Re: [spctools-discuss] TPP v7.1.0 Albedo - Works on Bookworm (Deb 12)! - Comment on Docs

['Luis Mendoza' via spctools-discuss]

Hi Robert,
Glad that you got it to install successfully, and thanks for the notes!
We'll integrate them into ours.
Do note that the official release of 7.1.0 is still pending a few minor
issues and testing; stay tuned for an announcement soon!
Cheers,
--Luis


On Tue, Jul 2, 2024 at 10:09 AM Robert Winkler <
robert.winkler.m...@gmail.com> wrote:

> Dear TPP team, thanks for your continuous work!
>
> I just successfully compiled and installed v7.1.0 Albedo on antiX Linux,
> which is based on Debian 12 Bookwork, following you instructions:
>
>
> http://tools.proteomecenter.org/wiki/index.php?title=TPP_7.0.0:_Installing_on_Ubuntu_22.04_LTS
>
> The installation and the tests work fine; congratulations!
>
> Just some minor comments on the documentation:
>
> ~~~
> ps aux | grep apache
> cd /usr/local/tpp sudo chown -R www-data.www-data log users
> cd /data
> sudo chown -R www-data.www-data .
> ~~~
> the `www-data.www-data` must be `www-data:www-data`
> (with : instead of . between user:group)
>
> And in the the test recipie:
> - Login with guest and password
>
> the password is 'guest' .
>
> Best, Robert
>
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Re: [spctools-discuss] Compilation on FreeBSD 14: Unable to determine target platform 

['Luis Mendoza' via spctools-discuss]

Hi Robert,
Sorry to hear about the FreeBSD issues.  And agree on boost.
Thanks again for the kind words.  Cheers.
--Luis


On Tue, Jul 2, 2024 at 10:16 AM Robert Winkler <
robert.winkler.m...@gmail.com> wrote:

> Thanks, Luis!
>
> Sure. TPP is the gold standard for MS-based proteomics and a long-going
> community project.
>
> Finally I had some other problems on FreeBSD (otherwise an excellent
> platform) and moved back to a Debionid system.
>
> I hate boost.
>
> Robert
>
> On Saturday 29 June 2024 at 04:01:09 UTC-6 Luis Mendoza wrote:
>
>> Hello Robert,
>>
>> Not sure that this is "elegant", but perhaps you can add the following
>> two lines to common.mk, starting after line 132 (additions in red) :
>>
>> else ifneq (,$(findstring linux, $(TARGET)))
>>OS := Linux
>> else ifneq (,$(findstring freebsd, $(TARGET)))
>>OS := Linux
>> else ifneq (,$(findstring darwin, $(TARGET)))
>>OS := Darwin
>>
>> Hope this does the trick!
>>
>> Did previous versions of TPP compile fine in the same system?  We don't
>> have much experience with FreeBSD.
>>
>> Thanks for MassyPup's continued support of TPP!
>> --Luis
>>
>> On Fri, Jun 28, 2024 at 11:03 AM Robert Winkler 
>> wrote:
>>
>>> Hi, I'm working on the next edition of MassyPup(64)
>>> 
>>>
>>> Of course,  the TPP should be included for proteomics data processing.
>>> As platform, I have chosen a FreeBSD 14 this time.
>>>
>>> In general, this is a very clean system for building. E.g. OpenMS is
>>> compiling since about 2 hours now without bothering me with
>>> warnings/errors. As well, R stuff (xcms, etc.) compiles well.
>>>
>>> With the 'bleeding-edge 7.0+ TPP' I got, however a problem with the
>>> build configuration:
>>> `gmake` results in
>>> ~~~
>>> common.mk:147: *** Unable to determine target platform using $(CXX)
>>> -dumpmachine. Stop.
>>> ~~~
>>> manually invoking `gcc -dumpmachine` gives `x86_64-portbld-freebsd14.0`
>>>
>>> Is there an elegant way for convincing TPP to build?
>>>
>>> Best, Robert
>>>
>>>
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>>> .
>>>
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Re: [spctools-discuss] Compilation on FreeBSD 14: Unable to determine target platform 

['Luis Mendoza' via spctools-discuss]

Hello Robert,

Not sure that this is "elegant", but perhaps you can add the following two
lines to common.mk, starting after line 132 (additions in red) :

else ifneq (,$(findstring linux, $(TARGET)))
   OS := Linux
else ifneq (,$(findstring freebsd, $(TARGET)))
   OS := Linux
else ifneq (,$(findstring darwin, $(TARGET)))
   OS := Darwin

Hope this does the trick!

Did previous versions of TPP compile fine in the same system?  We don't
have much experience with FreeBSD.

Thanks for MassyPup's continued support of TPP!
--Luis

On Fri, Jun 28, 2024 at 11:03 AM Robert Winkler <
robert.winkler.m...@gmail.com> wrote:

> Hi, I'm working on the next edition of MassyPup(64)
> 
>
> Of course,  the TPP should be included for proteomics data processing.
> As platform, I have chosen a FreeBSD 14 this time.
>
> In general, this is a very clean system for building. E.g. OpenMS is
> compiling since about 2 hours now without bothering me with
> warnings/errors. As well, R stuff (xcms, etc.) compiles well.
>
> With the 'bleeding-edge 7.0+ TPP' I got, however a problem with the build
> configuration:
> `gmake` results in
> ~~~
> common.mk:147: *** Unable to determine target platform using $(CXX)
> -dumpmachine. Stop.
> ~~~
> manually invoking `gcc -dumpmachine` gives `x86_64-portbld-freebsd14.0`
>
> Is there an elegant way for convincing TPP to build?
>
> Best, Robert
>
>
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> 
> .
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Re: [spctools-discuss] PepXML Schema v1.23

['Luis Mendoza' via spctools-discuss]

Hello Max,

Thank you for bringing this to our attention.  I have added the file and
updated the wiki.

Cheers,
--Luis


On Sat, Feb 17, 2024 at 9:20 AM Max Brazhnikov 
wrote:

> Hi all,
>
> pepXML_v123.xsd was committed almost two years ago [1], however pepXML
> wiki page [2] has ceased at v1.22, also the schema file is not available
> for referencing [3]. Is v1.23 officially released and ready for use? If so
> could you please update wiki and upload pepXML_v123.xsd?
>
> Thanks,
> Max
>
>
> [1] https://sourceforge.net/p/sashimi/code/8600/
> [2] http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML
> [3] https://sashimi.sourceforge.net/schema_revision/pepXML/
>
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Re: [spctools-discuss] PepXML > spectrum > top hits viewer issue - Comet

['Luis Mendoza' via spctools-discuss]

Hi Sam,
It does sound like potentially an issue with the mzML file path(s) inside
the comet pepXML results, though there could be other issues.

As for troubleshooting, you can inspect the URL of those troublesome links
and look for the Dta= (or File=) parameter -- is the filepath the same that
you expect on the local drive?  You can also compare that to one of the
links that do work to look for differences, as sometimes they might be
subtle -- e.g. a missing slash etc.

Hope this helps,
--Luis


On Mon, Feb 19, 2024 at 7:41 PM Sam Whedon  wrote:

> Hi all,
>
> I am using the Pep.XML viewer with Comet data in the Comet pipeline. If I
> click a link in the ions column Lorikeet produces an annotated spectrum as
> anticipated. If I click on the spectrum link in the same row, navigating to
> a page showing comet hits, then none of the spectrum viewer links work
> (individual links in the 'ions' column or the lower 'view and compare top
> hits'). The comet hits window shows multiple top hits, and correctly
> annotates the ion count for each hit.
> I am running comet on a cluster, then downloading the pep.xml, and
> correcting the mzML and fasta filepaths in the xml text before viewing in
> the trans proteomic pipeline.
> Please let me know if there is anything I can try to troubleshoot this
> problem.
> Thanks.
>
> Best,
> Sam
>
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Re: [spctools-discuss] Trouble converting Waters.RAW with TPP msconvert

['Luis Mendoza' via spctools-discuss]

Hello Alex,
Glad that you were able to get to the bottom of this issue and hope you
have been able to process your data.

I  just wanted to add that when installing TPP on Windows, the entire
ProteoWizard set of tools (including msConvert GUI) is also bundled -- so
there is typically no need to re-download/install unless you want a newer
version.  You can find the software under  C:/Program Files/ProteoWizard/
on standard installs.  Note that one is able to install multiple versions
side-by-side, and you may even notice multiple ones there already if you
have updated TPP on that machine before.

Cheers,
--Luis

On Thu, Jan 18, 2024 at 7:53 AM Alex Gao  wrote:

> Dear David,
>
> So after a long troubleshooting process with msConvert and Waters team as
> well as testing it by myself, I found the best way to convert Waters.raw
> files is to use this Waters proprietary software
> https://microapps.on-demand.waters.com/home/showmarkdown/data-as-a-product
>  to convert Waters file to mzML (convert to 32 bit). Alternatively, one
> could convert the file with msConvert GUI (the actual software, not the one
> embedded in TPP), with only the settings "write index" and "TPP compatible"
> checked, convert to mzML 32-bit (mzXML 32-bit for Maxquant compatibility),
> and most importantly, exclude the negative values (which are EMR spectra
> from UV or PDA detector inline with the system) by adding a subset filter
> for MS-Level "1-", which allows the mz(X)ML to keep only MS1 and MS2 data.
> Thanks for your help!
>
> Best,
> Alex
> On Thursday, January 11, 2024 at 2:40:07 AM UTC+1 David Shteynberg wrote:
>
>> Hello Alex,
>>
>> This is pointing to a bug in either the Waters library for access to the
>> raw data or in msconvert. Perhaps you can contact Waters and msconvert
>> developers to see if they have patched the problem.  My suspicion as to the
>> nature of the problem is use of signed (as opposed to unsigned) variables
>> internally for the representation of intensities.  Once the intensities get
>> large enough they roll over to the negative representations of the values
>> in C++.  Let us know when you find a solution to this issue!
>>
>> Thanks,
>> -David
>>
>> On Jan 10, 2024, at 4:24 AM, Alex Gao  wrote:
>>
>> Hi David,
>>
>> I do not know why. The data was acquired on MassLynx by a Waters Xevo
>> QTOF set to fast DDA, with scan times of MS1 and MS2 set to both 1s with 10
>> MS2 scans. The lockspray mass is also included. The settings, besides the
>> scan times, were not changed from the last time I ran the data, which
>> worked the last time. On MassLynx, the intensities look normal as well,
>> with a dome of increasing intensities over the gradient, typical of bottom
>> up proteomics. Is there a way to solve this?
>>
>> On Wednesday, January 10, 2024 at 1:56:19 AM UTC+1 David Shteynberg wrote:
>>
>>> Hello Alex,
>>>
>>> I was able to download your file, convert the data to mzML using
>>> msconvert and read a few spectra using the command line tool readMzXml
>>> (works on mzML too).  Unfortunately, I am finding many intensities these
>>> files that are encoded with negative values, which is likely causing
>>> problems for the downstream tools like comet.  Do you know why negative
>>> intensities are in these files?  It is possible this is a bug with the raw
>>> encoding.  Are you able to visualize these files using Waters software to
>>> check the intensities and compare to those output by msconvert?
>>>
>>> Thanks,
>>> -David
>>>
>>> On Jan 5, 2024, at 4:17 AM, Alex Gao  wrote:
>>>
>>> Hi David,
>>>
>>> Thank you for your prompt feedback! The file can be found at the link
>>> below.
>>>
>>>
>>> https://drive.google.com/file/d/1QulcwZ3UP7pcMtECNwubd4DysqaDq4UN/view?usp=sharing
>>>
>>> Looking forward to your inputs!
>>>
>>> Best,
>>> Alex
>>>
>>> On Friday, January 5, 2024 at 1:09:03 AM UTC+1 David Shteynberg wrote:
>>>
 Hello Alex,

 Thanks for trying the TPP pipeline to solve your proteomics
 computational needs.  Sorry, you are having trouble converting and
 analyzing Waters raw data.  Have you tried using the latest version of
 msconvert to do the conversion to mzML?  If you are able to upload your
 file to an online drive and give me access to it, I can pull it down and
 try to convert it myself.  Let me know what works for you.

 Cheers!
 -David

 On Jan 3, 2024, at 4:32 AM, Alex Gao  wrote:

 Hi guys,

 So I've used TPP before to convert bottom up proteomic Thermo raw files
 in msconvert, comet search with custom params file, and xinteract to
 perform protein prophet with no issues. Earlier this year, I performed the
 same with Waters. Raw file, although in the beginning there was an issue
 with size, shrinking the size of my raw file from 25 to 5-6GB did the
 trick.

 However, recently, I reinstalled TPP (v6.3.3), and was trying to
 perform the same task to convert 5-6GB of Waters.raw but failed. 

Re: [spctools-discuss] TPP installation tutorials 404 errors?

