Hi, it sounds like you question is related to DNA sequencing, not
proteomics. The TPP tools are designed for mass spectrometry proteomics,
not for DNA/RNA sequencing. Let me know if I’ve misunderstood.
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Tuan Anh Nguyen Van
*Sent:*
Hi Debojyoti, we will see if we see if we can add that feature to Libra,
but you’re probably best off exporting the data from Libra to MSstatsTMT,
which you cite below, itself. It has many nice features in addition to
normalization, and so a good workflow would be to compute the raw TMT
values
Hi Will, thanks for the question. There no easy answer. An SSD is good
because there’s a lot of disk I/O processing data. Comet itself is pretty
thrifty with memory, so you won’t need lots of memory for Comet. The
Prophets can use a lot of memory if you process huge experiments at once,
although
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
Hi Felipe, we just updated our servers to https with SSL since that seems
to be the standard now, and I think this is problem related to that.
Would you try to see if this URL works:
https://tppms.systemsbiology.net/tools/ptm/Ferries2017.zip
thanks,
Eric
*From:*
uld be a great help
> if you could share the text file of the parameter.
> Thank you
> Priti
> PhD Scholar
> Animal Biotechnology Centre, NDRI
> Karnal
>
>
> On Wed, Feb 22, 2023 at 10:05 AM 'Eric Deutsch' via spctools-discuss <
> spctools-discuss@googlegroups.com>
MSFragger itself can generate one for you, just run something like:
/usr/bin/java -jar msfragger-3.2.one-jar.jar --config closed
mv closed_fragger.params msfragger.params
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Priti Panchal
*Sent:* Tuesday, February 21, 2023 8:32 PM
Upgrading to TPP 6.1.0 is definitely recommended, however, as there are
many additional benefits to upgrading than just more TMT channels:
http://tools.proteomecenter.org/wiki/index.php?title=TPP:6.1.0_Release_Notes
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Aarthie
y
I appreciate your prompt help with this,
-Will
On Thursday, September 8, 2022 at 2:32:17 PM UTC-4 Eric Deutsch wrote:
Hi Will, I think the answer is yes, although I’d need to test on a fresh
computer for the exact protocol. I think you can launch the TPP Tray app
and then use
Hi Will, I think the answer is yes, although I’d need to test on a fresh
computer for the exact protocol. I think you can launch the TPP Tray app
and then use that to start Apache and then you’re good to go. Is this for
Windows computers?
Eric
*From:* spctools-discuss@googlegroups.com
*On
Centre
National Dairy Research Institute, Karnal
On Tue, 26 Jul 2022, 11:01 am 'Eric Deutsch' via spctools-discuss, <
spctools-discuss@googlegroups.com> wrote:
Correct, if you did not use iodoacetamide, then change it to 0.0
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Anju
not include any alkylation step?
Do I need to change it to 0?
On Mon, Jul 25, 2022 at 8:26 PM 'Eric Deutsch' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:
Since Cys is almost always alkylated with iodoacetamide in most experiments:
http://www.unim
Since Cys is almost always alkylated with iodoacetamide in most experiments:
http://www.unimod.org/modifications_view.php?editid1=4
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Anju Nagpal
*Sent:* Monday, July 25, 2022 1:59 AM
*To:* spctools-discuss
*Subject:*
Hi Malcolm, thank you for the corrections, the page is now updated. Let me
know if you find any other problems.
http://tools.proteomecenter.org/wiki/index.php?title=TPP_6.1.0:_Installing_on_Ubuntu_20.04_LTS
Thanks!
Eric
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Malcolm
Hi, the problem is that the version of msconvert that you are using does
not know how to recognize your model of the Eclipse instrument. You could
specify the ignoreUnknownInstrumentError flag to ignore that problem. A
better solution is to download the latest ProteoWizard toolkit and use that
Hi, the problem is that the version of msconvert that you are using does
not know how to recognize your model of the Eclipse instrument. You could
specify the ignoreUnknownInstrumentError flag to ignore that problem. A
better solution is to download the latest ProteoWizard toolkit and use that
Hi Philip, while I am not completely certain, I don’t think SpectraST has
any options for multi-threaded execution in the library import/conversion
steps. I recall Henry saying in the past that these operations tend to be
I/O bound mostly so multi-threading wouldn’t help very much? Maybe that was
I’m thinking that a very large mzXML file with “UDMSE” in it might be DIA
data, and thus Comet is not the right tool? Could this be MS^e data instead
of DDA data?
