86_64/artifacts/libpng-1.5.19

$ aclocal

$ automake

$ make

I have automake-1.15 and the above steps helped me go past that issue.

Now I am at this compile issue, which seems to be very difficult to
resolve.

touch config.h.in

cd . && /bin/bash ./config.status config.h

config.status: creating config.h

/bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-DPNG_CONFIGURE_LIBPNG -g -O2 -MT libpng15_la-png.lo -MD -MP -MF
.deps/libpng15_la-png.Tpo -c -o libpng15_la-png.lo `test -f 'png.c' || echo
'./'`png.c

libtool: Version mismatch error. This is libtool 2.4.2, but the

libtool: definition of this LT_INIT comes from libtool 2.4.6.

libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2

libtool: and run autoconf again.

Makefile:797: recipe for target 'libpng15_la-png.lo' failed

make[1]: *** [libpng15_la-png.lo] Error 63

make[1]: Leaving directory
'/local/svn/release_5-1-0/build/gnu-x86_64/artifacts/libpng-1.5.19'

extern/Makefile:893: recipe for target
'/local/svn/release_5-1-0/build/gnu-x86_64/lib/libpng.a' failed

make: *** [/local/svn/release_5-1-0/build/gnu-x86_64/lib/libpng.a] Error 2

Googling libtool issues, I am not getting anywhere.

Any help would greatly be appreciated: Has anyone tried building in Ubuntu
17?

Thanks

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RE: [spctools-discuss] Re: Help! - The requested URL /tpp/cgi-bin/tpp_gui.pl was not found on this server.

2018-01-30 Thread Eric Deutsch

Those should be functionally equivalent, I think, so that is puzzling. Did
you completely clean the build area between these two runs, or was it
already partly built when you ran the second? As noted in the instructions,
there seems to be some intermittent issue with building where sometimes it
works all the way through but sometimes it halts, but then immediately
doing another `make` allows completion. Maybe you hit that intermittent
stoppage on the first run, but not the second?

Thanks for reporting your experience!

Eric

*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Stanislav Luban
*Sent:* Tuesday, January 30, 2018 4:54 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Re: Help! - The requested URL /tpp/cgi-bin/
tpp_gui.pl was not found on this server.

Hi,

Update:

Following instructions at
http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.1.0:_Installing_on_Ubuntu_16.04_LTS

Instead of doing:
sudo make libgd
sudo make all
sudo make install

Did:

sudo su
make libgd
make all
make install

and the installation seemed to complete without error.

After following the rest of instructions including for Apache, navigating
to http://localhost:10401/tpp/cgi-bin/tpp_gui.pl to login with guest / guest
We seem to have bypassed the problem previously being encountered.

Thanks greatly,
s luban

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RE: [spctools-discuss] spectrast produces empty output file

2017-10-27 Thread Eric Deutsch

Dear Hannes, sorry for this problem you had, and thanks so much for
tracking this down exactly and sending us the offending code and solution.
After investigating this a bit more we’ve determined that the problem was
introduced in a check-in to trunk on Oct 2. Yesterday we checked in some
new code that fixes this problem and adds some additional functionality as
well from other development. We did not use your patch exactly as is, but
thank you for sending it.

Please try updating to the latest trunk and using that code, and let us
know if you have further trouble with it.

A note to everyone else: if you compiled TPP yourself from trunk during the
month of October, please recompile with the latest trunk to fix this
problem. Official TPP releases are not affected by this problem as far as
we know. We plan to release TPP 5.1 next week and this will be fixed.

Thanks,

Eric

*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Hannes Roest
*Sent:* Tuesday, October 24, 2017 7:38 AM
*To:* spctools-discuss <spctools-discuss@googlegroups.com>
*Subject:* Re: [spctools-discuss] spectrast produces empty output file

Dear Eric

I have now tracked down the problem to a bit of logic in TPP
in mzParser/RAMPface.cpp

 501   scanHeader->precursorMZ = ( p.isoMZ > 0 ? p.monoMZ : p.mz );

basically what this assumes is that whenever p.isoMZ is set, then the
precursorMZ is best set to p.monoMZ. The problem is that this logic fails
for the files that I have tested where p.isoMZ is set but p.monoMZ is set
to zero.  This happens for the attached mzML and mzXML files both. It seems
for the mzML file there is some quirky logic
in ./mzParser/saxmzmlhandler.cpp which sets m_precursorIon.isoMZ when the
tag MS:1000827 is encountered but this leads further down to not
settting m_precursorIon.monoMZ since neither of the conditions is
fulfilled. In the end, both parsers fail to ensure that if p.isoMZ is
larger than zero that p.monoMZ is set. This of course leads to setting the
precursorMZ of the scanHeader to zero on which spectrast relies.

I attach a patch  that ensures that in either case the monoMZ is set if the
isoMZ is set.

Best

Hannes

On Saturday, October 21, 2017 at 2:24:29 AM UTC-4, Hannes Roest wrote:

Dear Eric

I see now the same thing:

$ /home/hr/openmsall/source/THIRDPARTY/Linux/64bit//spectrast -V
-sLtestLib.splib spectra.mzXML
SpectraST started at Sat Oct 21 02:18:54 2017.
VERBOSE MODE...
Library File loaded: "testLib.splib".
Sorting query spectra in all mzXML files by precursor m/z before
searching...DONE!