['Luis Mendoza' via spctools-discuss]

Hi Will,
Thanks for the reply and extra info.  This strange redirects may be
connected to IT changes that took place recently; I'll follow up with them.
--Luis


On Fri, Jan 12, 2024 at 9:57 AM Will Comstock  wrote:

> Thanks Luis, your direct link works for me!
>
> Looks like clicking the hyperlinks on the tutorials page is redirecting me
> to URLs like the following for some reason:
>
> https://cytoscape.org/wiki/index.php?title=Linux_Installation_Guides
>
> Copying the link address from those hyperlinks sends me to the correct
> place though... may just be an issue on my end.
>
> Appreciate your help regardless!
> -Will
>
> On Friday, January 12, 2024 at 12:40:59 PM UTC-5 Luis Mendoza wrote:
>
>> Hi Will,
>> The following three links do work for me at the moment:
>> [image: image.png]
>>
>> e.g.
>> [image: image.png]
>>
>> I'll check with our internal IT to see if there have been any changes to
>> the web servers or network that may be affecting access from external users.
>>
>> In the meantime, here is the direct link, in case that helps:
>>
>> http://tools.proteomecenter.org/wiki/index.php?title=Running_the_TPP_docker_image
>>
>> Thanks for reporting the issue!
>> --Luis
>>
>> On Fri, Jan 12, 2024 at 9:34 AM Will Comstock  wrote:
>>
>>> Hi all, the link to the Docker Installation Tutorial appears to be
>>> broken. Is there another place for me to find this tutorial?
>>>
>>> Actually, the first three links on this page all lead to 404 errors for
>>> me:
>>> http://www.tppms.org/tutorials/
>>>
>>> Thank you!
>>> -Will
>>>
>>> [image: Screenshot 2024-01-12 at 12.30.17 PM.png]
>>>
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>>> .
>>>
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Re: [spctools-discuss] Problem with PeptideProphet

['Luis Mendoza' via spctools-discuss]

Hello Tanmay,
How did you generate the input pepXML files?  Which search engine did you
use?  Are you able to open both of those files and verify that they have
results?
Can you process results from another search engine (e.g. Comet or X!Tandem)
of the same mzML data?
Cheers,
--Luis

On Wed, Jul 26, 2023 at 8:01 AM Tanmay Singh  wrote:

> Dear all
> I keep trying to run PeptideProphet on two * pep.xml files but keep
> getting this error. What could the issue be and how can I solve it?
>
> Error
> C:/TPP/bin/xinteract (TPP v6.3.2 Arcus, Build 202305092202-8951
> (Windows_NT-x86_64)) using MAXTHREADS=1 for PeptideProphet... running:
> "C:/TPP/bin/InteractParser "interact.pep.xml"
> "OR20080317_S_SILAC-LH_1-1_01.pep.xml"
> "OR20080320_S_SILAC-LH_1-1_11.pep.xml" -L"7"" file 1:
> OR20080317_S_SILAC-LH_1-1_01.pep.xml file 2:
> OR20080320_S_SILAC-LH_1-1_11.pep.xml processed altogether 17620 results
> command "C:/TPP/bin/InteractParser "interact.pep.xml"
> "OR20080317_S_SILAC-LH_1-1_01.pep.xml"
> "OR20080320_S_SILAC-LH_1-1_11.pep.xml" -L"7"" failed: Unknown error
> command "C:/TPP/bin/InteractParser "interact.pep.xml"
> "OR20080317_S_SILAC-LH_1-1_01.pep.xml"
> "OR20080320_S_SILAC-LH_1-1_11.pep.xml" -L"7"" exited with non-zero exit
> code: -1073741819 QUIT - the job is incomplete
>
> Any help would be appreciated
>
> Many thanks
> Tanmay
>
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Re: [spctools-discuss] converting prot.xml to tsv/something else

['Luis Mendoza' via spctools-discuss]

Hi Emma,
The ProtXMLViewer is under the cgi-bin/ directory of the image.  However,
the version in 6.2.0 does not have the command-line capability of exporting
protXML to TSV.  We introduced this feature in 6.3.0, and will be available
once we produce the related image.  (well, after fixing some bugs and
releasing 6.3.3, soon).

Do note that if using the viewer interactively, you can export to TSV via
the File & Info tab of ProtXMLViewer.

We can gladly help convert a few files for you if you are able to share
those; just contact me directly if so.

Thanks,
--Luis


On Wed, Jul 26, 2023 at 2:52 AM Emma Whittington  wrote:

> Hi,
>
> I am running TPP 6.2.0 via a singularity image. I have been using the
> EXCELXX option in ProteinProphet to a tab-separated file. However, that is
> for some reason not working at the moment (tried today and yesterday). I
> tried to also use ProtXMLViewer.pl but it doesn't seem to exist in the
> singularity image. How else can I convert the prot.xml files?
>
> Thank you!
>
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Re: [spctools-discuss] Variable mod query in COMET

['Luis Mendoza' via spctools-discuss]

This should already be possible with, e.g.

variable_mod02 = 40.000 C 0 3 -1 0 0 0.0
add_C_cysteine = 50.000

(Of course using whatever masses are appropriate.)

Or does this not work?


On Mon, Jul 31, 2023 at 9:31 PM Debojyoti Pal 
wrote:

> Thanks Luis. I have asked this on the COMET group as well. They will
> probably come up with an update or something to enable it.
> On Tuesday, August 1, 2023 at 8:47:46 AM UTC+5:30 Luis Mendoza wrote:
>
>> Hi Debojyoti,
>> Yes, I would say this is the most straightforward way of conducting this
>> search.
>> Note that you may need to make further adjustments to the variable mod
>> string settings if, say, a given peptide must have *all* of its Cysteines
>> in one state (+50) or the other (+90).  The default is to allow for mixed
>> Cysteines in the peptide, e.g. PEPC[50]TIDEC[90]R.
>> Hope this helps,
>> --Luis
>>
>>
>> On Mon, Jul 31, 2023 at 11:04 AM Debojyoti Pal 
>> wrote:
>>
>>> Hello everyone
>>>
>>> I have a specific scenario where I want to search for peptide in which
>>> cysteine must either have +50 or +90 mod. Basically:
>>> 1) Cys can only have one of +50 or +90
>>> 2) Cys much have one of +50 or +90 (ie It cannot be unmodified)
>>>
>>> Only way I can achieve this is to put a static mod of +50 and variable
>>> mod of +40 (40+50 = +90). Is there any better way to do this.
>>>
>>> Regards
>>> Debojyoti
>>>
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>>> 
>>> .
>>>
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Re: [spctools-discuss] Variable mod query in COMET

['Luis Mendoza' via spctools-discuss]

Hi Debojyoti,
Yes, I would say this is the most straightforward way of conducting this
search.
Note that you may need to make further adjustments to the variable mod
string settings if, say, a given peptide must have *all* of its Cysteines
in one state (+50) or the other (+90).  The default is to allow for mixed
Cysteines in the peptide, e.g. PEPC[50]TIDEC[90]R.
Hope this helps,
--Luis


On Mon, Jul 31, 2023 at 11:04 AM Debojyoti Pal 
wrote:

> Hello everyone
>
> I have a specific scenario where I want to search for peptide in which
> cysteine must either have +50 or +90 mod. Basically:
> 1) Cys can only have one of +50 or +90
> 2) Cys much have one of +50 or +90 (ie It cannot be unmodified)
>
> Only way I can achieve this is to put a static mod of +50 and variable mod
> of +40 (40+50 = +90). Is there any better way to do this.
>
> Regards
> Debojyoti
>
> --
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> 
> .
>

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Re: [spctools-discuss] Access to Mascot file results

['Luis Mendoza' via spctools-discuss]

Hello Carlo,
I recall seeing a report like this years ago, and I think it has to do with
configuring the Mascot server to open its port.  I forget the details of
how this is done, and we don't have a Mascot server in-house where we can
test; perhaps someone else is able to provide help on this.

But you can otherwise copy the output .dat file (and database used to
search) over to the TPP area, and execute the analysis there.

Cheers,
--Luis


On Wed, Jul 26, 2023 at 9:54 AM Carlo de Oliveira Martins <
carlol...@gmail.com> wrote:

> Dear all,
> I have access to the Mascot Daemon Server through my institution.
> However, when I try to type in the URL of the Mascot Server URL, I get an
> error saying that the server seems not to exist. Is this related to any
> specific format, e.g., the URL has to end with /cgi/, or something of the
> sort? Or is my URL inaccessible from Petunia?
> Any specific instruction on how to retrieve my search data?
> Thank you,
> -Carlo
>
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> 
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Re: [spctools-discuss] Re: Upcoming Trans-Proteomic Pipeline (TPP) course

['Luis Mendoza' via spctools-discuss]

Hello,
Please find the Word document attached to the original course
announcement.  You can also find it on the archived google-groups chat:
https://groups.google.com/g/spctools-discuss/c/Hnkw6NKsrgA/m/mn7hfOhfCQAJ

Cheers,
--Luis


On Fri, Jul 21, 2023 at 1:24 AM Aparna Agarwal 
wrote:

> Dear  Luis,
>
> Please send the link of the registration form.
>
> Regards
>
> On Fri, Jul 21, 2023 at 1:42 PM 'Luis Mendoza' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> Hello Emma, Manuela, and others interested in attending virtually,
>>
>> We have decided to provide a remote option to attend the course via Zoom
>> on a limited basis.  Please fill out and send me the registration form, and
>> note in the comments that you would like this option.
>>
>> Please do note the following:
>>
>>- The course will be held 8am-430pm local Seattle time (with breaks
>>throughout); please make sure that you can attend.
>>- You will need to install TPP and download data to a 64-bit Windows
>>machine so that you can execute the tutorials.  This is typically quite
>>straightforward, and we'll be happy to help you install before the course
>>begins, but we'll be limited in that ability after that.
>>- We plan on having remote participants muted, but will be happy to
>>take questions via chat.
>>- One-on-one assistance will not be possible, or very limited at best.
>>
>> More information regarding course materials and links will be sent to
>> those who successfully register by Monday afternoon.
>>
>> Thank you for your continued support and interest in this course!
>> -- Luis
>>
>>
>> On Thu, Jul 20, 2023 at 2:42 AM Manuela Piazzi 
>> wrote:
>>
>>> Awesome! I would really like to attend to get an update and to refresh
>>> my TPP skills, but I'm not based in the US as well and I might only attend
>>> virtually
>>>
>>> Cheers,
>>> Manuela
>>>
>>> Il giorno gio 20 lug 2023 alle ore 11:13 Emma Whittington <
>>> emawh...@gmail.com> ha scritto:
>>>
>>>> Thank you for offering this. Will there be an option to attend
>>>> virtually? I am not based in the US so would find it impossible to attend
>>>> on short notice.
>>>>
>>>> All the best,
>>>> Emma
>>>>
>>>> On Thursday, 20 July 2023 at 01:50:49 UTC+2 Luis Mendoza wrote:
>>>>
>>>>> Hi everyone, the next Trans-Proteomic Pipeline (TPP) course will be
>>>>> held next week.
>>>>>
>>>>>
>>>>> More info below.
>>>>>
>>>>> --Luis
>>>>>
>>>>>
>>>>> *Proteomics Informatics Course at ISB in Seattle, Washington: July 26
>>>>> – 28, 2023 * Course Objective:
>>>>>
>>>>> The SPC is pleased to offer a three-day intensive course in the use of
>>>>> a suite of open-source software tools designed for the analysis,
>>>>> validation, storage and interpretation of data obtained from large-scale
>>>>> quantitative proteomics experiments using various labeling methods,
>>>>> multi-dimensional chromatography and tandem mass spectrometry.  Through
>>>>> daily lectures and tutorials, each course participant should become
>>>>> proficient in the use of the tools.
>>>>> Prerequisites:
>>>>>
>>>>> Prerequisite for participation in the course is a demonstrated
>>>>> understanding in the operation of tandem mass spectrometers, the basic
>>>>> structure and interpretation of peptide MS/MS spectra and proficiency in
>>>>> the use of computers.*  A* *commitment to attend the entire course is
>>>>> also required.*
>>>>>
>>>>> Participants must provide their own (64-bit Windows) laptop, and have
>>>>> the TPP software pre-installed.
>>>>>
>>>>> *Registrations must be completed by July 24, 2023.*
>>>>> Location:
>>>>>
>>>>> *Institute for Systems Biology*
>>>>> 401 Terry Ave North
>>>>> Seattle, WA 98109
>>>>>
>>>>> Dates:
>>>>>
>>>>> Wednesday, July 26, 8:00 am through Friday, July 28, 5:00 pm.
>>>>>
>>>>> Participants must commit to attending the entire course and bring
>>>>> their own laptop with the TPP software pre-installed.
&

Re: [spctools-discuss] Re: Upcoming Trans-Proteomic Pipeline (TPP) course

['Luis Mendoza' via spctools-discuss]

Hello Emma, Manuela, and others interested in attending virtually,

We have decided to provide a remote option to attend the course via Zoom on
a limited basis.  Please fill out and send me the registration form, and
note in the comments that you would like this option.

Please do note the following:

   - The course will be held 8am-430pm local Seattle time (with breaks
   throughout); please make sure that you can attend.
   - You will need to install TPP and download data to a 64-bit Windows
   machine so that you can execute the tutorials.  This is typically quite
   straightforward, and we'll be happy to help you install before the course
   begins, but we'll be limited in that ability after that.
   - We plan on having remote participants muted, but will be happy to take
   questions via chat.
   - One-on-one assistance will not be possible, or very limited at best.