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Jason Winget
*Sent:* Friday, September 17, 2021 10:02 AM
*To:*
I have not yet created a container for 6 but I should. I could try to do
that soon if there is demand to use it/test it.
Thanks,
Eric
*From:* 'Alastair Skeffington' via spctools-discuss <
spctools-discuss@googlegroups.com>
*Sent:* Monday, June 21, 2021 8:59 AM
*To:* spctools-discuss
:* Eric Deutsch
*Sent:* Monday, May 10, 2021 2:42 PM
*To:* spctools-discuss@googlegroups.com
*Cc:* Eric Deutsch
*Subject:* RE: [spctools-discuss] Re: Exporting StPeter´s ng to mzid
Hi Valdemir, the tpp2mzid is indeed the preferred and recommended tool, not
idconvert.
I think the problem
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
You can convert the sptxt format to msp with:
rename mylibrary.sptxt mylibrary.msp
sptxt and msp are effectively the same thing. There is no specification on
exactly what msp is and it has evolved a little over time, and sptxt is
essentially the same as one of the variations.
Eric
Hi Sud, I think you can just use this parameter with Comet:
search_enzyme_number = 0 # choose from list at end of this
params file
where 0 is defined at the bottom of the comet.params:
[COMET_ENZYME_INFO]
0. Cut_everywhere 0 - -
1. Trypsin
. Regards.
On Thu, Oct 22, 2020 at 3:46 AM 'Eric Deutsch' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:
Hi Aziz, there is no specific maximum size. In general, the larger your
database, the greater the memory requirements and CPU time needed for the
software tools and the
Hi Aziz, there is no specific maximum size. In general, the larger your
database, the greater the memory requirements and CPU time needed for the
software tools and the lower your sensitivity, although it depends on the
degree of redundancy in your database. Hundreds of MB and hundreds of
Hi Juergen, this sounds like a sensible idea, but as far as I’m aware, this
functionality does not yet exist.
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Juergen Bartel
*Sent:* Monday, October 19, 2020 3:50 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] SpectraST
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:
g.*
Any help?
Thanks
On Wednesday, July 8, 2020 at 2:19:24 AM UTC-4 Eric Deutsch wrote:
I’ve never tried to import into PD, so I can’t help there. Presumably the
ADD DECOY doesn’t change things like M[147], so I also do not understand
why PD would recognize M[147] in a library wi
at 1:29:08 PM UTC-4 Eric Deutsch wrote:
Yes, M[147] is the TPP notation for oxidized methionine. The total mass of
oxidized methionine rounds to 147 Da.
*From:* spctools...@googlegroups.com *On
Behalf Of *RS
*Sent:* Tuesday, July 7, 2020 9:38 AM
*To:* spctools-discuss
*Subject:* [spctools
Yes, M[147] is the TPP notation for oxidized methionine. The total mass of
oxidized methionine rounds to 147 Da.
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *RS
*Sent:* Tuesday, July 7, 2020 9:38 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Re: SpectraST: Missing
Hi Srikanth, I suggest after your step “I have convert the results
individually to pepxml using Mascot2XML, Tandem2XML and Idconvert and then
apply peptideprophet on each file” (which is good), the next step is merge
the 3 PeptideProphet outputs into a single PepXML file with iProphet. Then
build
Sounds like an XY Problem here.
If it’s spectral clustering you want to do, and within the TPP, perhaps
consider SpectraST:
http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#Spectral_Archive_.28Unidentified_Spectral_Library.29_Building
You won’t need to fool around
to the mzIdentML format
- Spectrum-centric DIA analysis and quantitation with DISCO
- Kojak PeptideProphet support and de Bruijn decoys
- Using the Universal Spectrum Identifier in TPP
We hope to see to there!
Mike Hoopmann
David Shteynberg
Eric Deutsch
--
You received this message
Hi Ray, I suspect that SpectraST will recognize this notation:
n[42]MFLVNSFLK
N terminal modifications are shown after an n. Side-chain modifications are
shown after the residue.
Eric
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *RayS
*Sent:* Saturday, April 25, 2020 3:01
Hi Srikanth, I can confirm that SpectraST supports mzML files. In fact we
always/only use mzML files.
As far as the iRT error, I am not familiar with this. I could only
speculate. Maybe Henry or David have ideas?