Now searching query: spectra.1.1.536870927 (PrecursorMZ =
8.98729e-315; PrecursorCharge = 536870927)
Found 0 candidate(s)...  Comparing...  DONE! Top hit: NO_MATCH
Now searching query: spectra.2.2.0 (PrecursorMZ =
8.98729e-315; PrecursorCharge = 2,3,4,5,6)
Found 0 candidate(s)...  Comparing...  DONE! Top hit: NO_MATCH
Now searching query: spectra.3.3.0 (PrecursorMZ = 8.98729e-315)
Found 0 candidate(s)...  Comparing...  DONE! Top hit: NO_MATCH
Finished searching "spectra.mzXML" (3 spectra searched.)
Output written to "/home/hr/openmsall/builds/openms/spectra.pep.xml".
Total Number of Searches Performed = 3; Run Time per Search = 0.6667
seconds.
Total Run Time = 2 seconds.
SpectraST finished at Sat Oct 21 02:18:56 2017 without error.

so clearly there is a parsing error with the mzXML file. It seems that
precursor charge and precursormz are not initialized properly here,
but they are in the file. Do you see what is going on here? The mzXML
file is based on this file:
https://github.com/OpenMS/OpenMS/blob/develop/src/tests/topp/THIRDPARTY/spectra_comet.mzML
which I converted to mzXML. The file appears to be an LTQ Velos file
that was generated by XCalibur and converted with proteowizard.

Thanks for looking into this

Hannes

On Fri, Oct 20, 2017 at 6:57 PM, Eric Deutsch
> I ran SpectraST on your file with –V and it seems to show that it is not
> reading the precursor mz from you file somehow. All the precursormzs in
the
> verbose output are 0. I peeked in the file and I do see precursor mzs in
> there, but I don’t know if they are encoded correctly.
>
>
>
> Where did this mzXML file come from?
>
>
>
>
>
> From: spctools-discuss@googlegroups.com
> [mailto:spctools-discuss@googlegroups.com] On Behalf Of Hannes Roest
> Sent: Friday, October 20, 2017 3:15 PM
> To: spctools-discuss <spctools-discuss@googlegroups.com>
> Subject: Re: [spctools-discuss] spectrast produces empty output file
>
>
>
> Dear Eric
>
>
>
> Thanks for your analysis
>
>
>
> 1. I found that mzXML worked better with SpectraST and the mzML file did
not
> work at all:
>
>
>
> $ spectrast  -sLtestLib.splib spectra.mzML
>
> SpectraST started at Fri Oct 20 18:06:1

RE: [spctools-discuss] Peptide identification using AB SCIEX Raw data

2017-10-25 Thread Eric Deutsch

Regarding “can I trust this?”, I’m certain there is an error rate
associated with those calls, but I do not know what it is. Many spectra are
chimeric and thus the charge assignment may not be valid for all of the
precursors.



Good luck!

Eric







*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Naiping Dong
*Sent:* Wednesday, October 25, 2017 4:58 PM
*To:* spctools-discuss@googlegroups.com
*Subject:* RE: [spctools-discuss] Peptide identification using AB SCIEX Raw
data



Hi Eric,



Thanks for your suggestion, it's very valuable for me.



I noticed that AB SCIEX assigned charge states to precursors, even
fragments. But can I trust this? ProteinPilot tries several charge states
for each tandem mass spectrum, so I think we can ignore those charges
evaluated by AB. I am now setting very wide range of charge in Comet search.



Thanks again.



Regards,



Ellen.



2017年10月25日 下午11:56，"Eric Deutsch" <edeut...@systemsbiology.org>写道：

Hi Elkan, every converter will do things a little differently. It’s hard to
say which is better. I think we did some tests a while back and the SCIEX
conversion of 5600 DDA data yielded slightly more IDs than with msconvert
converter, but they were pretty similar. For most datasets, it should not
matter much. I think SCIEX’s converter can produce mzML files as well, so I
would recommend mzML instead of MGF. You could do both and compare. But
you’ll likely be fine just to pick one and go with it.



In reviewing some notes I have, it looks like the msconvert tool does not
have access to the precursor charge states, while the SCIEX converter does.
So the SCIEX convert to mzML is probably the best option because you will
get charge states, while a search with msconverted mzML will be guessing
charge states. Just a problem with the SCIEX API that msconvert has access
to.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Elkan Dong
*Sent:* Tuesday, October 24, 2017 10:08 PM
*To:* spctools-discuss <spctools-discuss@googlegroups.com>
*Subject:* [spctools-discuss] Peptide identification using AB SCIEX Raw data



Dear all,



I have raw data derived from AB SCIEX TripleTOF 5600 and protein
identification results obtained from ProteinPilot using MGF files converted
by AB SCIEX MS Converter.

Now I want to use other search engines like Comet or X!Tandem to search the
data again. So I converted to raw data to ..mzML files using ProteoWizard
MSConvert and then searched by Comet.

The question is that I found the spectra in ..mzML files are different with
those in MGF peak lists generated by AB SCIEX MS Converter, what should I
do? Still use ..mzML files generated by MSConvert or use AB SCIEX's MGF
peak list?

The helper of AB SCIEX MS Converter says that a signal processing procedure
is applied when the converter is used to convert raw data to MGF peak list.
Can I consider this as a preprocessing procedure of AB SCIEX search engine
(i.e., ProteinPilot) to improve the identification? If so, I think I should
use the ..mzML as Comet applies its own preprocessing procedure. But if
not, I will use AB SCIEX's MGF peak list and skip the preprocessing
procedure when Comet is used. How can I do this?



Can you help me on this?



Thanks.



Elkan

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RE: [spctools-discuss] Peptide identification using AB SCIEX Raw data

2017-10-25 Thread Eric Deutsch

Hi Elkan, every converter will do things a little differently. It’s hard to
say which is better. I think we did some tests a while back and the SCIEX
conversion of 5600 DDA data yielded slightly more IDs than with msconvert
converter, but they were pretty similar. For most datasets, it should not
matter much. I think SCIEX’s converter can produce mzML files as well, so I
would recommend mzML instead of MGF. You could do both and compare. But
you’ll likely be fine just to pick one and go with it.