More information regarding course materials and links will be sent to those
who successfully register by Monday afternoon.

Thank you for your continued support and interest in this course!
-- Luis


On Thu, Jul 20, 2023 at 2:42 AM Manuela Piazzi 
wrote:

> Awesome! I would really like to attend to get an update and to refresh my
> TPP skills, but I'm not based in the US as well and I might only attend
> virtually
>
> Cheers,
> Manuela
>
> Il giorno gio 20 lug 2023 alle ore 11:13 Emma Whittington <
> emawh...@gmail.com> ha scritto:
>
>> Thank you for offering this. Will there be an option to attend virtually?
>> I am not based in the US so would find it impossible to attend on short
>> notice.
>>
>> All the best,
>> Emma
>>
>> On Thursday, 20 July 2023 at 01:50:49 UTC+2 Luis Mendoza wrote:
>>
>>> Hi everyone, the next Trans-Proteomic Pipeline (TPP) course will be
>>> held next week.
>>>
>>>
>>> More info below.
>>>
>>> --Luis
>>>
>>>
>>> *Proteomics Informatics Course at ISB in Seattle, Washington: July 26 –
>>> 28, 2023 * Course Objective:
>>>
>>> The SPC is pleased to offer a three-day intensive course in the use of a
>>> suite of open-source software tools designed for the analysis, validation,
>>> storage and interpretation of data obtained from large-scale quantitative
>>> proteomics experiments using various labeling methods, multi-dimensional
>>> chromatography and tandem mass spectrometry.  Through daily lectures and
>>> tutorials, each course participant should become proficient in the use of
>>> the tools.
>>> Prerequisites:
>>>
>>> Prerequisite for participation in the course is a demonstrated
>>> understanding in the operation of tandem mass spectrometers, the basic
>>> structure and interpretation of peptide MS/MS spectra and proficiency in
>>> the use of computers.*  A* *commitment to attend the entire course is
>>> also required.*
>>>
>>> Participants must provide their own (64-bit Windows) laptop, and have
>>> the TPP software pre-installed.
>>>
>>> *Registrations must be completed by July 24, 2023.*
>>> Location:
>>>
>>> *Institute for Systems Biology*
>>> 401 Terry Ave North
>>> Seattle, WA 98109
>>>
>>> Dates:
>>>
>>> Wednesday, July 26, 8:00 am through Friday, July 28, 5:00 pm.
>>>
>>> Participants must commit to attending the entire course and bring their
>>> own laptop with the TPP software pre-installed.
>>>
>>>
>>> Lodging, Meals and Transportation:
>>>
>>> These expenses and arrangements are the responsibility of the
>>> participants.
>>> Fees:
>>> No fee for this three-day course
>>>
>>> Register:
>>>
>>> *Please fill out the attached document and send directly to
>>> luis.m...@isbscience.org*
>>>
>>>
>>> Preliminary Schedule: [image: image.png]
>>>
>>> --
>> You received this message because you are subscribed to the Google Groups
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to spctools-discuss+unsubscr...@googlegroups.com.
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>> https://groups.google.com/d/msgid/spctools-discuss/bf286ca2-e741-4efa-bd0c-678beedc6de6n%40googlegroups.com
>> 
>> .
>>
>
>
> --
> Dr Manuela Piazzi, PhD
> IGM-CNR c/o Rizzoli Orthopedic Institute
> via di Barbiano 1/10
> 40136 Bologna -IT-
> off. +390516366769
> mob. +393495101877
>
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> 
> .
>

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

['Luis Mendoza' via spctools-discuss]

Hi Don,
We'll look into setting up a Zoom option and get back to you soon.
Thank you for your interest in the course!
--Luis


On Tue, Jul 18, 2023 at 1:52 PM don johann  wrote:

> Luis,
> Will there be a virtual option?
> It's very difficult to schedule travel (via university rules) on such
> short notice.
> Thanks,
> Don
>
> On Tue, Jul 18, 2023 at 3:44 PM 'Luis Mendoza' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> Hello all,
>> Based on the survey of dates that Eric sent out, we will hold a short TPP
>> course next week, July 26 - 28, at ISB.
>> We will send a link to registration and more info in the next couple of
>> days, but expect to go 8am - 4:30pm on those three days.
>> Hope this date works for most of you!
>> --Luis
>>
>>
>> On Mon, Jul 17, 2023 at 11:38 AM don johann  wrote:
>>
>>> Any further info (dates) on when the next TPP course may be offered?
>>> Thx,
>>> Don
>>>
>>> On Tue, Jun 27, 2023 at 11:04 PM 'Eric Deutsch' via spctools-discuss <
>>> spctools-discuss@googlegroups.com> wrote:
>>>
>>>> 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 <
>>>> 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!
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "spctools-discuss" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to spctools-discuss+unsubscr...@googlegroups.com.
>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/spctools-discuss/a68bc81c-e40a-4406-9098-929230e3388fn%40googlegroups.com
>>>> <https://groups.google.com/d/msgid/spctools-discuss/a68bc81c-e40a-4406-9098-929230e3388fn%40googlegroups.com?utm_medium=email_source=footer>
>>>> .
>>>>
>>>> --
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>>>> Groups "spctools-discuss" group.
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Re: [spctools-discuss] Re: Next proteomics informatics course?

['Luis Mendoza' via spctools-discuss]

Hello all,
Based on the survey of dates that Eric sent out, we will hold a short TPP
course next week, July 26 - 28, at ISB.
We will send a link to registration and more info in the next couple of
days, but expect to go 8am - 4:30pm on those three days.
Hope this date works for most of you!
--Luis


On Mon, Jul 17, 2023 at 11:38 AM don johann  wrote:

> Any further info (dates) on when the next TPP course may be offered?
> Thx,
> Don
>
> On Tue, Jun 27, 2023 at 11:04 PM 'Eric Deutsch' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> 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 <
>> 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!
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to spctools-discuss+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/spctools-discuss/a68bc81c-e40a-4406-9098-929230e3388fn%40googlegroups.com
>> 
>> .
>>
>> --
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>> "spctools-discuss" group.
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>> 
>> .
>>
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> 
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Re: [spctools-discuss] TPP Tandem input files

['Luis Mendoza' via spctools-discuss]

Hello Emma,
According to this, X!Tandem is indeed able to process MGF files:
https://www.thegpm.org/tandem/tandem_install_faq.html#faq6

Do note that the TPP GUI (Petunia) only allows you to choose mzML/mzXML
files as input, so you will have to run via the command-line.  Also, any
downstream TPP analysis also requires mzML/mzXML files.

Hope this helps!
 --Luis

On Mon, Jun 19, 2023 at 6:57 AM Emma Whittington  wrote:

> Hi,
>
> Is it possible to use MGF files as an input for X!Tandem? I noted that
> comet will accept MGF files but can't see anything about tandem.
>
> All the best,
> Emma
>
> --
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> 
> .
>

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[spctools-discuss] TPP @ ASMS 2023 -- Posters, Tuesday Workshop, and Bioinformatics Hub

['Luis Mendoza' via spctools-discuss]

 Hello everyone,

Next week the TPP software tools team will be attending and giving several
presentations at ASMS in Houston.

Please feel free to find us and say hello to me (Luis), David, and Michael,
and bring your PeptideAtlas/TPP-related software and/or installation
questions.  We also have information on the recent TPP 6.3 release, as well
as on upcoming updates in our posters.

We will be conducting an evening *Workshop *on *Tuesday June 6th at 5:45pm
in room 351CF*.  We'll give a brief intro to the existing TPP tools and
then encourage discussion about them and about future directions for the
TPP.  Topic leads for discussion are: *mining for rare PTMs* in your data,
cleavable crosslinker data analysis with *Ving*, and overview of the *Cloud
and cluster* enabled TPP.  So please come and learn about TPP and be part
of the discussion about its future.

We also plan to spend extended time at the *Bioinformatics Hub
*, including
participating in a session on *open science practices on Tuesday 6 June,
10:30 - 12:30*. The Bioinformatics Hub will be located at the
Poster/Exhibit Hall, next to the main entrance; it is open each day during
exhibit hall hours.  Please check the program and drop by to participate in
the various discussions, or to just seek advice, knowledge, and/or support
from leading bioinformaticians.

Lastly, we will be presenting several *posters*:

   - *How Well Did You Capture that Ion? Find Out with PeptidePrisoner!*
   Luis Mendoza

*MP 376 *


   - *Ving: A New Tool in the Trans-Proteomic Pipeline for XL-MS Using
   Cleavable Cross-Linking Reagents*
   Michael Hoopmann


*TP 174 *
   - * Modification Specific Modeling in PeptideProphet Improves Validation
   of Rare PTM Containing Peptides in Complex Samples*
   David Shteynberg
   *ThP 610*


Other posters related to TPP and our lab:

   - *Proteomics Standards Initiative (PSI) proposed peak annotation format
   (mzPAF) and spectral library format (mzSpecLib) standards*
   Henry Lam
   *TP 39*0

   - *Borrelia PeptideAtlas: A proteome resource for the Lyme disease
   community*
   Helisa Wippel
   *MP 697*


   - * Achieving robust quantitative analysis of proteomes using Vacuum
   insulated probe heated electrospray ionization (VIP-HESI) coupled with
   microflow chromatography and timsTOF-Mass-Spectrometer*
   Mukul Midha
   *WP 133*


More information at:
* http://www.tppms.org/asms/  *

Please let your colleagues or any other interested people know, too!

Also, please let us know if you have a poster or oral presentation of
research that makes use of the TPP; we'll try to drop by and visit.

Thanks,
--Luis, David, Eric, and Michael

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[spctools-discuss] TPP 6.3.0 Release is now available

['Luis Mendoza' via spctools-discuss]

Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.3.0
"Arcus"

We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP)
software, release 6.3.0.  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:6.3.0_Release_Notes


*Getting the TPP Software*
Download the TPP version 6.3.0 native windows installer from the Sashimi
SourceForge project file release page:
  https://sourceforge.net/

projects/sashimi/files/Trans-
Proteomic
Pipeline (TPP)/


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 6.3.0 source
code .zip package
or, check out the code directly from svn:
  svn export svn://svn.code.sf.net/p/sashimi/code/tags/release_6-3-0

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] protein validation

['Luis Mendoza' via spctools-discuss]

Hello Felipe,

There may be several reasons why you see the viral protein in your
analysis, e.g.

   - Did you only run Comet, or did you validate using the TPP/Prophets?
   If the latter, what was the probability of the protein(s) in question?
   - What were the contents of the database that you used to search?  Did
   they contain only "the sequence of my protein of interest"/virus protein,
   or did you use a full proteome database?  Did you use decoys?  Contaminants?
   - Does the virus protein contain peptides that may be shared with
   proteins in the sample itself?   Do you observe unique/proteotypic peptides
   from that protein?

Cheers,
--Luis



On Sun, Apr 30, 2023 at 7:13 PM felipe velasquez  wrote:

> Hello
>
> I have a question about protein validation. I am trying to use TPP to
> identify post-translational modifications of certain proteins. I performed
> a Comet search using the sequence of my protein of interest. However, while
> exploring another database, I performed a search using a protein that is
> not in the experimental design, as it comes from a virus. Surprisingly,
> this protein appeared in my analysis. Is this normal?
>
> thanks,
>
> Felipe Ignacio Velásquez Salinas
> Bioquímico
> Doctor en Microbiología
>
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> 
> .
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Re: [spctools-discuss] Problem with PTMprophet

['Luis Mendoza' via spctools-discuss]

Hello Felipe,

The top message seems to indicate a permissions error; perhaps the files
under /tmp are not accessible to the Apache/web user?  Since this looks
like a Linux install, it depends on how that part of your system is set up.

The large error may or may not be related to the previous one, but it is
telling you that the pepXML file is not valid PepXML.  There can be many
reasons for this, so it depends on how that file was initially generated.

What steps did you take to go from your Thermo raw file to this pepXML?
Do you get any other errors or warnings before this step?  Have you been
able to run other data as a test of your TPP install?

Cheers,
--Luis


On Fri, Apr 28, 2023 at 11:25 AM felipe velasquez 
wrote:

> Hello luis, thanks.
>
> [image: image.png]
>
>
> This is one of the messages... there is something I can do to fix it?
>
> Thanks again,
>
> Felipe
>
> El vie, 28 abr 2023 a las 4:58, 'Luis Mendoza' via spctools-discuss (<
> spctools-discuss@googlegroups.com>) escribió:
>
>> Hello Felipe,
>>
>> It is in general not normal to not find "any results" with TPP when other
>> platforms do find some, as there is often partial, if not significant,
>> overlap.  Typically when no results are found, it points to either bad data
>> (presumably not in this case) or incorrect parameters (including choice of
>> database if doing sequence searching).
>>
>> For your specific case, we would need to know more specifics if you are
>> looking for help in your TPP analysis -- e.g. what kind of data you have,
>> what components are you using, what parameters were set, etc.
>>
>> We do note that in some instances other software does tend to inflate the
>> number of results provided to the user, albeit with either a very high or
>> otherwise poorly characterized error rate.
>>
>> Again, without knowing specifics, it is impossible to tell what could be
>> going on.
>>
>> Cheers,
>> --Luis
>>
>>
>> On Thu, Apr 27, 2023 at 8:04 PM felipe velasquez 
>> wrote:
>>
>>> hello again
>>>
>>> I am trying to analyze some samples from thermo raw data, but I cannot
>>> find any results. However, another person analyzed the same data using
>>> another platform and found some results. Is this normal?
>>>
>>>
>>> Felipe
>>>
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>>> .
>>>
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Re: [spctools-discuss] Problem with PTMprophet

['Luis Mendoza' via spctools-discuss]

Hello Felipe,

It is in general not normal to not find "any results" with TPP when other
platforms do find some, as there is often partial, if not significant,
overlap.  Typically when no results are found, it points to either bad data
(presumably not in this case) or incorrect parameters (including choice of
database if doing sequence searching).