Thanks,
Eric
*From:* spctools-discuss@googlegroups.com
*On Behalf Of
ORCiD: -0001-8732-0928
Office: +1-206-732-1397
Fax: +1-206-732-1260
WWW: https://www.systemsbiology.org/eric-deutsch
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You received this message because you are subscribed to the Google Groups
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To unsubscribe from this group and stop receiving emails fro
Thanks for the clarification, Jimmy!
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Jimmy Eng
*Sent:* Friday, December 13, 2019 8:27 AM
*To:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Interpretation of stats from pepXML viewer
Regarding inputs and output
Hi Alistair, thanks for posting your questions. Although it’s possible
something problematic is happening, I think the answers to your questions
are:
1) Most search engines including Comet have a minimum spectrum quality
threshold to even search the spectrum, e.g. minimum of 10 peaks. There are
http://www.perl.org/, the Perl Home Page.
cd bin
./test_tpi.pl
Now shows me that all the libraries have been installed!
Looks like I might have had an error typing the PERL5LIB pathway. Thanks a
lot!
-Shagun
On Tuesday, December 3, 2019 at 2:27:07 PM UTC-5, Eric Deutsch wrote:
Okay, w
didn't change anything and didn't have any issues with make
install!
On Monday, December 2, 2019 at 10:51:54 PM UTC-5, Eric Deutsch wrote:
So then you did:
cd /home/tpp/bin
export PERL5LIB=/home/tpp/lib/perl
./test_tpi.pl
?
*From:* spctools...@googlegroups.com <
spcto
7
Hi Eric
I did do make install step. TPP was installed in /home/tpp and I changed
all the directory specs accordingly!
On Friday, November 22, 2019 at 3:25:50 PM UTC-5, Eric Deutsch wrote:
Hi Shagan, did you perform the `make install` step? Was TPP actually
installed in /usr/local/tpp
Hi Shagan, did you perform the `make install` step? Was TPP actually
installed in /usr/local/tpp? Or was it installed somewhere else?
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Shagun Gupta
*Sent:* Friday, November 22, 2019 11:33 AM
*To:* spctools-discuss
*Subject:*
Thanks for reporting, Oliver. We have not seen this issue ourselves.
Regards,
Eric
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *oliveralka
*Sent:* Tuesday, November 5, 2019 1:34 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] Re: Question: mzML parsing issue
stina
Am Montag, 23. September 2019 17:48:10 UTC+2 schrieb Eric Deutsch:
Hi Kristina, I am not so sure about answers to your questions. It would be
ideal to use SpectraST 5.0 in all your processing if you can easily do
this, yes, but in some cases it would not matter much. In general,
Hi Nikita, perhaps someone has some better answers than I do, but here is
what I can say based on your description.
Regarding the cutoff, I wonder if in your combined analysis you are using a
peptide-level FDR of 1%, whereas in the single analyses you are using an
PSM-level FDR of 1%? A
s of older software versions imported with a newer one?
Thank you and kind regards,
Kristina
Am Freitag, 20. September 2019 20:49:28 UTC+2 schrieb Eric Deutsch:
Hi Kristina, I’m not certain I fully understand your issue, but maybe I can
answer some questions:
Partial old:
Name: DIETIIQK/2 *
Hi Kristina, I’m not certain I fully understand your issue, but maybe I can
answer some questions:
Partial old:
Name: DIETIIQK/2 *(old entry, original library)*
308.1581 226.5 ?
309.0826 359.4 ?
325.6734 1596.8b6-35^2/0.000,b6-36^2/0.492
329.1945 141.2 a6^2/0.000
Hi Virginie, thank you for your interest in TPP.
That command assumes that the user account that you will be installing tpp
as is called “tpp” with group “tpp”.
You could either create a Linux user “tpp” and a group “tpp” first, or you
could replace that with the current user and group that
Eric
--
Eric W. Deutsch
Senior Research Scientist
Institute for Systems Biology
401 Terry Ave North
Seattle WA 98109
Email: edeut...@systemsbiology.org
ORCiD: -0001-8732-0928
Office: +1-206-732-1397
Fax: +1-206-732-1260
WWW: https://www.systemsbiology.org/eric-deutsch
--
You re
Hi Alejandro, which checkout did you do? Was it this?
svn checkout -r 7909
http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline
Or a little different?