In reviewing some notes I have, it looks like the msconvert tool does not
have access to the precursor charge states, while the SCIEX converter does.
So the SCIEX convert to mzML is probably the best option because you will
get charge states, while a search with msconverted mzML will be guessing
charge states. Just a problem with the SCIEX API that msconvert has access
to.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Elkan Dong
*Sent:* Tuesday, October 24, 2017 10:08 PM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Peptide identification using AB SCIEX Raw data



Dear all,



I have raw data derived from AB SCIEX TripleTOF 5600 and protein
identification results obtained from ProteinPilot using MGF files converted
by AB SCIEX MS Converter.

Now I want to use other search engines like Comet or X!Tandem to search the
data again. So I converted to raw data to ..mzML files using ProteoWizard
MSConvert and then searched by Comet.

The question is that I found the spectra in ..mzML files are different with
those in MGF peak lists generated by AB SCIEX MS Converter, what should I
do? Still use ..mzML files generated by MSConvert or use AB SCIEX's MGF
peak list?

The helper of AB SCIEX MS Converter says that a signal processing procedure
is applied when the converter is used to convert raw data to MGF peak list.
Can I consider this as a preprocessing procedure of AB SCIEX search engine
(i.e., ProteinPilot) to improve the identification? If so, I think I should
use the ..mzML as Comet applies its own preprocessing procedure. But if
not, I will use AB SCIEX's MGF peak list and skip the preprocessing
procedure when Comet is used. How can I do this?



Can you help me on this?



Thanks.



Elkan

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RE: [spctools-discuss] spectrast produces empty output file

2017-10-20 Thread Eric Deutsch

I ran SpectraST on your file with –V and it seems to show that it is not
reading the precursor mz from you file somehow. All the precursormzs in the
verbose output are 0. I peeked in the file and I do see precursor mzs in
there, but I don’t know if they are encoded correctly.



Where did this mzXML file come from?





*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Hannes Roest
*Sent:* Friday, October 20, 2017 3:15 PM
*To:* spctools-discuss <spctools-discuss@googlegroups.com>
*Subject:* Re: [spctools-discuss] spectrast produces empty output file



Dear Eric



Thanks for your analysis



1. I found that mzXML worked better with SpectraST and the mzML file did
not work at all:



$ spectrast  -sLtestLib.splib spectra.mzML

SpectraST started at Fri Oct 20 18:06:18 2017.

Library File loaded: "testLib.splib".

Total Number of Searches Performed = 0; Run Time per Search = inf seconds.

Total Run Time = 2 seconds.

SpectraST finished at Fri Oct 20 18:06:20 2017 without error.



$ spectrast  -sLtestLib.splib spectra.mzXML

SpectraST started at Fri Oct 20 18:07:06 2017.

Library File loaded: "testLib.splib".

Sorting query spectra in all mzXML files by precursor m/z before
searching...DONE!

Searching...10%...20%...30%...DONE!

Finished searching "spectra.mzXML" (3 spectra searched.)

Output written to "/home/hr/openmsall/builds/openms/spectra.pep.xml".

Total Number of Searches Performed = 3; Run Time per Search = 0.6667
seconds.

Total Run Time = 2 seconds.

SpectraST finished at Fri Oct 20 18:07:08 2017 without error.



2. Yes there are only two as comet did only find matches for 2 spectra.
However, searching a  library of 2 spectra against a file of 3 spectra
should still work?

3. These are "MaxQuant compatible CR". I have removed those but without any
change in result. Unfortunately.



Hannes


On Friday, October 20, 2017 at 5:57:45 PM UTC-4, Eric Deutsch wrote:

Hi Hannes, I had a quick peek at your file and while I didn’t do any
testing a few things come to mind.



1) It could be that because you’re using mzXML (you meant to use mzML,
didn’t you? ;-) SpectraST might not be not detecting that these are HCD
spectra when building the library? The peptides are labeled (CID) when I
they should be labeled (HCD) I assume? When creating the library, maybe
-cIHCD would help? Just guessing



2) Unless I mis-count, there are only 2 spectra in the sptxt?



3) The mzML has some unusual carriage returns in the third spectrum. It
could be causing some problem possibly..



I would investigate those first, but maybe it’s something else..



Eric









*From:* spctools...@googlegroups.com  [mailto:
spctools...@googlegroups.com ] *On Behalf Of *Hannes Roest
*Sent:* Friday, October 20, 2017 1:58 PM
*To:* spctools-discuss <spctools...@googlegroups.com >
*Subject:* [spctools-discuss] spectrast produces empty output file



Dear Henry

I am trying to set up a minimal example for a spectral library search, but
I cannot get it to work. I have a spectral library and a corresponding
mzXML file:

$ spectrast  -sLtestLib.splib spectra.mzXML
SpectraST started at Fri Oct 20 16:43:54 2017.
Library File loaded: "testLib.splib".
Sorting query spectra in all mzXML files by precursor m/z before
searching...DONE!
Searching...10%...20%...30%...DONE!
Finished searching "spectra.mzXML" (3 spectra searched.)
Output written to "/home/hr/openmsall/builds/openms/spectra.pep.xml".
Total Number of Searches Performed = 3; Run Time per Search = 1 seconds.
Total Run Time = 3 seconds.
SpectraST finished at Fri Oct 20 16:43:57 2017 without error.

however, the resulting file spectra.pep.xml appears to be empty. Is there
any reason for this or any parameter I can change to make this example
work? Note that I generated the spectral library from that same mzXML file
(searched with comet) and I expect that the spectra match perfectly, so I
find an empty result file an unexpected outcome.

Thanks

Hannes

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RE: [spctools-discuss] "- Search progress: Error - database file, expecting definition line here." Error with custom database

2017-09-29 Thread Eric Deutsch

Greater than symbol should be first on the line. Instead of:



sp>|Q13547|HDAC1_HUMAN



must be:



>sp|Q13547|HDAC1_HUMAN



Eric





*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Adam R
*Sent:* Thursday, September 28, 2017 8:41 PM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] "- Search progress: Error - database file,
expecting definition line here." Error with custom database



Hi Everyone,

I am trying to assemble a customized fasta database to search spectra
against. I believe I had the correct format as:

sp>|Q13547|HDAC1_HUMAN Histone deacetylase 1 OS=Homo sapiens GN=HDAC1 PE=1
SV=1

MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKAN

AEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAS

AVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHG

DGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAI

FKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGG

GGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLE

KIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEDDPDKRISICSSDKRIACEEEF

SDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVK

LA



With all over the other proteins following the same format. I haven't had
issues with the past when copying and pasting in sequences from the GPM
crapome database

so I am not sure what is wrong about it...