For your specific case, we would need to know more specifics if you are
looking for help in your TPP analysis -- e.g. what kind of data you have,
what components are you using, what parameters were set, etc.

We do note that in some instances other software does tend to inflate the
number of results provided to the user, albeit with either a very high or
otherwise poorly characterized error rate.

Again, without knowing specifics, it is impossible to tell what could be
going on.

Cheers,
--Luis


On Thu, Apr 27, 2023 at 8:04 PM felipe velasquez  wrote:

> hello again
>
> I am trying to analyze some samples from thermo raw data, but I cannot
> find any results. However, another person analyzed the same data using
> another platform and found some results. Is this normal?
>
>
> Felipe
>
> --
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> "spctools-discuss" group.
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> 
> .
>

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Re: [spctools-discuss] SILAC quantification with targeted SIM

['Luis Mendoza' via spctools-discuss]

Hi Will,
Glad you got this to work!

A potentially quicker solution is to enter those extra flags in the
"additional options" box in Petunia:

[image: image.png]

You can find a full set of available options at the Proteowizard msconvert
info page:
https://proteowizard.sourceforge.io/tools/msconvert.html

At some point we'll add more options to this page as well.

Cheers,
--Luis


On Fri, Apr 7, 2023 at 10:55 AM Will Comstock  wrote:

> Okay I got it to work. For the record, my solution was the following:
>
>
>1. Rather than use the msConvert packaged with the TPP, I downloaded
>it separately from ProteoWizard.
>2. I converted my RAW file with the following parameters:
>
>
>- [image: SIM_msConvert.PNG]
>- (I am not sure if "SRM as spectra" is required, but "SIM as spectra"
>was key as all my MS1 scans were classified as SIM-MS scans)
>
>   3. I then searched the resulting mzML file as normal.
>
> Thanks again, Jimmy!
> -Will
>
> On Friday, April 7, 2023 at 1:04:44 PM UTC-4 Will Comstock wrote:
>
>> Good catch, I will try to redo the RAW conversion to include my MS1
>> scans. Thanks Jimmy!
>>
>> -Will
>>
>> On Fri, Apr 7, 2023 at 12:50 PM Jimmy Eng  wrote:
>>
>>> Will,
>>>
>>> XPRESS extracts precursor intensities from MS1 scans and your mzXML file
>>> contains only MS/MS scans.  So that's why XPRESS is failing because it's
>>> expecting to parse MS1 scans which aren't present in this file.
>>>
>>> Jimmy
>>>
>>> On Fri, Apr 7, 2023 at 8:57 AM Will Comstock  wrote:
>>>
 Hi all,

 I'm trying to use tSIM-ddMS2 to identify specific peptides in my
 sample, but I also want SILAC quantification of those peptides using
 XPRESS. I've made sure the MS1 isolation window is wide enough to see both
 Light and Heavy peptide peaks for everything in my inclusion list (30
 daltons, so my heavy peptides which are +8 or +10 are detected). However,
 when I search with Comet and XPRESS, there is no quantitative ratio
 provided, just -1.0. XPRESS appears to be looking in the wrong place for
 the light and heavy peptides, but I am not sure why or how to redirect it
 to the right parts of my MS1 spectra. If I look at the precursor scans
 manually via QualBrowser, both peaks are definitely being detected.

 Has anyone here tried using XPRESS to do SILAC quantitation in targeted
 runs before?


 Here is a folder with my data, search parameters, and database just in
 case.

 https://drive.google.com/drive/folders/1142YHaxB1RC6HMcfuy_MdEN8T-sSLDSl?usp=sharing

 Thanks!
 -Will

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Re: [spctools-discuss] Re: Output sequence coverage info

['Luis Mendoza' via spctools-discuss]

Sure thing.

And to answer your original question: there is a command-line tool in TPP
called batchcoverage (look in the bin/ directory) that calculates this
residue coverage -- and is the one used by ProteinProphet to populate that
attribute in protXML.

It needs an input file of the form:
>PROTEIN_1
PEPTIDE
ANOTHERONE
ANDTHISONE
>PROTEIN_2
ELVIS
WASHERE
>PROTEIN_3
...

And you run it by providing a reference fasta file location and output file
name, like this:
batchcoverage   

The output file will contain a 2-column list of   values.

Hope this helps, and stay tuned for updates!
--Luis



On Tue, Mar 28, 2023 at 3:59 PM Yasir Ahmed  wrote:

> Thanks Luis, that's helpful. For now I'll just use an older version of TPP
> to get the coverage values.
>
> Cheers,
> Yasir
>
> On Tuesday, March 28, 2023 at 6:46:58 PM UTC-4 Luis Mendoza wrote:
>
>> Hello Yasir,
>>
>> We have recently identified a bug in ProteinProphet that mis-reports the
>> coverage as zero for all proteins.  This affects TPP versions 6.1.0 and
>> 6.2.0.  We will be releasing an update soon that corrects this and other
>> bugs.
>>
>> Even then, the value that is reported in protXML is the ratio of observed
>> amino acids to total.  There is no simple way to get the coverage based on
>> the digestible portion of the protein, though we could think about adding
>> that as a feature.
>>
>> Let me know if you would like to get a preview version of just
>> ProteinProphet in advance of our release and I can post that separately,
>> just specify if you use Linux or Windows.  Alternatively, if you have a
>> pre-6.1.0 version of TPP installed, you can run ProteinProphet and get the
>> coverage values reported.
>>
>> Cheers,
>> --Luis
>>
>>
>> On Tue, Mar 28, 2023 at 2:50 PM Yasir Ahmed  wrote:
>>
>>> I guess I have another question about coverage: using ProtXMLViewer
>>> (which is similar to the output from ProteinProphet), the coverage values
>>> are almost always zero. For example, the example I show above has Obs/Dig
>>> of 82%, but is showing percent coverage to be zero in the ProteinProphet
>>> output. Any idea why? And can one get those Obs/Dig values?
>>>
>>> On Tuesday, March 28, 2023 at 5:23:06 PM UTC-4 Yasir Ahmed wrote:
>>>
 Never mind, got it with ProtXMLViewer.pl (duh).

 On Tuesday, March 28, 2023 at 5:03:14 PM UTC-4 Yasir Ahmed wrote:

> Greetings Friends,
>
> Is there a command line tool within the TPP that can output sequence
> residue coverage percentages (Obs/Tot)? I can get those for individual
> proteins using the ProtXMLViewer GUI (see attached image), but would like
> to do this for every protein in my database.
>
> Cheers,
> Yasir
>
> [image: Screen Shot 2023-03-28 at 4.29.18 PM.png]
>
 --
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>>> 
>>> .
>>>
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Re: [spctools-discuss] Re: Output sequence coverage info

['Luis Mendoza' via spctools-discuss]

Hello Yasir,

We have recently identified a bug in ProteinProphet that mis-reports the
coverage as zero for all proteins.  This affects TPP versions 6.1.0 and
6.2.0.  We will be releasing an update soon that corrects this and other
bugs.

Even then, the value that is reported in protXML is the ratio of observed
amino acids to total.  There is no simple way to get the coverage based on
the digestible portion of the protein, though we could think about adding
that as a feature.

Let me know if you would like to get a preview version of just
ProteinProphet in advance of our release and I can post that separately,
just specify if you use Linux or Windows.  Alternatively, if you have a
pre-6.1.0 version of TPP installed, you can run ProteinProphet and get the
coverage values reported.

Cheers,
--Luis


On Tue, Mar 28, 2023 at 2:50 PM Yasir Ahmed  wrote:

> I guess I have another question about coverage: using ProtXMLViewer (which
> is similar to the output from ProteinProphet), the coverage values are
> almost always zero. For example, the example I show above has Obs/Dig of
> 82%, but is showing percent coverage to be zero in the ProteinProphet
> output. Any idea why? And can one get those Obs/Dig values?
>
> On Tuesday, March 28, 2023 at 5:23:06 PM UTC-4 Yasir Ahmed wrote:
>
>> Never mind, got it with ProtXMLViewer.pl (duh).
>>
>> On Tuesday, March 28, 2023 at 5:03:14 PM UTC-4 Yasir Ahmed wrote:
>>
>>> Greetings Friends,
>>>
>>> Is there a command line tool within the TPP that can output sequence
>>> residue coverage percentages (Obs/Tot)? I can get those for individual
>>> proteins using the ProtXMLViewer GUI (see attached image), but would like
>>> to do this for every protein in my database.
>>>
>>> Cheers,
>>> Yasir
>>>
>>> [image: Screen Shot 2023-03-28 at 4.29.18 PM.png]
>>>
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> 
> .
>

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[spctools-discuss] TPP 6.2.0 Release is now available

['Luis Mendoza' via spctools-discuss]

Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.2.0
"Nacreous"

We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP)
software, release 6.2.0.  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:6.2.0_Release_Notes


*Getting the TPP Software*
Download the TPP version 6.2.0 native windows installer from the Sashimi
SourceForge project file release page:
  https://sourceforge.net/projects/sashimi/files/Trans-Proteomic Pipeline
(TPP)/TPP v6.2 (Nacreous) 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 6.2.0 source
code .zip package
or, check out the code directly from svn:
  svn export svn://svn.code.sf.net/p/sashimi/code/tags/release_6-2-0

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] Analyzing Metaproteomic Data

['Luis Mendoza' via spctools-discuss]

Hello,

The version of msconvert that is shipped with TPP is a couple of years old
and does not know about that instrument.  You have three options to convert
your files:

1. Download and install a newer version of ProteoWizard, run the
conversion, and use that mzML file in Comet.  This is likely the simplest
and most expedient.

2. Use the command-line to convert the file, using the
--ignoreUnknownInstrumentError flag, for example:
  msconvert.exe --ignoreUnknownInstrumentError
c:\TPP\data\TMT_Microbiome\Xu_20210512_IRIstudy_Concentration_TMT_Plate1_D.raw


3. We will be releasing a new version of TPP later this week.  If you are
able to wait, then just update to the new version, which includes a more
recent version of msconvert.   This is recommended as long as you can wait
a few days to process your data.

Hope this helps,
--Luis


On Mon, Feb 13, 2023 at 8:32 AM Aarthie Senathirajah <
animallover@gmail.com> wrote:

> Hi I'm currently trying to analyze the raw files from this metaproteomic
> dataset of the human gut microbiome. Which uses maxquant usually but i
> would like to use Comet.
> Firstly I am getting this error when trying to convert the raw file into
> mzml
> processing file:
> c:/TPP/data/TMT_Microbiome\Xu_20210512_IRIstudy_Concentration_TMT_Plate1_D.raw
> [Reader_Thermo::fillInMetadata] unable to parse instrument model; please
> report this error to the ProteoWizard developers with this information:
> model(Orbitrap Exploris 480) name(Orbitrap Exploris Slot #162); if want to
> convert the file anyway, use the ignoreUnknownInstrumentError flag
>
>
> Which I'm not sure how to solve.. Any help would be great!
>
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> 
> .
>

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Re: [spctools-discuss] protein prophet failing on Eclipse searches

['Luis Mendoza' via spctools-discuss]

Hi,
Congrats on the new instrument, and happy holidays as well!

The error seems to indicate that there is no input data for ProteinProphet
to work with; can you verify that the input file contains validated search
results with probabilities above 0.2 ?  Are there any other errors or
warnings in the previous steps?

Feel free to directly send me the interact.pep.xml file and I can have a
look as well.