Thanks,
Eric
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Alejandro
*Sent:* Friday, May 17, 2019 2:57
I think the SeeMS tool from ProteoWizard may be your best bet. If you have
TPP installed, it may already be installed with TPP. Or otherwise, it is
easy to download and install. Install all of ProteoWizard, and then from
the Start menu under the ProteoWizard folder will be SeeMS.
Regards,
Eric
Hi Jason, I have no solution yet, but I have one more data point. It seemed
to work well when I used all the default TPPGUI settings. But then in
another run when I fiddled with several of the settings, I had a similar
result as you describe. So I think there is a bug in one of the settings
that
Hi Ankit, both strategies would likely work okay. I would prefer first
combining all your data with iProphet and then creating the library with
SpectraST. An issue to consider: if you combine several libraries that have
been processed or thresholded individually, the final FDR will be higher
for
Hi Jeff, thanks for sharing these tips on the list!
Regards,
Eric
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *jeffreyavansan...@gmail.com
*Sent:* Monday, February 4, 2019 4:15 PM
*To:* spctools-discuss
*Subject:* [spctools-discuss] mzXML - peak encoding/decoding
Hello
Hi Ankit, I suppose the first question to ask is: how many iRT peptides are
in your iRT.txt file and how many of those have a corresponding entry in
the library?
Regards,
Eric
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Ankit Balhara
*Sent:* Tuesday, January 29, 2019 1:22 AM
t; 23 minutes ago Up 23
minutes 0.0.0.0:10401->10401/tcp quizzical_bhabha
# docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
docker.io/spctools/tpp latest 73727a87cff0 8 days ago 2.86 GB
Best, Robert
On Dec 3 2018, at 6:29 pm, Eric Deutsch wrote:
Hi Robert, when you get an error
Hi George, I haven’t had a chance to test this more thoroughly yet, but I
wonder if it might be Shared Drives setting in Docker, like this?
[image: image]
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *guoguodigi...@msn.com
*Sent:* Monday, December 3, 2018 2:26 PM
*To:*
CREATED STATUS PORTS NAMES
799753202ce1ebf55696681a"apache2ctl -DFORE..." 11 hours
agoUp 11 hours 0.0.0.0:10401->10401/tcp dazzling_mahavira
Am Donnerstag, 29. November 2018 01:32:55 UTC+1 schrieb
+1 schrieb Eric Deutsch:
Hi Robert, great, thanks for the testing! Can you elaborate a little on
what the symptoms are here for the file access through the GUI? I think the
file access worked fine in my testing. Maybe one potential fix is setting
some more permissive privileges in the directory
Hi Robert, no this was unintentional. But it is now fixed. Try another pull
and see if that works better. We changed things a little based on feedback.
See the updated tutorial for changes in calling sequence:
http://tools.proteomecenter.org/wiki/index.php?title=Running_the_TPP_docker_image
Hi Robert, good idea, thanks! We have added vim and nano to the image.
docker pull spctools/tpp
Regards,
Eric
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Robert
*Sent:* Wednesday, November 21, 2018 12:09 AM
*To:* spctools-discuss
*Subject:* [spctools-discuss] simple
Hi Robert, great, thanks for the testing! Can you elaborate a little on
what the symptoms are here for the file access through the GUI? I think the
file access worked fine in my testing. Maybe one potential fix is setting
some more permissive privileges in the directory you’re mapping into the
The parameter for X!Tandem is “spectrum, threads”. Set that to 8 or
whatever is appropriate for your machine.
The parameter for Comet is “num_threads”. The default is 0, which is to
detect how many CPUs you have and use them all. Or you can set it to a
number you like.
I don’t know the state
Hi Robert, I think this warning comes when the FASTA database has
unexpected characters in it. Is there anything unusual about the FASTA
database you’re using? Unusual spaces or something?
Regards,
Eric
*From:* spctools-discuss@googlegroups.com
*On Behalf Of *Robert
*Sent:* Tuesday,
you suggest any better to handle it?
-Kamal
On Mon, Nov 19, 2018 at 9:45 AM Eric Deutsch
wrote:
Hi Kamal, you could try downloading and trying to run these binaries
compiled under CentOS 7.5:
cd ~
wget http://www.tppms.org/sw/TPP5.2RC4/tppUsrLocalTpp-CentOS7.5.tgz
tar -zxf tppUsrLocalTpp
9:27 AM
*To:* Eric Deutsch
*Cc:* spctools-discuss@googlegroups.com
*Subject:* Re: [spctools-discuss] Linux version of TPP
Hi Eric,
I heard the following reply from our system administrator. Can you please
go through it and suggest me some alternative.