Thanks,

Adam

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[spctools-discuss] Upcoming TPP courses

2017-06-26 Thread Eric Deutsch

Hi everyone, I would like to let you know about various TPP course related
events:



There is still room to register attend the TPP course here at ISB July
19-21. This was originally designed as an advanced course, but we have
altered it to be more of an introductory course due to various requests.
See agenda and registration information and lodging options at:

https://moritz.systemsbiology.org/courses/proteomics-informatics-course/july-2017-seattle-washington/



Please note also that this course immediately follows the two-day Cascadia
Proteomics Symposium. It may be fun to attend both! For more information,
please see:

http://www.cascadiaproteomics.org/



We have also confirmed that the next TPP course will be held September
12-16 in Dublin in the week prior to the HUPO World Congress. Registration
is not yet open, but will in soon. Please examine the information we have
so far and mark your calendar if you’re thinking of attending:



Course Information page:

https://moritz.systemsbiology.org/courses/proteomics-informatics-course/september-2017-dublin-ireland/



World HUPO Congress site.

http://hupo2017.ie/



Please let me know if you have any questions!



Please forward this message to any colleagues who might be interested in
attending.



Regards,

Eric

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RE: [spctools-discuss] SpectraST question about different charge states of candidate library spectra and query spectra

2017-06-26 Thread Eric Deutsch

Hi Jianqiao, although I am not 100% certain, I do not recall any SpectraST
feature where it will try to match a spectrum to a library entry outside
the normal tolerance window, but corrected for an alternate charge state.



This is an interesting idea for a feature, I hadn’t thought about this
before. It might be successful in matching some additional spectra, at
least for 2+ and 3+, which often look similar. But not yet possible.



Maybe Henry can correct me or provide additional thoughts.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Jianqiao Shen
*Sent:* Sunday, June 25, 2017 1:45 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] SpectraST question about different charge
states of candidate library spectra and query spectra



Hi,



I am using SpectraST to build a spectral library. I know that the precursor
m/z of candidate library spectrum should be in tolerance of query spectrum.
My question is whether SpectraST can match the candidate library spectrum
with the query spectrum if their precursor have different charge states.



For example, we have spectrum A in library and its corresponding peptide
sequence is X with mass 1000, and the charge of precursor is 2 so the
precursor m/z is 500. We also have the query spectrum B and its peptide
sequence is X with mass 1000 as well but the charge of precursor is 3
so the precursor m/z is 333. Can SpectraST match the candidate library
spectrum A with query spectrum B regardless of their different charge?



Thank you!

Jianqiao Shen



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RE: [spctools-discuss] Re: Can't open spctools wiki

2017-05-24 Thread Eric Deutsch

Hi Jamie, thanks for letting us know about the problem. It was a different
problem than before. It is back up now.



Although we do plan to upgrade the Wiki software, so it will have to go
down again for maintenance sometime soon, but not scheduled yet.





*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Jamie Walters
*Sent:* Wednesday, May 24, 2017 11:54 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Re: Can't open spctools wiki



I'm sorry to say it looks like the wiki is still down. I can't access any
of the pages -- I just keep getting blank pages. I am also looking to
install on Linux, so tutorials/directions would be helpful.

Thanks,  Jamie


On Wednesday, May 10, 2017 at 1:06:02 PM UTC-5, xu wrote:

Hello

   I attempted to install TPP on my linux. So I want to get some tutorials
to read about installation. But I couldn't open spctools wiki through the
link on this website



   http://tools.proteomecenter.org/software.php



   And here is the message I got when I tried to open wiki:







 Does anyone can help me solve this problem?

 Thanks a lot.









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RE: [spctools-discuss] Can't open spctools wiki

2017-05-10 Thread Eric Deutsch

Hi, our MySQL back-end to the wiki was acting up yesterday at the time your
email was sent (although your email just landed in my inbox now). This was
fixed yesterday and should all be fine now. You might find this page of
guides useful:



http://tools.proteomecenter.org/wiki/index.php?title=Linux_Installation_Guides



Regards,

Eric





*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *xu
*Sent:* Tuesday, May 9, 2017 3:25 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Can't open spctools wiki



Hello

   I attempted to install TPP on my linux. So I want to get some tutorials
to read about installation. But I couldn't open spctools wiki through the
link on this website



   http://tools.proteomecenter.org/software.php



   And here is the message I got when I tried to open wiki:



[image: Image removed by sender.]




 Does anyone can help me solve this problem?

 Thanks a lot.









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RE: [spctools-discuss] Parameters in X!tandem inputfile for itraq 8

2017-04-06 Thread Eric Deutsch

Yes, but note that the documentation you quote is for SILAC data. While in
your original message, you were asking about iTRAQ data. SILAC and iTRAQ
are completely different. These SILAC settings don’t apply to iTRAQ. Unless
you’re combining the two..