Cheers,
--Luis


On Tue, Nov 29, 2022 at 10:31 AM cabarnes...@gmail.com <
cabarnescabar...@gmail.com> wrote:

> Hi all,
>
> Happy holidays!  I have a new Eclipse in the lab and have been running my
> Comet + TPP pipeline successfully on a lot of data downloaded from PRIDE
> lately, but have run into an error with the new DDA data generated on the
> Eclipse.  It seems to be failing at the protein prophet step and the error
> doesn't make much sense to me.  Any idea what is going on?
>
> I'm running TPP 6.1 and Comet 2022.01 rev. 1 although the error below is
> from the output of the Comet search through the TPP interface.  I get a
> similar error on the command line at the same step.
>
>
> Here's the error message:
>
> WARNING: no data - output file will be empty
>
> command "C:/TPP/bin/ProteinProphet "interact.pep.xml" "interact.prot.xml""
> failed: Operation not permitted
>
> command "C:/TPP/bin/ProteinProphet "interact.pep.xml" "interact.prot.xml""
> exited with non-zero exit code: 1
> QUIT - the job is incomplete
>
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> 
> .
>

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Re: [spctools-discuss] Xpress ratio in pepXML do not match those in XPressPeptideUpdateParser.cgi

['Luis Mendoza' via spctools-discuss]

Hello,
That is quite odd; Are you able to share a pepXML file so we can
troubleshoot?  You can contact me directly to arrange a file transfer.
Thanks,
--Luis


On Tue, Oct 18, 2022 at 12:21 PM 2kl...@gmail.com <2kl...@gmail.com> wrote:

> Hi all,
>
> I am using the TPP v6.1.0 Parhelion, Build 202108271510 for analyzing
> dimethylation following Comet (or MSFragger) search with the light label
> set as fixed and the heavy mass difference as variable. Xpress settings
> include mass tolerance of 20 ppmת a Minimum number of chromatogram points
> needed for quantitation:3 and Number of isotopic peaks to sum is set to 0.
>
> When I open the interact.pep.xml file with the viewer and filter the
> results based on probability, for some of the peptides there is a
> discrepancy between the ratio shown in the pepXML and the one in the
> XPressPeptideUpdateParser. The differences can be relatively large (for
> example, 0.1 versus 1.5)
>
> Similar results are obtained if the Number of isotopic peaks to sum is
> set to 1, 2 or 3.
>
> Can you please advise?
> Many thanks,
> OK
>
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> 
> .
>

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Re: [spctools-discuss] Windows 11 Compatibility

['Luis Mendoza' via spctools-discuss]

Hi Will,
We tested it on Windows 11 a few months ago and noticed no issues.  Please
do let us know if you run into any.
Cheers,
--Luis


On Thu, Oct 13, 2022 at 12:24 PM Will Comstock  wrote:

> Hi all,
>
> Very quick question: Is the TPP 6.1.0 fully compatible with Windows 11?
>
> Thanks!
> -Will
>
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> 
> .
>

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Re: [spctools-discuss] Libra quantification on TMT 16-plex returns zeros only

['Luis Mendoza' via spctools-discuss]

Great, glad that it is now working for you!  We will remove references to
that deprecated parameter from our documentation.
Cheers,
--Luis


On Fri, Sep 9, 2022 at 1:54 PM Yasir Ahmed  wrote:

> Thanks Eric and Luis! Turns out I was using the wrong/older syntax in the
> condition file (targetMS level = “3”). The quantification works now. Thanks
> for your help!!!
>
> Cheers,
> Yasir
>
> On Sep 8, 2022, at 6:15 PM, 'Luis Mendoza' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
> Hi Yasir,
> Is your data Thermo SPS where the reporter ions are in MS3?  If so, please
> check the relevant box when producing the condition file:
>
> 
>
>
> As Eric noted, it does not seem like your MS2 spectra contain reporter ion
> signals, at least from the one spectrum you posted.  Are there others where
> this is not the case?
>
> Cheers,
> --Luis
>
>
> On Thu, Sep 8, 2022 at 2:28 PM 'Eric Deutsch' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> I’m thinking that ion trap spectra are usually unsuitable for TMT:
>>
>>
>> 
>>
>>
>> I think you would want to acquire fragmentation spectra with Orbitrap HCD?
>>
>>
>>
>> *From:* spctools-discuss@googlegroups.com <
>> spctools-discuss@googlegroups.com> *On Behalf Of *Yasir Ahmed
>> *Sent:* Thursday, September 8, 2022 2:19 PM
>> *To:* spctools-discuss@googlegroups.com
>> *Subject:* Re: [spctools-discuss] Libra quantification on TMT 16-plex
>> returns zeros only
>>
>>
>> Hi Luis,
>>
>>
>> Just to follow up: I found a handful of cases where one of the channels
>> has super high quantification and observable reporter ions (see screenshots
>> below), albeit it should be way more than this, I believe. I’ll keep
>> digging, but let me know if you have any other ideas.
>>
>>
>> Again, thanks for you suggestions.
>>
>>
>> Cheers,
>>
>> Yasir
>>
>>
>> 
>>
>>
>> 
>>
>>
>> 
>>
>>
>>
>> On Sep 8, 2022, at 5:07 PM, Yasir Ahmed  wrote:
>>
>>
>> Hi Luis,
>>
>>
>> Thanks a lot for the response.
>>
>>
>> Can you try re-running Libra without the centroiding option?  (i.e. set
>> type="0") Or are your mzML data not centroided?
>>
>>
>>
>> I just tried that, but no difference in outcome.
>>
>>
>>
>> Another thing to try: are you able to open the PeptideProphet + Libra
>> results in the PepXMLViewer?  You should be able to see if there are a
>> significant number of quantified PSMs -- you should also be able to examine
>> a few individual spectra and zoom in on the reporter ion signals.
>>
>>
>>
>> I’m able to look at a few individual spectra, and I think they all look
>> mostly good—but frankly I’m not too sure how to evaluate their suitability
>> (see example screenshots below).
>>
>>
>>
>> Lastly, what version of TPP are you running?
>>
>>
>>
>> 6.1.0
>>
>>
>> Thanks again!
>>
>> Yasir
>>
>>
>> 
>>
>>
>> 
>>
>>
>>
>>
>>
>>
>> Cheers,
>>
>> --Luis
>>
>>
>>
>> On Thu, Sep 8, 2022 at 12:02 PM Yasir Ahmed  wrote:
>>
>> Greetings,
>>
>>
>> I'm having difficulty performing TMT quantification using Libra on a
>> 16-plex dataset. Basically, the "quantification.tsv" file that Libra
>> outputs only contains zeros for both peptides and proteins. The Comet
>> search runs just fine. I'm at a loss for where things are going wrong. The
>> Mass Spec facility used ProteomeDiscoverer for the quantification, and it
>> worked fine so the issue is not the raw data.
>>
>>
>> My TPP run repository can be found here
>> <https://github.com/YazBraimah/TPP_TMT_proteomics_pipeline>, and the
>> "condition.xml" file for Libra—along with the Comet params file—is in the
>> "params" folder. The commands used to run the TPP processes can be found in
>> the file called "Snakefile". I'm happy to provide any additional
>> information needed to help troubleshoot this. Any pointers/advise would be
>> greatly appreciated.
>>
>>
>> Cheers,
>>
>> Yasir
>>
>>
>> --
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Re: [spctools-discuss] Libra quantification on TMT 16-plex returns zeros only

['Luis Mendoza' via spctools-discuss]

Hello Yasir,

Can you try re-running Libra without the centroiding option?  (i.e. set
type="0") Or are your mzML data not centroided?
Another thing to try: are you able to open the PeptideProphet + Libra
results in the PepXMLViewer?  You should be able to see if there are a
significant number of quantified PSMs -- you should also be able to examine
a few individual spectra and zoom in on the reporter ion signals.
Lastly, what version of TPP are you running?

Cheers,
--Luis


On Thu, Sep 8, 2022 at 12:02 PM Yasir Ahmed  wrote:

> Greetings,
>
> I'm having difficulty performing TMT quantification using Libra on a
> 16-plex dataset. Basically, the "quantification.tsv" file that Libra
> outputs only contains zeros for both peptides and proteins. The Comet
> search runs just fine. I'm at a loss for where things are going wrong. The
> Mass Spec facility used ProteomeDiscoverer for the quantification, and it
> worked fine so the issue is not the raw data.
>
> My TPP run repository can be found here
> , and the
> "condition.xml" file for Libra—along with the Comet params file—is in the
> "params" folder. The commands used to run the TPP processes can be found in
> the file called "Snakefile". I'm happy to provide any additional
> information needed to help troubleshoot this. Any pointers/advise would be
> greatly appreciated.
>
> Cheers,
> Yasir
>
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> 
> .
>

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Re: [spctools-discuss] Tandem Analysis

['Luis Mendoza' via spctools-discuss]

Hello Priti,
You can specify non-enzymatic cleavage by setting the *protein, cleavage
site* parameter to *[X]|[X]* .

More info at the X!Tandem site:
https://www.thegpm.org/TANDEM/api/pcs.html
https://www.thegpm.org/TANDEM/api/pcsemi.html

Hope this helps,
--Luis


On Wed, Aug 3, 2022 at 10:59 PM Priti Panchal 
wrote:

> Hello
> I am trying to do tandem analysis. I am uncertain whether we can perform a
> tandem analysis for the lc-ms/ms data of non enzymatically digested sample
> since in the tandem parameter file there is not any option available for
> "no cleavage" or "no cut" as found in comet parameters. In tandem, there is
> "semi tryptic" digestion option only.
> If we can perform the analysis in tandem please suggest how to edit the
> parameter file to perform analysis of non digested data.
> Thank you
> Priti
>
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> 
> .
>

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Re: [spctools-discuss] Comet Params file for MS2 and MS3 TMT11-plex, comet won't load any spectra when mslevel=3

['Luis Mendoza' via spctools-discuss]

Hello,
It seems that your issue may be caused by this parameter:
ms_level = 2-3   # MS level to analyze, valid are
levels 2 (default) or 3
Please specify it as a single value, e.g.
ms_level = *3*   # MS level to analyze, valid are
levels 2 (default) or 3

Hope this helps,
--Luis


On Fri, Jul 15, 2022 at 9:17 AM Aarthie Senathirajah <
animallover@gmail.com> wrote:

> Hi
> I'm currently having an issue with comet in TPP where I use my MZXML file
> and when I set my comet params mslevel= 3 it does not load any spectra.
>
> I've check the mzxml file and it does contain MS3 spectra so I'm not sure
> why this is occurring. Here is a copy of my comet params file .
> # comet_version 2018.01 rev. 4
> # Generated via Petunia/TPP by guest on Fri Jul 15 11:43:46 2022
> # Comet MS/MS search engine parameters file.
> # Everything following the '#' symbol is treated as a comment.
>
> database_name = /some/path/db.fasta
> decoy_search = 1   # 0=no (default), 1=concatenated
> search, 2=separate search
> peff_format = 0# 0=no (normal fasta, default),
> 1=PEFF PSI-MOD, 2=PEFF Unimod
> peff_obo = # path to PSI Mod or Unimod OBO file
>
> num_threads = 0# 0=poll CPU to set num threads;
> else specify num threads directly (max 128)
>
> #
> # masses
> #
> peptide_mass_tolerance = 50.00
> peptide_mass_units = 2 # 0=amu, 1=mmu, 2=ppm
> mass_type_parent = 1   # 0=average masses, 1=monoisotopic
> masses
> mass_type_fragment = 1 # 0=average masses, 1=monoisotopic
> masses
> precursor_tolerance_type = 1   # 0=MH+ (default), 1=precursor m/z;
> only valid for amu/mmu tolerances
> isotope_error = 3   # 0=off, 1=0/1 (C13 error),
> 2=0/1/2, 3=0/1/2/3, 4=-8/-4/0/4/8 (for +4/+8 labeling)
>
> #
> # search enzyme
> #
> search_enzyme_number = 1   # choose from list at end of this
> params file
> num_enzyme_termini = 2 # 1 (semi-digested), 2 (fully
> digested, default), 8 C-term unspecific , 9 N-term unspecific
> allowed_missed_cleavage = 2# maximum value is 5; for enzyme
> search
>
> #
> # Up to 9 variable modifications are supported
> # format:<0=variable/else binary>
>
> # e.g. 79.966331 STY 0 3 -1 0 0
> #
> variable_mod01 = 15.9949 M 0 3 -1 0 0
> variable_mod02 = 0.0 X 0 3 -1 0 0
> variable_mod03 = 0.0 X 0 3 -1 0 0
> variable_mod04 = 0.0 X 0 3 -1 0 0
> variable_mod05 = 0.0 X 0 3 -1 0 0
> variable_mod06 = 0.0 X 0 3 -1 0 0
> variable_mod07 = 0.0 X 0 3 -1 0 0
> variable_mod08 = 0.0 X 0 3 -1 0 0
> variable_mod09 = 0.0 X 0 3 -1 0 0
> max_variable_mods_in_peptide = 5
> require_variable_mod = 0
>
> #
> # fragment ions
> #
> # ion trap ms/ms:  1.0005 tolerance, 0.4 offset (mono masses),
> theoretical_fragment_ions = 1
> # high res ms/ms:0.02 tolerance, 0.0 offset (mono masses),
> theoretical_fragment_ions = 0, spectrum_batch_size = 1
> #
> fragment_bin_tol = 1.0005  # binning to use on fragment ions
> fragment_bin_offset = 0.4  # offset position to start the
> binning (0.0 to 1.0)
> theoretical_fragment_ions = 1  # 0=use flanking peaks, 1=M peak
> only
> use_A_ions = 0
> use_B_ions = 1
> use_C_ions = 0
> use_X_ions = 0
> use_Y_ions = 1
> use_Z_ions = 0
> use_NL_ions = 0# 0=no, 1=yes to consider NH3/H2O
> neutral loss peaks
>
> #
> # output
> #
> output_sqtstream = 0   # 0=no, 1=yes  write sqt to
> standard output
> output_sqtfile = 0 # 0=no, 1=yes  write sqt file
> output_txtfile = 0 # 0=no, 1=yes  write tab-delimited
> txt file
> output_pepxmlfile = 1  # 0=no, 1=yes  write pep.xml file
> output_percolatorfile = 0  # 0=no, 1=yes  write Percolator
> tab-delimited input file
> print_expect_score = 1 # 0=no, 1=yes to replace Sp with
> expect in out & sqt
> num_output_lines = 5   # num peptide results to show
> show_fragment_ions = 0 # 0=no, 1=yes for out files only
>
> sample_enzyme_number = 1   # Sample enzyme which is possibly
> different than the one applied to the search.
># Used to calculate NTT & NMC in
> pepXML output (default=1 for trypsin).
>
> #
> # mzXML parameters
> #
> scan_range = 0 0   # start and end scan range to
> search; either entry can be set independently
> precursor_charge = 0 0 # precursor charge range to
> analyze; does not override any existing charge; 0 as 1st entry ignores
> parameter
> override_charge = 0# 0=no, 1=override precursor charge
> states, 2=ignore precursor charges outside precursor_charge range, 3=see
> online
> ms_level = 2-3   # MS level to analyze, valid are
> levels 2 (default) or 3
> activation_method = CID

Re: [spctools-discuss] account management

['Luis Mendoza' via spctools-discuss]

Hi Malcolm,
Yes, those instructions for adding new accounts are still valid; I find it
simplest to follow the ones under your second link ("TPP Login
Credentials").

Please do note that those passwords are only as secure as the server
protocol under which you install TPP -- i.e. things are not at all secure
unless using https.  The passwords are never stored locally; instead a
one-way encryption with a locally-settable salt are used to generate a
hash.  You may also wish to disable the default "guest" account in order to
avoid unwanted access.

Cheers,
--Luis


On Mon, Jun 13, 2022 at 4:47 PM Malcolm Cook  wrote:

> I wonder if thee exchanges are the state of the are for TPP account
> management and its documentation:
>
>  - [add/create account for GUI](
> https://groups.google.com/g/spctools-discuss/c/hUhyzVSBR3Y/m/kBgM6muh43UJ)
>  - [TPP Login Credentials](
> https://groups.google.com/g/spctools-discuss/c/Av6dBdemrVg/m/JAzFH4TXdwUJ)
>
> Cheers,
> Malcolm
>
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> 
> .
>

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

['Luis Mendoza' via spctools-discuss]

Very nice, thank you!


On Fri, Jun 10, 2022 at 4:18 PM Malcolm Cook  wrote:

> I just finished successful install on CentOS7 with the following notes:
>
> https://github.com/malcook/tpp_sandbox/blob/main/tpp_install_centos7.org
>
> I hope it might help someone else
>
> On Monday, October 12, 2020 at 11:02:33 PM UTC-5 Eric Deutsch wrote:
>
>> 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...@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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>> 
>> .
>>
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Re: [spctools-discuss] Re: TPP 6.1.0 Release is now available

['Luis Mendoza' via spctools-discuss]

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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> 
> .
>

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[spctools-discuss] TPP @ ASMS 2022 -- Posters and Monday Workshop

['Luis Mendoza' via spctools-discuss]

 Hello everyone,

The SPC software tools team will be leading an evening *Workshop on Monday
June 6th at 5:45pm in room M100 BC *during the ASMS Annual Conference.

We will give a brief intro to the existing TPP tools, including new
features in *TPP 6.1.0*, and then encourage discussion about them and about
future directions for the TPP.

Topic leads for discussion are: *cluster deployment*, running and analyzing
open-search engine results with *Magnum and PTMProphet*, use of *entrapment
databases *to benchmark validation workflows, and deploying the TPP
using *Docker
containers & cloud computing platforms*.

We will also present several posters:

   - Michael Hoopmann:  "Incorporating digestion efficiency analysis to
   improve shotgun proteomics analytical pipelines"

*MP271 *
   - David Shteynberg: "PTMProphet + Magnum: Localization of Open-Mass
   Search Adducts and Mass Differences in Search Engine Results" *TP 437*


Please let your coworkers or any other interested people know, too!

Also, please let us know if you have a poster or oral presentation of
research that makes use of the TPP; we'll try to drop by and visit.

More information and reprints at:  http://www.tppms.org/asms/

Thanks,
--Luis, David, Eric, and Michael

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[spctools-discuss] TPP 6.1.0 Release is now available

['Luis Mendoza' via spctools-discuss]

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] MzXML2Search does not create files

['Luis Mendoza' via spctools-discuss]

Hello Max,
There seems to be an issue with running this command via the UI (Petunia).
Can you check if you get the same behavior when running on the command-line?
Thanks for reporting this.
--Luis


On Wed, Mar 2, 2022 at 3:56 PM Maxence Le Vasseur <
levasseurmaxe...@gmail.com> wrote:

> Hi there,
>
> It seems that the MzXML2Search function does not create .dta (and possibly
> other) files. Running the function from the Petunia web interface creates
> the folder but the folder is empty after completion of the task although
> the script seemingly finishes 'successfully' without triggering any error
> message. Anyone else is having this issue?
>
> Thanks,
>
> Max
>
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> 
> .
>

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Re: [spctools-discuss] MzXML2Search does not create files

['Luis Mendoza' via spctools-discuss]

On Wed, Mar 2, 2022 at 3:56 PM Maxence Le Vasseur <
levasseurmaxe...@gmail.com> wrote:

> Hi there,
>
> It seems that the MzXML2Search function does not create .dta (and possibly
> other) files. Running the function from the Petunia web interface creates
> the folder but the folder is empty after completion of the task although
> the script seemingly finishes 'successfully' without triggering any error
> message. Anyone else is having this issue?
>
> Thanks,
>
> Max
>
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> 
> .
>

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Re: [spctools-discuss] TPP offline version?

['Luis Mendoza' via spctools-discuss]

Hello Jill,

Yes, the TPP tools are run on your computer and no internet connection is
required other than to download it.  Or you can install from a flash drive
or other similar media as well.  The only time you might need internet is
to follow certain links to extra information from the various viewers;
there are also a few utilities that make use of the internet to download
and install other special software (such as spectral libraries), but are
not required to run the core TPP validation tools.

You can find a link to various tutorials at www.tppms.org

Hope this helps,
--Luis


On Fri, Nov 5, 2021 at 6:58 AM j.l.r...@gmail.com 
wrote:

> Hello! I was wondering if it is possible to run TPP without an internet
> connection? If someone could direct me to a tutorial it would be greatly
> appreciated!
>
> Thank you,
> Jill
>
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Re: [spctools-discuss] Cannot execute 'tpp_models.pl' by 'ProphetModels.pl' in TPP_5.2.0

['Luis Mendoza' via spctools-discuss]

Hello,
Is /usr/local/tpp/bin/  in your PATH?  If not, please add it and try
again.  You can test by typing  which tpp_models.pl

We would also recommend installing the latest version of TPP (6.0.0), which
we recently released.

Hope this helps,
--Luis


On Mon, Aug 23, 2021 at 9:53 AM Huang xiaoxiang 
wrote:

>   I installed the TPP_5.2.0 in my Ubuntu platform, every thing seems to
> going well until an error occurs.  I used the command
> '/usr/local/tpp/bin/xinteract -OPd -Nall -ddecoy_ -ip -p0 -eN *.pep.xml' to
> run ProteinProphet on the iProphet results, but an error occured below.  
> [image:
> hjaoapebbapijiaf.png]
> And below is the location of the error in file 'ProphetModels.pl'[image:
> 2.png]
>
> The files 'tpp_models.pl' and 'ProphetModels.pl' are both in the 'bin'
> directory. So, what is wrong with it? I need help, thanks a lot!
>
> --
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> 
> .
>

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[spctools-discuss] TPP 6.0.0 Release is now available

['Luis Mendoza' via spctools-discuss]

*Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.0.0
"OmegaBlock".*

We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP)
software, release 6.0.0.  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 with the most important new features, changes, and known
issues are available at:

http://tools.proteomecenter.org/wiki/index.php?title=TPP:6.0.0_Release_Notes


*Getting the TPP Software*

Download the TPP version 6.0.0 native windows installer from the Sashimi
SourceForge project file release page:
  https://sourceforge.net/projects/sashimi/files/Trans-Proteomic Pipeline
(TPP)/

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 6.0.0 source
code .zip package
or, check out the code directly from svn:
  svn export svn://svn.code.sf.net/p/sashimi/code/tags/release_6-0-0

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] Re: Exporting StPeter´s ng to mzid

['Luis Mendoza' via spctools-discuss]

Hello Valdemir,
You can run the ProtXMLViewer on the command-line to do this.

If you want one protein per line, with peptides as a comma-separated list:
/FULL/PATH/TO/tpp/cgi-bin/ProtXMLViewer.pl -file
 -action ExportExcel

If you want one peptide per line, with per-peptide stats as well:
/FULL/PATH/TO/tpp/cgi-bin/ProtXMLViewer.pl -file
 -action ExportExcel -peps

Just replace the start of the path to match the location of the viewer file
on your system, and make sure you use the full path to the input protXML
file; the output file will be named the same as the input, but with a *.tsv*
extension instead of .xml (e.g. myfile.prot.tsv).

Hope this helps,
--Luis


On Tue, May 11, 2021 at 5:00 PM mele...@gmail.com 
wrote:

> Thank you Eric for the clarification.
> Exporting prot.xml to TSV would be palliative in my case.
> May I ask you if it is possible to export prot.xml to TSV by command line
> (I just know how to do it with Petunia)?
> I am grateful for your help.
> Valdemir
>
> Em segunda-feira, 10 de maio de 2021 às 19:10:09 UTC-3, Eric Deutsch
> escreveu:
>
>> 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...@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...@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] TPP working directory - how to change

['Luis Mendoza' via spctools-discuss]

Hello Laco,
The simplest way is to select the location of the data at the time you
install TPP.   If you already installed TPP, you can just run the installer
again, making sure to specify the location of the data directory.  (You can
leave the actual TPP installation in C:\TPP if you'd like).
Hope this helps,
--Luis


On Mon, Feb 1, 2021 at 4:49 PM Ladislav Cséfalvay 
wrote:

>
> Hi all,
> Id like to ask, how can I change the working directory of TPP to another
> harddrive? The installation of TPP software is on C:\ and I need to set up
> the working directory to D:\Data, if it is possible. How can I manage that?
> Thank you!
> BR
> Laco
>
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Re: [spctools-discuss] Error generation while converting raw files

['Luis Mendoza' via spctools-discuss]

Hello Giangiacomo,

You can use the Lib2html tool to convert an splib into a webpage with
clickable links to library spectra.  You can launch this tool from
SpectraST Tools -> Convert Libraries to HTML.

Hope this helps,
--Luis


On Thu, Jan 21, 2021 at 12:09 AM giangiacomo beretta <
giangiacomo.berett...@gmail.com> wrote:

> Hi David, sorry for the mistypos!
>
> Yes I run PeptideProphet under Analyze Peptides, and no relevant messages
> were generated :)
>
> However, I forgot to mention that the problem is related to
> interact.pep.xml processing in SpectraST in its command line version
> (independent from TPP).
>
> I am sorry, I did not notice that TPP includes an option for spectral
> library generation that works perfectly fine, and this is what I needed..!
>
> Just last question, is there any tool for visualisation/inpection of
> spectra in splib libraries ?
>
> Lots of thanks,
>
> Giangiacomo
>
> Il giorno giovedì 21 gennaio 2021 alle 01:24:47 UTC+1 David Shteynberg ha
> scritto:
>
>> I am not sure I know a tool called "ProptideProphet" ;) Perhaps you tried
>> to run PeptideProphet but it generated no results for you?  When you run
>> "Analyze Peptides" in the TPP interface, it should create a file called
>> interact.pep.xml by default, that will contain probabilities among other
>> information.  Did you run "Analyzed Peptides"?  Were there any messages
>> reported by the analysis?
>>
>> On Wed, Jan 20, 2021 at 1:30 AM giangiacomo beretta <
>> giangiacom...@gmail.com> wrote:
>>
>>> Hi David! It works nicely, thank you !
>>>
>>> Now I am experiencing another issue of mine :)
>>>
>>> I run ProptideProphet on the XML fiel generated by XTandem. I need this
>>> file presuming that PP will add probabilities to the identified peptides as
>>> this is requested by SpectraST to generate the corresponding spectral
>>> library (this is actually my final goal).
>>>
>>> However, when I try to do it, SpectraST reports: WARNING -- PEPXML
>>> IMPORT: Importing a .pep.xml file with no probabilities. PeptideProphet
>>> probably needs to be run on .pep.xml first.
>>>
>>> Maybe probabilities are used for data processing but not appendend to
>>> the XML output file?
>>>
>>> Thanks a lot in advance!
>>>
>>> G
>>>
>>> Il giorno martedì 19 gennaio 2021 alle 20:53:57 UTC+1 David Shteynberg
>>> ha scritto:
>>>
 Dear Giangiacomo,

 Thanks for trying the TPP and reporting the problem.  TPP uses the
 proteowizard's msconvert tools for this step.  You can remedy the problem
 by either upgrading to a newer version of proteowizard's msconvert tool or
 use  --ignoreUnknownInstrumentError option with your current version.  On
 the generate mzML page you can specify this option in the"Enter
 additional options to pass directly to the command-line" text box, just
 enter the text  --ignoreUnknownInstrumentError

 Hope it works!