*From:* richard chiang [mailto:9richardchi...@gmail.com]
*Sent:* Thursday, April 6, 2017 9:03 PM
*To:* spctools-discuss <spctools-discuss@googlegroups.com>
*Cc:* edeut...@systemsbiology.org
*Subject:* Re: [spctools-discuss] Parameters in X!tandem inputfile for
itraq 8

Thank you! I am not quite understand your meaning. I just modified it
according follows, although I am not sure if it was right.
residue, modification mass <http://www.thegpm.org/TANDEM/api/rmm.html>:

In order to facilitate the analysis of SILAC data, the capability of having
multiple sets of modifications analyzed simultaneously has been added. To
specify additional sets of modifications, use the same parameter name with
the addition of an incrementing count (starting at 1):

residue, modification mass 1
residue, modification mass 2
...
residue, modification mass N
I will do a further reading to bettter understand it. And your anwser give
me another confussion,if a signal modification is enough, how should the
libra program to differentiate the proteins for quantification later.
在 2017年4月7日星期五 UTC+8上午10:53:51，Eric Deutsch写道：

Hi, I don’t think that will get you anything useful, although you could try
it to see if you get anything that way. All you want is a single
modification on n-term and K as in the other thread.

I’m guessing what happens is that the reporter ions like to hold the charge
and most peptides will still fragment somewhere along the backbone. So.. if
the reporter ion stays attached, then you see the mass of both the reporter
and balance group plus residues until the break. But, if the reporter ions
breaks off, then the charge stays on the reporter ion and you see it, while
the molecule with the residues plus the balance group has no charge and so
you don’t see it. So the molecules you’re thinking of are there, but they
rarely carry a charge so you don’t see them. That’s my guess. If anyone who
really knows can set us straight, that would be great.

Regards,

Eric

*From:* spctools...@googlegroups.com [mailto:
spctools...@googlegroups.com ] *On Behalf Of *richard chiang
*Sent:* Thursday, April 6, 2017 7:16 PM
*To:* spctools-discuss <spctools...@googlegroups.com >
*Subject:* [spctools-discuss] Parameters in X!tandem inputfile for itraq 8

Hi,
I am trying to anlysis itraq8 Ms/Ms data with xtandm, and got confused by
a previouse disscussion iTRAQ data through xtandem! using TPP.
<https://groups.google.com/forum/#!searchin/spctools-discuss/tandem$20parameters%7Csort:date/spctools-discuss/e4wihr_i8JE/1SNYto9jMVgJ>
Should not the parameters in tandem.paraams.xml like follows,since balance
groups have been removed by the second Ms

57.0...@C>

15.9...@M,8.014199@K,10.008269@R>
113@K
114@K
116@K
117@K
118@K
121@K

You can specify a variable modification only when present in
a motif. For instance, 0@N!{P}[ST ] is a deamidation
modification on N only if it is present in an N[any but P][S or T] motif
(N-glycosite).
113@K
114@K
116@K
117@K
118@K
121@K

Sincerely,
Richard

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RE: [spctools-discuss] Parameters in X!tandem inputfile for itraq 8

2017-04-06 Thread Eric Deutsch

Hi, I don’t think that will get you anything useful, although you could try
it to see if you get anything that way. All you want is a single
modification on n-term and K as in the other thread.



I’m guessing what happens is that the reporter ions like to hold the charge
and most peptides will still fragment somewhere along the backbone. So.. if
the reporter ion stays attached, then you see the mass of both the reporter
and balance group plus residues until the break. But, if the reporter ions
breaks off, then the charge stays on the reporter ion and you see it, while
the molecule with the residues plus the balance group has no charge and so
you don’t see it. So the molecules you’re thinking of are there, but they
rarely carry a charge so you don’t see them. That’s my guess. If anyone who
really knows can set us straight, that would be great.



Regards,

Eric







*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *richard chiang
*Sent:* Thursday, April 6, 2017 7:16 PM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Parameters in X!tandem inputfile for itraq 8



 Hi,
 I am trying to anlysis itraq8 Ms/Ms data with xtandm, and got confused by
a previouse disscussion iTRAQ data through xtandem! using TPP.

Should not the parameters in tandem.paraams.xml like follows,since balance
groups have been removed by the second Ms

57.021464@C
  
15.994915@M,8.014199@K,10.008269@R
113@K
114@K
116@K
117@K
118@K
121@K

 You can specify a variable modification only when present in
a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N
only if it is present in an N[any but P][S or T] motif (N-glycosite).

113@K
114@K
116@K
117@K
118@K
121@K

Sincerely,
Richard

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RE: [spctools-discuss] tpp_gui.pl: Error: invoking tpp_hostname to look up installation property 'HomePath!'

2017-03-17 Thread Eric Deutsch

It might be no problem. The installation instructions say:

If it compiles and you get an error about being unable to find HomePath
then you're fine. However, if you get an error not being able to find a
module, then go back to cpan and install it.

*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Luis Mendoza
*Sent:* Friday, March 17, 2017 5:50 PM
*To:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] tpp_gui.pl: Error: invoking tpp_hostname
to look up installation property 'HomePath!'

Hello Mike,

Are you able to run the following? If so do you get the version string?

/usr/local/tpp/tpp_hostname versionInfo!

Make sure that all of the binaries in bin/ have executable permissions.

Do you also get the error if you try to access via the web interface?

Cheers,

--Luis

On Tue, Feb 21, 2017 at 3:49 AM, Mike Rightmire
wrote:

Good Morning All,

I'm installing TPP-5.0.0 following the instructions here:
http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.0.0:_Installing_on_Ubuntu_16.04

I'm using Ubuntu on a Vmware Fusion virtual machine (running on OSX):
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=16.04
DISTRIB_CODENAME=xenial
DISTRIB_DESCRIPTION="Ubuntu 16.04.1 LTS"

I got the distribution via:

svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_5-0-0

Everything seemed to install normally, but after the 'make install'
and installing the Perl tools via cpanm, I do the step to ensure 'all
the Perl tools are installed' and I get the error message:
root@ubuntu:/usr/local/tpp/cgi-bin# perl tpp_gui.pl
[Tue Feb 21 03:42:58 2017] tpp_gui.pl: Error: invoking tpp_hostname to
look up installation property 'HomePath!'

Any ideas?

Thx!

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RE: [spctools-discuss] Database search of heavy isotope labeled peptides

2017-03-05 Thread Eric Deutsch

There’s no trivial solution, I think. But here are some non-trivial
possibilities:

1) Search the whole dataset with variable heavy label

2) Create a spectral library with the heavy labeled peptides and merge that
library with a normal human library and search with SpectraST

3) Replace all the heavy labeled amino acids in your peptides with some
letters such as B and J and then set Comet or whatever search engine to
have the correct masses for B and J.

4) Eventually the optimal solution will be to use the PEFF format which can
support such modifications right in the PEFF file. Comet and the TPP will
support this sometime this year I hope but not super soon.

5) X!Tandem has a mechanism to specify a file containing proteins with
certain mass modifications. I can’t seem to find the documentation on how
to do it at the moment, but X!Tandem can do it.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Sim Kae Hwan
*Sent:* Thursday, March 02, 2017 10:07 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Database search of heavy isotope labeled
peptides



Hi,



I have spiked in 10 in-house heavy isotope labeled standard peptides into a
non-labeled complex human peptide mixtures (trypsin-digested whole cell
lysate). Can anyone advise me how to perform the database search? and also
the creation of fasta database for this specific task?

Many thanks!



Best regards,

KH

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RE: [spctools-discuss] Re: tandem.exe command line parameters (other than the input.xml file)

2017-03-01 Thread Eric Deutsch

Hi Mike, great, since this is a question that comes up fairly often, would
you post your solution once you get it working?



Thanks,

Eric





*From:* Mike Rightmire [mailto:mike.rightm...@biocomsoftware.com]
*Sent:* Wednesday, March 1, 2017 9:16 AM
*To:* spctools-discuss@googlegroups.com
*Cc:* Eric Deutsch <edeut...@systemsbiology.org>
*Subject:* Re: [spctools-discuss] Re: tandem.exe command line parameters
(other than the input.xml file)



Hi Eric,

Thanks for the reply. Actually, the OpenMS wrapper seems to let me change
the parameters at it's command line...so I think we're good.

Thanks for the info!

Eric Deutsch wrote:

For clarification - is the input.xml file the ONLY way to pass parameters
to the tandem.exe...or can it be done at the command line.



-- 

*Michael Rightmire*

B.Sci. Molecular Biotechnology

MCSE, MCP+I, HPUXCA, CompTIA, VDE, SIAM, ISCB

Skype: RightmireM

+49-721-1320-2562 (DE)

+1-408-890-2121 (USA)

*Biocom Biotechnology and Software*
BiocomSoftware.Com 

BiocomSoftware.De <http://Biocomsoftware.de>



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RE: [spctools-discuss] Re: tandem.exe command line parameters (other than the input.xml file)

2017-03-01 Thread Eric Deutsch

Hi Mike, nothing has changed, this is still the current state. We are not
the authors of this tool, we just bundle it and use it. I think it is
unlikely that the original author would change this, and I don’t think we
will ever change it.



*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Mike Rightmire
*Sent:* Wednesday, March 1, 2017 3:49 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Re: tandem.exe command line parameters (other
than the input.xml file)



I mean defailt_input.xml. Sorry :)

On Wednesday, March 1, 2017 at 12:30:24 PM UTC+1, Mike Rightmire wrote:

I know this question has been asked before, but the answer always seems to
end up with 'use the input.xml file'). So, I appreciate your patience a
with it again.



For clarification - is the input.xml file the ONLY way to pass parameters
to the tandem.exe...or can it be done at the command line.



The reason I ask is; I'm using a Luigi(Sciluigi) pipeline to call
tandem.exe...and it would be much, much easier to pass in command ine
variables than have to edit an XML file on the fly.



Thanks!



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RE: [spctools-discuss] Error while conversion of files

2017-01-24 Thread Eric Deutsch

Aha, that’s probably the problem. During your conversion from wiff to mzML,
you should turn ON peak picking. Otherwise your profile mode data will be
huge and the searches will take a very long time.



Regards,

Eric





*From:* Joel Christie [mailto:joel.jo.chris...@gmail.com]
*Sent:* Tuesday, January 24, 2017 10:42 AM
*To:* Eric Deutsch
*Subject:* Re: [spctools-discuss] Error while conversion of files



One more thing, the .mzML file after the conversion from .Wiff was of
nearly 18 GB.





On Wed, Jan 25, 2017 at 12:01 AM, Joel Christie <joel.jo.chris...@gmail.com>
wrote:

Hi,



I am using the params files that were taught at TPP workshop at Delhi
except the SILAC modifications.



Other thing I would like to ask is what specifications of Computer you are
suggesting me to use to analyse a IDA run of cancer cell line, where around
2000 proteins with 95% confidence are assigned using Protein Pilot of Ab
Sciex.



Today I have started searching for Tandem as well, till the time I left the
lab it was still loading the spectra.



For Comet, I am attaching one screenshot with this post. Please have a look
at it. When I tried to kill the Job, I couldn't.



Thank you very much for your support.



regards,

Joel.





On Tue, Jan 24, 2017 at 11:48 PM, Eric Deutsch <edeut...@systemsbiology.org>
wrote:

Well, normally it should not, but depending on your data file(s) and
parameters you’ve set as well as the computer you’re running on, it
certainly may. Comet very rarely just keeps running without making
progress, so the search you’ve specified is probably just too expensive for
the computing power you’re making available to it. Using more threads,
fewer mass mods, fully tryptic search, large MS2 binsize, smaller sequence
database may all help. But without posting specifics, it is hard to guess
what the problem might be. Posting your comet.params file might help.



Regards,

Eric





*From:* Joel Christie [mailto:joel.jo.chris...@gmail.com]
*Sent:* Tuesday, January 24, 2017 9:55 AM
*To:* spctools-discuss
*Cc:* edeut...@systemsbiology.org
*Subject:* Re: [spctools-discuss] Error while conversion of files



Thanks it worked for me. Now I have different problem.Its been two days
still Comet search is not over. I don't know whether it should take this
much of time?