 Cheers,
 -David


 On Tue, Jan 19, 2021 at 8:10 AM giangiacomo beretta <
 giangiacom...@gmail.com> wrote:

> Hi, when I try to convert raw files, the conversion tool stops
> immediately reporting the following error:
>
> Reader_Thermo::fillInMetadata] 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
>
> It appears that the system is not recognizing the instrument model
> that produced the raw files. Is there any option to overcome this issue?
>
> Actually I have converted the same files with ProteoWizard without
> troubles.
>
> Thanks in advance!
>
> G
>
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Re: [spctools-discuss] Is there a threshold of min. peptide probability that ProteinProphet uses to pick the peptides?

['Luis Mendoza' via spctools-discuss]

Hello James,

Yes, these values are still hard-coded.  If you wish to test alternative
values, you can edit lines 958-959 and recompile:

https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/src/Validation/ProteinProphet/ProteinProphet.cpp

  MIN_WT = 0.5;
  MIN_PROB = 0.2;


Let us know if you find anything interesting!
Cheers,
--Luis



On Wed, Dec 23, 2020 at 3:04 PM James Go  wrote:

> Hi Luis,
>
> Is this option still hardcoded in the most up to date version of
> ProteinProphet?
>
> On Tuesday, November 22, 2011 at 5:39:54 PM UTC-8 Luis wrote:
>
>> Hello Xiao,
>> You are correct: there is a lower limit in ProteinProphet to disregard
>> peptides below a certain probability and assigned weight.  These values
>> (0.2 and 0.5, respectively) are unfortunately hard-coded in the program and
>> cannot be set by the user; in order to change them you would have to alter
>> the code and recompile the software.
>> Cheers,
>> --Luis
>>
>>
>> On Mon, Nov 21, 2011 at 8:23 AM, Xiao  wrote:
>>
>>> Dear all,
>>>
>>> I have a question about the ProteinProphet. From the link of "More
>>> Analysis Info" in the ProteinProphet results view window, I found the
>>> "min peptide probability" to be 0.2. Is 0.2 the probability threshold
>>> that ProteinProphet uses to select the peptides? If yes, can I set a
>>> different value (if necessary)?
>>>
>>> Thanks,
>>>
>>> Xiao
>>>
>>
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>>>
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Re: [spctools-discuss] Related to St Peter tool in TPP

['Luis Mendoza' via spctools-discuss]

Hello Mehar,
It seems that there was an issue with reading your user session cookie --
perhaps you followed an old link, reinstalled TPP while logged in, or your
browser does not support cookies.
I suggest starting a new browser session and try to run TPP again; let us
know if the issue persists.  Has this happened more than once?
Cheers,
--Luis


On Mon, Dec 14, 2020 at 8:56 AM Mehar Un Nissa 
wrote:

> Hello TPP Team,
> I want to use St. Peter tool in TPP for Label free quantification of some
> dataset.
> Once I go to TPP Tools--> Quantify Label Free (MS2), the web page
> redirected to the login page when I login again some error is coming as
> under:
>
> [image: image.png]
>
> Could you please through some light in this regard.
> Looking forward to hearing from you.
> Thanks and regards,
>
> *Mehar Un Nissa*
> Research Scholar,
> Proteomics Lab.
> Department of Biosciences and Bioengineering,
> Indian Institute of Technology, Bombay-400076
>
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Re: [spctools-discuss] TPP seems never stop in windows......

['Luis Mendoza' via spctools-discuss]

Hello,
This is likely an issue with the webserver not realizing that X!Tandem has
finished running.

Can you see if there are any "tandem.exe" processes running by opening the
Task Manager?
- If you do not see any and if you can see .tandem output files, it means
that the job is done, but the connection to the interface timed out.  You
can (in most cases) safely move on to converting this .tandem file to
pepXML and then continue your analysis.
- If Tandem is still running, then check the parameters (are there too many
variable modifications, for example), or try using a more powerful machine.

Furthermore, to tell the interface to consider the job as finished, click
on the *Jobs *link in Petunia, find the "Running" job and click on "*View*"
under the *Output *column.  Then, in that page click on the following link: If
your commands have actually completed, or the queue did not work, *click
here*.


Another situation in which this may happen is if the computer shuts down or
goes into sleep mode before the job is finished, so make sure that is not
the case.  If so, you will need to re-start the search.

Hope this helps,
--Luis


On Thu, Nov 19, 2020 at 6:32 PM na jiang <16622080...@163.com> wrote:

> Hi,
> I'm new to TPP.Recently, I intend to use TPP and I have tested my data on
> TPP(my operation system is windows.).It seems that TPP  is always  runing
> for 2 days and there's only 1 data.I intend to use Tandem Pipeline. What
> could be the reason why the TPP never stopped running?
>
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Re: [spctools-discuss] Not all the proteins in PeptideProphet appear in ProteinProphet

['Luis Mendoza' via spctools-discuss]

 Hello Soroush,

Great!  Good to verify that it is working as designed.  And you will not
miss those zero probability proteins; they would just add even more time to
the processing and make a larger output file, but with no gain in high
quality results.

Cheers,
--Luis


On Tue, Nov 17, 2020 at 9:32 PM Soroush F  wrote:

> Dear Luis,
>
> Thanks so much for your insight. It is very much appreciated.
>
> I can see that the proteins that are not outputted in the ProteinProphet
> have PeptideProphet probability of <0.05.
>
> All the best,
> Soroush
>
>
>
>
> On Tuesday, November 17, 2020 at 2:42:17 PM UTC-5 Luis wrote:
>
>> Hello Soroush,
>>
>> ProteinProphet has baked-in defaults in the code that will skip over any
>> peptide with (initial) probability < 0.05 (and won't use those below 0.20
>> post-NSP adjustment).  Do any of those peptides that point to the missing
>> proteins violate that rule?
>>
>> This is certainly something that can be changed in the code on your local
>> copy, but it is not recommended.
>>
>> Cheers,
>> --Luis
>>
>>
>>
>> On Mon, Nov 16, 2020 at 6:31 PM Soroush F  wrote:
>>
>>> Dear all,
>>>
>>> I noticed that not all the proteins that exist in my PeptideProphet file
>>> will appear in the ProteinProphet output. Obviously I expect some proteins
>>> to be determined as having very low probability by the ProteinProphet, but
>>> why they don't appear in the ProteinProphet altogether? How can I keep them
>>> in the output of the ProteinProphet?
>>>
>>> Also, I am not setting anything to be excluded in the ProteinProphet
>>> setting (which I run through TPP).
>>>
>>> Many thanks for your help.
>>>
>>> Soroush
>>>
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>>> 
>>> .
>>>
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Re: [spctools-discuss] Not all the proteins in PeptideProphet appear in ProteinProphet

['Luis Mendoza' via spctools-discuss]

Hello Soroush,

ProteinProphet has baked-in defaults in the code that will skip over any
peptide with (initial) probability < 0.05 (and won't use those below 0.20
post-NSP adjustment).  Do any of those peptides that point to the missing
proteins violate that rule?

This is certainly something that can be changed in the code on your local
copy, but it is not recommended.

Cheers,
--Luis



On Mon, Nov 16, 2020 at 6:31 PM Soroush F  wrote:

> Dear all,
>
> I noticed that not all the proteins that exist in my PeptideProphet file
> will appear in the ProteinProphet output. Obviously I expect some proteins
> to be determined as having very low probability by the ProteinProphet, but
> why they don't appear in the ProteinProphet altogether? How can I keep them
> in the output of the ProteinProphet?
>
> Also, I am not setting anything to be excluded in the ProteinProphet
> setting (which I run through TPP).
>
> Many thanks for your help.
>
> Soroush
>
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Re: [spctools-discuss] Re: Initiating Petunia GUI after TPP installation Windows Server 2019

['Luis Mendoza' via spctools-discuss]

Hi Miguel,
Glad that you were able to solve this, and sorry we could not help, as we
do not have access to a WS2019 machine.
Thanks for the update, and hope TPP keeps being useful to your research!
--Luis


On Mon, Nov 9, 2020 at 4:17 PM Miguel Cosenza  wrote:

> Hello,
>
> I managed to solve this. Now I am describing what I did in case someone
> else has the same issue:
>
> Uninstalled the previous installation of TPP.
>
> 1. Installed it again on the default location (C:/TPP) (the first time I
> have installed it on a different location/drive).
> 2. Set the data folder into a different drive.
> 3. Restarted the server.
> 4. Opened 'cmd' as an admin and executed ttptray.
> 5. Then Petunia opened as normal.
>
> I hope this is helpful to someone.
>
> Best wishes,
> Miguel
> El miércoles, 4 de noviembre de 2020 a las 16:12:38 UTC+1, Miguel Cosenza
> escribió:
>
>> Hello all,
>>
>> I just installed TPP on a Windows Server 2019 machine.
>>
>> I defined the default local host for the Apache web server (
>> http://localhost:10401/tpp) but when trying to access it through the web
>> browser I am receiving a
>>
>> "Forbidden" error "You don't have permission to access /tpp on this
>> server.
>>
>> I don't have the same problems with my TPP installation on my Windows 10
>> Desktop machine.
>>
>> I would be very greateful if someone could help me understand what might
>> be happening.
>>
>> Many thanks in advance,
>> Miguel
>>
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Re: [spctools-discuss] Linux Build Error

['Luis Mendoza' via spctools-discuss]

Hi Nathan,

In case you want to build something that closely resembles 5.2.0, you can
follow the steps on this page:
http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS

making sure to use revision 7909.   Alternatively, you can use an older
compiler to build 5.2.0 :
"*The release version of TPP 5.2.0 was discovered to have a minor bug that
prevented a clean compile under the version of GCC in Ubuntu 18.04, so in
this example below we actually pull from revision 7909, which is just after
the 5.2.0 release. Under older versions of GCC, the stock 5.2.0 will
compile fine.*"

HTH,
--Luis



On Fri, Nov 6, 2020 at 1:29 PM 'David Shteynberg' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

> Hi Nathan,
>
> These are some bugs in the TPP externals that have been fixed in the more
> recent versions of the code.   You can either pull the offending files from
> a more recent version of the code, use an up-to-date trunk version of the
> code (and report any bugs you find ;), or wait until we make an official
> release.
>
> Cheers,
> -David
>
> On Fri, Nov 6, 2020 at 12:59 PM Nathan Wamsley 
> wrote:
>
>>
>> I have extracted version 5.2.0 on my computer and am running Ubuntu
>> 20.04.1. I have also followed the instructions on the BUILD_LINUX file that
>> comes with the distribution. I believe I have installed the dependencies.
>> When I navigate into the "release_5-2-0" directory and run "make all," I
>> see the following:
>>
>> (base) nathan@NathanLaptop:~/release_5-2-0$ make all
>> cd
>> /home/nathan/release_5-2-0/build/gnu-x86_64/artifacts/comet_source_2018014;
>> make
>> make[1]: Entering directory
>> '/home/nathan/release_5-2-0/build/gnu-x86_64/artifacts/comet_source_2018014'
>>
>> g++ -O3 -Wall -Wextra -static -Wno-char-subscripts -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -D__LINUX__ -IMSToolkit/include -IComet
>> Search Comet.cpp -c
>> In file included from CometSearch/Common.h:40,
>> from Comet.cpp:18:
>> MSToolkit/include/MSReader.h:96:80: error: invalid conversion from ‘char’
>> to ‘char*’ [-fpermissive]
>>   96 |   void writeFile(const char* c, MSFileFormat ff, MSObject& m,
>> char* sha1Report='\0');
>>  |
>>
>> ^~~~
>>  |
>>
>> |
>>  |
>>
>> char
>> Comet.cpp: In function ‘void LoadParameters(char*,
>> CometInterfaces::ICometSearchManager*)’:
>> Comet.cpp:235:24: warning: passing argument 1 to restrict-qualified
>> parameter aliases with argument 3 [-Wrestrict]
>>  235 |sprintf(szVersion, "%s %s %s", szVersion, szRev1,
>> szRev2);
>>  |^  ~
>> Comet.cpp:1037:9: warning: ignoring return value of ‘char* fgets(char*,
>> int, FILE*)’, declared with attribute warn_unused_result [-Wu
>> nused-result]
>> 1037 |fgets(szParamBuf, SIZE_BUF, fp);
>>  |~^~
>> Comet.cpp:1077:12: warning: ignoring return value of ‘char* fgets(char*,
>> int, FILE*)’, declared with attribute warn_unused_result [-W
>> unused-result]
>> 1077 |   fgets(szParamBuf, SIZE_BUF, fp);
>>  |   ~^~
>> make[1]: *** [Makefile:20: Comet.o] Error 1
>> make[1]: Leaving directory
>> '/home/nathan/release_5-2-0/build/gnu-x86_64/artifacts/comet_source_2018014'
>>
>> make: *** [extern/Makefile:353:
>> /home/nathan/release_5-2-0/build/gnu-x86_64/artifacts/comet_source_2018014/comet]
>> Error 2
>> (base) nathan@NathanLaptop:~/release_5-2-0$ sudo make all
>> cd
>> /home/nathan/release_5-2-0/build/gnu-x86_64/artifacts/comet_source_2018014;
>> make
>> make[1]: Entering directory
>> '/home/nathan/release_5-2-0/build/gnu-x86_64/artifacts/comet_source_2018014'
>>
>> g++ -O3 -Wall -Wextra -static -Wno-char-subscripts -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -D__LINUX__ -IMSToolkit/include -IComet
>> Search Comet.cpp -c
>> In file included from CometSearch/Common.h:40,
>> from Comet.cpp:18:
>> MSToolkit/include/MSReader.h:96:80: error: invalid conversion from ‘char’
>> to ‘char*’ [-fpermissive]
>>   96 |   void writeFile(const char* c, MSFileFormat ff, MSObject& m,
>> char* sha1Report='\0');
>>  |
>>
>> ^~~~
>>  |
>>
>> |
>>  |
>>
>> char
>> Comet.cpp: In function ‘void LoadParameters(char*,
>> CometInterfaces::ICometSearchManager*)’:
>> Comet.cpp:235:24: warning: passing argument 1 to restrict-qualified
>> parameter aliases with argument 3 [-Wrestrict]
>>  235 |sprintf(szVersion, "%s %s %s", szVersion, szRev1,
>> szRev2);
>>  |^  ~
>> Comet.cpp:1037:9: warning: ignoring return value of ‘char* fgets(char*,
>> int, FILE*)’, declared with attribute warn_unused_result [-Wu
>> nused-result]
>> 1037 |fgets(szParamBuf, SIZE_BUF, fp);
>>  |~^~
>> Comet.cpp:1077:12: warning: ignoring return value of ‘char* fgets(char*,
>> int, FILE*)’, declared with attribute warn_unused_result [-W
>> 

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

['Luis Mendoza' via spctools-discuss]

Hello Emily,

This is not a problem that we have seen much of.  Do you know which version
of ProteinProphet / TPP you are using?

One potential issue is the large number of proteins (and peptides) that it
is trying to process -- can you either monitor the memory usage of the
machine when you run this dataset, and/or try on one with more memory?

Hope this helps,
--Luis


On Tue, Oct 6, 2020 at 6:32 PM Emily Kawaler  wrote:

> Hello! I've been running ProteinProphet as part of the Philosopher
> pipeline for a while now with no problems. However, one of my datasets
> seems to be getting stuck in the middle of this function. It doesn't throw
> an error or anything - just stops advancing (the last
> line of the output is "Computing degenerate peptides for 69919 proteins:
> 0%...10%...20%...30%...40%...50%"). Has anyone run into this problem before?
>
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Re: [spctools-discuss] LFQ

['Luis Mendoza' via spctools-discuss]

The other alternative is to run XPRESS in Label-free mode.  For peaks where
it can extract intensities, it will report two results: one for the
integrated area with corresponding scan range, and one for the maximum peak
intensity along with the scan number of that peak.  You can view and export
these values in the PepXMLViewer.  Unfortunately, they cannot be used for
quantitation of proteins within TPP tools.

If you are looking to quantify proteins, we do recommend that you give
StPeter a try.  Its main algorithm is based of fragment ion intensities
from corresponding PSMs, although it can also report a value based on
spectral counting.

Hope this helps.
--Luis

On Fri, Oct 2, 2020 at 12:06 AM vipulb...@gmail.com 
wrote:

> I am a using  TPP v5.2.0 Flammagenitus  to analyze label free data
> generated on a Thermo QExactive machine. I  want to perform LFQ, is there
> anyway to get Intensity values from the TPP. I am not sure about using
> StPeter since it is based on spectral counting. How can I perform LFQ in
> TPP ?
>
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Re: [spctools-discuss] ProtyQuant for comparing TPP samples (.pepXML)

['Luis Mendoza' via spctools-discuss]

This looks great!  Thank you. Robert!

--Luis


On Fri, Sep 25, 2020 at 1:34 PM Robert 
wrote:

> Hi, I just published a software for  post-processing TPP .pepXML files
> (validated by PeptideProphet). The GUI software has the following functions:
>
> - Calculation of protein inference/ probability
> - Quantification; kind of spectral counting, but using peptide
> probabilities
> - Compilation of tables in simple CSV format, for direct comparison of
> protein presence/ quantity in the different samples.
>
> Most functions are implemented in the graphical user interface (Windows
> installer, Python, Docker.) For the experts, the code repository (
> https://bitbucket.org/lababi/protyquant/) also contains some scripts ;-).
>
> "ProtyQuant: Comparing label-free shotgun proteomics datasets using
> accumulated peptide probabilities"
>
> https://doi.org/10.1016/j.jprot.2020.103985
>
> Have fun, Robert
>
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> 
> .
>

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Re: [spctools-discuss] Query related to PTMprophet results in TPP

['Luis Mendoza' via spctools-discuss]

Hello Mehar,

Unfortunately PTMProphet does not calculate the protein position of the
modified amino acids; we may add this to a future version of TPP.

In the meantime, you would need to determine it from mapping the peptide
sequence onto its corresponding protein, with the caveat that the peptide
sequence may map to more than one protein (or in rare cases more than once
to the same protein) and thus have different positions.

Cheers,
--Luis



On Fri, Aug 7, 2020 at 12:38 AM Mehar Un Nissa 
wrote:

> Dear Sir/Madam,
>
>
> I have a query related to PTMprophet analysis.
>
>
> I performed comet search for an mzml file and put it for further analysis
> as under:
>
>
>
> -Using TPP tools Analyse peptides Checked for iprophet proteinprophet
> PTMprophet
>
>
> -Mass added for PTMs were:
>
>
> - 79.966 Da for Phosphorylation- STY
>
>
>
> I filtered the data on the basis of error table values.
>
>
> - I exported the excel showing results as under.
>
>
> [image: image.png]
>
>
>   *Query: Everything is fine except that the position of modified amino
> acid is not there, only the mass is there and amino acid is highlighted. *
>
>
>
> *How can I get to know the modified site (I mean exact position of
> modified amino acid?*
>
>
> *Is there a way that I can get these modified sites with respect to
> protein. e.g. S27 or T82 etc. *
>
>
>
> Could you please help me for this.
>
>
> Thanks and regards,
>
> *Mehar Un Nissa*
> Research Scholar,
> Proteomics Lab.
> Department of Biosciences and Bioengineering,
> Indian Institute of Technology, Bombay-400076
>
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> 
> .
>

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Re: [spctools-discuss] Percolator Error in TPP

['Luis Mendoza' via spctools-discuss]

Hi Gabby,

So since Percolator is not actually running, it just means that the
interface is confused.  On that page where you see the command list, click
on "View" (instead of "Kill Job"), and at the bottom of the page that comes
up you will find a small link (at the end of "If your commands have
actually completed but the server timed out, click here") that will allow
you to explicitly tell the interface to consider this job "finished".

Cheers,
--Luis


On Tue, Jun 9, 2020 at 6:47 AM Gabrielle H  wrote:

> Hello Luis,
>
> Percolator is no longer running in Task Manager, so it definitely timed
> out. I tried to "kill job" in the command page and I keep getting the same
> error. Is there a way around this? Thank you for the help.
>
> - Gabby
>
> On Monday, June 8, 2020 at 6:36:45 PM UTC-4, Luis wrote:
>>
>> Hello,
>>
>> Is this running on your local machine?  If so, you can see if Percolator
>> is still running by either opening the Task Manager (if on Windows) or
>> executing the "ps" command (in Linux).
>>
>> Most likely, the command might have timed out due a very long running
>> time, and the interface (Petunia) is not aware of this.  On the command
>> output page, you can find a button that overrides the status and marks it
>> as "finished".
>>
>> Hope this helps,
>> --Luis
>>
>>
>>
>> On Mon, Jun 8, 2020 at 3:22 PM Gabrielle H  wrote:
>>
>>> Hello,
>>>
>>> I exported a Comet search as a txt file to search with percolator and
>>> the percolator has now been "running" for three days. When I try to kill
>>> the job, it gives me "Unable to kill command 8760! ()." I'm guessing
>>> it's stuck in a loop, but I was wondering what the best way of ending
>>> job/fixing the program would be. Thank you for your help.
>>>
>>> --
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>>> Groups "spctools-discuss" group.
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>>> an email to spctools...@googlegroups.com.
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>>> 
>>> .
>>>
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Re: [spctools-discuss] Percolator Error in TPP

['Luis Mendoza' via spctools-discuss]

Hello,

Is this running on your local machine?  If so, you can see if Percolator is
still running by either opening the Task Manager (if on Windows) or
executing the "ps" command (in Linux).

Most likely, the command might have timed out due a very long running time,
and the interface (Petunia) is not aware of this.  On the command output
page, you can find a button that overrides the status and marks it as
"finished".

Hope this helps,
--Luis



On Mon, Jun 8, 2020 at 3:22 PM Gabrielle H  wrote:

> Hello,
>
> I exported a Comet search as a txt file to search with percolator and the
> percolator has now been "running" for three days. When I try to kill the
> job, it gives me "Unable to kill command 8760! ()." I'm guessing it's
> stuck in a loop, but I was wondering what the best way of ending job/fixing
> the program would be. Thank you for your help.
>
> --
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> 
> .
>

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Re: [spctools-discuss] Kojak File not Found

['Luis Mendoza' via spctools-discuss]

Hi Lindsey,

It seems that Kojak did not finish successfully, and it may be the reason
why there is no output file.  If you scroll down in the command-line output
sub-window (the one in your screenshot, just scroll down more), you should
be able to see diagnostic messages that may be helpful in troubleshooting
the issue.

Cheers,
--Luis


On Fri, Mar 27, 2020 at 2:27 PM Lindsey Ulmer 
wrote:

> Hi,
>
> I've run Kojak with the same settings on other data files with no problem,
> but for some reason with this particular data file I keep getting the error
> that the pep.xml file cannot be found and am not sure why this one file
> would be different.
>
> Thanks!
> Lindsey
>
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> 
> .
>

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Re: [spctools-discuss] TPP 5.2 in Ubuntu 18.04 not showing plots/images in PepProphet nor ProtProphet models

['Luis Mendoza' via spctools-discuss]

Hello Alejandro,

Can you share the html source?  The most likely culprit is that it has the
wrong location of the javascript files.

It may also be the case that if you re-installed TPP after you generated
the models files, they may need to be updated.  The simplest way to do this
is to delete the html models file (only!) and re-open the pepXML file in
PepXMLViewer to trigger the generation of the models file.

Hope this helps,
--Luis


On Sun, Mar 8, 2020 at 5:58 PM Alejandro  wrote:

> Dear all,
>
> I'm running TPP 5.2 both build 202003062318-8034 as well as have tried the
> release 5.2 in Ubuntu 18.04, installed using the recommended instructions.
> Everything that I have tested seems to work except the generation of the
> plots of the models in both PeptideProphet and ProteinProphet results. I
> can see the Sens/Error tables but in the model charts in the place were the
> graph should go there is just white. I have checked the source of the html
> and it seems to have the info. I don't know how to troubleshoot this and/or
> if it is a common thing. Hope you can give me some advice, as the visual
> interpretation of the graph is quite useful as a first look in the analysis.
>
>
>
> [image: screen.png]
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Best,
>
> Alejandro
>
>
>
>
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> 
> .
>

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Re: [spctools-discuss] Re: Query related to Lorikeet viewer PTMprophet results in TPP

['Luis Mendoza' via spctools-discuss]

Hello,

It seems that Lorikeet is unable to find the mzML file to extract and
display the spectrum.  Did you move the files after you conducted the
analysis?

If you look at the bottom of your screenshot, you can see that the file
must be located under "/proteomics/jpanga/."  Can you confirm that the
file is in that location on your file server?

Cheers,
--Luis


On Thu, Mar 5, 2020 at 7:40 AM Mehar Un Nissa 
wrote:

> Dear Sir/Madam,
> Please reply to my query in the above mail.
> Thanks and regards,
>
> *Mehar Un Nissa*
> Research Scholar,
> Proteomics Lab.
> Department of Biosciences and Bioengineering,
> Indian Institute of Technology, Bombay-400076
>
>
> On Wed, Mar 4, 2020 at 11:38 AM Mehar Un Nissa <
> meharunnissako...@gmail.com> wrote:
>
>> Hello Sir/Madam,
>> We used TPP and PTMprophet for PTM analysis.
>> PTM  taken (Phosphorylation- STY).
>> *I want to see the spectra in Lorikeet viewer but it is showing following
>> error.*
>> [image: image.png]
>>
>> Please help me solve this.
>> Looking forward to hearing from you.
>>
>> Thanks and regards,
>>
>> *Mehar Un Nissa*
>> Research Scholar,
>> Proteomics Lab.
>> Department of Biosciences and Bioengineering,
>> Indian Institute of Technology, Bombay-400076
>>
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> 
> .
>

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Re: [spctools-discuss] Failed, error code 256 when I want to run LIBRA with TPP

['Luis Mendoza' via spctools-discuss]

Hello Cindy,

Please note that raw to mzML conversion via the msconvert program only
works on Windows systems.  Once the file is in the mzML format, you can
carry on with analysis on Linux.

Cheers,
--Luis


On Thu, Feb 20, 2020 at 4:48 AM Cindy Dieryckx 
wrote:

> Hello,
>
> Thanks a lot but now, I obtained this error:
>
>
> Cindy
>
>
>

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