On Saturday, 21 January 2017 00:25:08 UTC+5:30, Eric Deutsch wrote:

Hi Joel, the problem is a space in your folder names. Some tools are
confused by this. If you rename “Joel Data” to “JoelData” (without the
space) and remove any other spaces in file name  and folder names, things
should work a lot better.



Regards,

Eric





*From:* spctools...@googlegroups.com [mailto:spctools...@googlegroups.com
<spctools...@googlegroups.com>] *On Behalf Of *Joel Christie
*Sent:* Friday, January 20, 2017 9:14 AM
*To:* spctools-discuss <spctools...@googlegroups.com>
*Subject:* [spctools-discuss] Error while conversion of files



Dear all,



I am facing an error while converting files from Sciex's .wiff files to
MzML, I am uploading an error msg with this post. Please check and suggest
me a solution.



I am just beginning to use TPP.



Much Thanks in Advance,

Joel

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RE: [spctools-discuss] Error while conversion of files

2017-01-24 Thread Eric Deutsch

Well, normally it should not, but depending on your data file(s) and
parameters you’ve set as well as the computer you’re running on, it
certainly may. Comet very rarely just keeps running without making
progress, so the search you’ve specified is probably just too expensive for
the computing power you’re making available to it. Using more threads,
fewer mass mods, fully tryptic search, large MS2 binsize, smaller sequence
database may all help. But without posting specifics, it is hard to guess
what the problem might be. Posting your comet.params file might help.



Regards,

Eric





*From:* Joel Christie [mailto:joel.jo.chris...@gmail.com]
*Sent:* Tuesday, January 24, 2017 9:55 AM
*To:* spctools-discuss
*Cc:* edeut...@systemsbiology.org
*Subject:* Re: [spctools-discuss] Error while conversion of files



Thanks it worked for me. Now I have different problem.Its been two days
still Comet search is not over. I don't know whether it should take this
much of time?



On Saturday, 21 January 2017 00:25:08 UTC+5:30, Eric Deutsch wrote:

Hi Joel, the problem is a space in your folder names. Some tools are
confused by this. If you rename “Joel Data” to “JoelData” (without the
space) and remove any other spaces in file name  and folder names, things
should work a lot better.



Regards,

Eric





*From:* spctools...@googlegroups.com  [mailto:
spctools...@googlegroups.com ] *On Behalf Of *Joel Christie
*Sent:* Friday, January 20, 2017 9:14 AM
*To:* spctools-discuss <spctools...@googlegroups.com >
*Subject:* [spctools-discuss] Error while conversion of files



Dear all,



I am facing an error while converting files from Sciex's .wiff files to
MzML, I am uploading an error msg with this post. Please check and suggest
me a solution.



I am just beginning to use TPP.



Much Thanks in Advance,

Joel

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RE: [spctools-discuss] Error while conversion of files

2017-01-20 Thread Eric Deutsch

Hi Joel, the problem is a space in your folder names. Some tools are
confused by this. If you rename “Joel Data” to “JoelData” (without the
space) and remove any other spaces in file name and folder names, things
should work a lot better.



Regards,

Eric





*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Joel Christie
*Sent:* Friday, January 20, 2017 9:14 AM
*To:* spctools-discuss 
*Subject:* [spctools-discuss] Error while conversion of files



Dear all,



I am facing an error while converting files from Sciex's .wiff files to
MzML, I am uploading an error msg with this post. Please check and suggest
me a solution.



I am just beginning to use TPP.



Much Thanks in Advance,

Joel

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RE: [spctools-discuss] Re: Spectrast slow processing with .msp file under Linux

2017-01-12 Thread Eric Deutsch

I cannot recall any other report like this and have never experienced
anything like this myself that I can recall. Can you describe in more
detail exactly what the origin and version of this executable is?



Is it true that other executables like Comet or X!Tandem do not suffer from
this huge slowdown using the same files/filesystems?



What distro/version of Linux are you using?



Regards,

Eric





*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Jianqiao Shen
*Sent:* Thursday, January 12, 2017 1:01 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Re: Spectrast slow processing with .msp file
under Linux



Hi Eric,



Thank you for your reply. I/O bound may be the problem. However, when I do
my search with Spectrast, the speed is also quite slow. Nearly 20 times
slower than my laptop. The CPU usage is only 3% as well. So, I am confused
whether it is because the linux standalone version of Spectrast.


在 2017年1月11日星期三 UTC-5下午2:43:42，Jianqiao Shen写道：

Hi,



I am using Spectrast Creat mode to convert my .msp file into .splib file. I
only build the stand-alone Spectrast on our cluster. The problem is that
Spectrast runs quite slow on our cluster and the cpu usage is only 3%. I
also try the same process on my laptop Windows, it is faster and finishes
in only 200 seconds. The command I use is 'spectrast -cNtest test.msp'. Can
anyone tell me how to solve it and is there any parameters I can set so
that Spectrast can be used with multi processors?



Thank you!



Jianqiao Shen

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RE: [spctools-discuss] Spectrast slow processing with .msp file under Linux

2017-01-11 Thread Eric Deutsch

Hi, although SpectraST has a few multi-threaded features, I don’t think the
msp conversion is multithreaded, so that is just one thread only. This
conversion is actually not very CPU intensive at all, but rather I/O bound,
i.e. the speed of your disks probably matters most. I’m guessing that on
your cluster, you’re probably accessing the data over NFS, which can be
quite slow. I also notice that often my laptop is faster at such operations
because I have an SSD on my laptop and therefore disk reads and writes are
really fast and that makes all the difference.



So, there are no parameters to make that operation faster. Running the
operation on a faster disk might help a lot. Running it on a local disk,
rather than on NFS might help quite a bit. But then there might be the
overhead of copying the files to and from local disk. RAMdisk would be even
faster.



But, then, on the other hand, does it matter that much? Usually you’ll just
have to do the msp -> splib conversion once, and then use that splib many
times. So really the searching is more important because that’s happening
many times. And I believe that part is multi-threaded.



Not very helpful, but those are my thoughts..



Regards,

Eric





*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Jianqiao Shen
*Sent:* Wednesday, January 11, 2017 11:43 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Spectrast slow processing with .msp file
under Linux



Hi,



I am using Spectrast Creat mode to convert my .msp file into .splib file. I
only build the stand-alone Spectrast on our cluster. The problem is that
Spectrast runs quite slow on our cluster and the cpu usage is only 3%. I
also try the same process on my laptop Windows, it is faster and finishes
in only 200 seconds. The command I use is 'spectrast -cNtest test.msp'. Can
anyone tell me how to solve it and is there any parameters I can set so
that Spectrast can be used with multi processors?



Thank you!



Jianqiao Shen

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RE: [spctools-discuss] PeptideProphet/iProphet Probability Distribution

2017-01-04 Thread Eric Deutsch

Hi Ali, my thoughts are that for this dataset and analysis,
PeptideProphet+iProphet (PP+iP) are discriminating between correct and
incorrect much better than the other analysis. The vast majority of
peptides are deemed by PP+iP as very likely to be correct or very likely
incorrect with a rather small population of IDs at intermediate confidence.
The other analysis seems to be unsure about many more. In fact the curve is
extremely steep indicating not very good discriminating power between
correct and incorrect. There are many more in the intermediate range.

The PP+iP analysis looks quite similar to what we are used to for modern
datasets. The steepness of the other analysis seems a bit worrying to me.
How are the PEPs calculated? Can you perform an independent analysis of the
PEPs to see if they agree with decoys or some other measure of errors? I
would say that in the range that matters (FDR < 1%) PP+iP is giving you a
better result. It is puzzling that the total number of correct hits at FDR
2.5% is so much lower fir PP+iP. I couldn’t say from the data shown why
that is. Maybe the PEPs are not correct or MQ is finding more IDs because
of different search parameters? I don’t know.

Regards,

Eric

*From:* Ali [mailto:sma.banijam...@gmail.com]
*Sent:* Wednesday, January 04, 2017 1:06 PM
*To:* spctools-discuss
*Cc:* edeut...@systemsbiology.org; david.shteynb...@systemsbiology.org
*Subject:* Re: [spctools-discuss] PeptideProphet/iProphet Probability
Distribution

Dear Eric and David

By accepting lower thresholds I actually mean accepting higher FDRs but
that is not so useful here because there is not so many hits after the very
high probabilities and I will not be gaining much by using lower
thresholds. PeptideProphet gives me a lot of PSMs with very high confidence
and very low FDR. But as I allow higher FDRs like 2-3% it falls behind PEP
from MaxQuant.

Here is another plot to better show my point. I have compared the combined
results above with Max Quant's results as I increase the FDR. As it can be
seen, number of unique peptides is more with PepPro/iPro for low FDR, but
in the end it falls behind PEP.

<https://lh3.googleusercontent.com/-VZgUOiAvvno/WG1ggpOR3uI/BBA/nyrjsBbLrGQ60eo3iqB3beMOVs4ZCXCAACLcB/s1600/Picture1.png>

And this can be understood from the following plot:

<https://lh3.googleusercontent.com/-jmsbfmBfbXA/WG1hNLP8e1I/BBI/SBnRc5-naTw09vjKk0K4m9xcCBgS-1Z8QCLcB/s1600/Picture2.png>

Do you have any thoughts on this?

Thank you very much,

Ali

On Wednesday, January 4, 2017 at 3:08:14 PM UTC-5, Ali wrote:

Dear David and Eric

Thanks for your replies and suggestions. I thought that I might be able to
increase identification by accepting hits with lower thresholds. I do
understand what you mentioned here.

Thanks again,

Ali

On Tuesday, January 3, 2017 at 1:57:38 PM UTC-5, Eric Deutsch wrote:

In the ideal case where the PeptideProphet and iProphet had perfect
discriminating power, i.e. the correct and incorrect PSM distributions do
not overlap, you would expect a large peak at P=0 and P=1 and nothing in
between. As a dataset diverges from this ideal and the correct and
incorrect distributions begin to overlap, you will still have very large
peaks near P=0 and near P=1, with a small number of intermediate values
where the probability is between 0 and 1.

So, in short, your distribution is exactly what you would expect based on
what you did. It is indicative of a great dataset. You should follow
David’s suggestion, and then if you replot, you will see huge peaks at 0
and 1 with rather little in between.

Regards,

Eric

*From:* spctools...@googlegroups.com [mailto:spctools...@googlegroups.com] *On
Behalf Of *David Shteynberg
*Sent:* Tuesday, January 03, 2017 10:36 AM
*To:* spctools-discuss
*Subject:* Re: [spctools-discuss] PeptideProphet/iProphet Probability
Distribution

These results are showing you that iProphet has great discriminating power
even when you restrict the input to only non-low probability PSMs
(filtering with PeptideProphet probability). The best way to run iProphet
is to give it all the data from PeptideProphet (use a PeptideProphet
minimum probability of 0).

-David

On Mon, Jan 2, 2017 at 9:26 PM, Ali <sma.ban...@gmail.com> wrote:

Dear all

I am plotting the distribution of the assigned PeptideProphet and iProphet
probabilities to my search results. I am seeing a rather strange pattern
shown below. Why am I seeing so many hits with very high confidence
(probability >0.98) but suddenly after that threshold the number of
assigned probabilities to the PSMs decrease abruptly? What could be the
reason for this pattern? One would expect to see all ranges of
probabilities for PSMs.

<https://lh3.googleusercontent.com/-BeikGpozjkw/WGsygFV83UI/BAg/DcG6lRxucM4IRclvdadal-eFSaA05sd6QCLcB/s1600/Picture1.png>

This figure is the combination of different search eng

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