"I would recommend not insta
install glibc-static
You probably need all of the packages I listed in the previous message
downthread. Can you check to see if those were installed?
Thanks,
Eric
*From:* Kamal Mandal
*Sent:* Saturday, November 17, 2018 11:31 PM
*To:* Eric Deutsch
*Cc:* spctools-discuss@googlegroups.com
-Kamal
On Thu, Nov 15, 2018 at 9:07 PM Eric Deutsch
wrote:
Hi Kamal, I’m not certain what would be best, but suppose you just install
the TPP in your own area under your username. So, based on the instructions
here:
http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing
Hi Kamal, I’m not certain what would be best, but suppose you just install
the TPP in your own area under your username. So, based on the instructions
here:
http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS
You could install TPP in a space off your
*On Behalf Of *Darryl Davis
*Sent:* Tuesday, October 23, 2018 3:30 AM
*To:* spctools-discuss
*Subject:* Re: [spctools-discuss] Running TPP/Petunia GUI with Docker
Hi Eric,
I also would very much like to sign up as a tester.
Thanks,
DD
On Monday, October 22, 2018 at 1:23:00 PM UTC-4, Eric Deutsch
Hi Robert, we just put up a new Docker image for beta testing, see these
notes:
http://tools.proteomecenter.org/wiki/index.php?title=Running_the_TPP_docker_image
Have a look at that, and try running what you’re trying to do in the latest
image and see if that works better. If not, would you
Hi Robert, there is a TPP Docker container available via BioContainers:
https://hub.docker.com/r/biocontainers/tpp/
However, I’m pretty sure that this does not contain the GUI layer, it is
just the tools. (correct me if I’m wrong!)
However, with the imminent release of TPP 5.2.0, we are
Email: edeut...@systemsbiology.org
ORCiD: -0001-8732-0928
Office: +1-206-732-1397
Fax: +1-206-732-1260
WWW: https://www.systemsbiology.org/eric-deutsch
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Oops, sorry, that should have been Sep 24-28. Information and registration
page is not up yet, but will be soon. We will announce here when it is open.
Thanks,
Eric
*From:* Eric Deutsch
*Sent:* Wednesday, June 6, 2018 7:11 AM
*To:* spctools-discuss@googlegroups.com
*Cc:* Eric Deutsch
The next course will be September 28-48 in Orlando, Florida. This is the
week before the World HUPO Congress (https://www.hupo2018.org/), also in
Orlando. So, if you will be attending HUPO this fall, it might be an ideal
opportunity to arrive early in Orlando and attend the course.
Regards,
Hi Sami, there are two kinds of SpectraST libraries, raw libraries and
consensus libraries. Raw libraries may have many replicates and that’s
fine. Consensus libraries will not have replicates. Replicates are
converted into a consensus by SpectraST when suitable flags are set. Note
that the same
file in that directory does not make the binaries. Do you know where I
could find them?
Thanks
On Tuesday, February 13, 2018 at 3:02:42 PM UTC-8, Eric Deutsch wrote:
Hi, we haven’t tried to install it on Ubuntu 17, only the 16.04 LTS, with
the recipe you found. So I can’t really help mu
Hi, we haven’t tried to install it on Ubuntu 17, only the 16.04 LTS, with
the recipe you found. So I can’t really help much at this point. I googled
a little and found this:
https://stackoverflow.com/questions/3096989/libtool-version-mismatch-error
Does this help maybe? If you do figure it
Those should be functionally equivalent, I think, so that is puzzling. Did
you completely clean the build area between these two runs, or was it
already partly built when you ran the second? As noted in the instructions,
there seems to be some intermittent issue with building where sometimes it
ted with proteowizard.
Thanks for looking into this
Hannes
On Fri, Oct 20, 2017 at 6:57 PM, Eric Deutsch
> I ran SpectraST on your file with –V and it seems to show that it is not
> reading the precursor mz from you file somehow. All the precursormzs in
the
> verbose output are
.
Thanks again.
Regards,
Ellen.
2017年10月25日 下午11:56，"Eric Deutsch" <edeut...@systemsbiology.org>写道：
Hi Elkan, every converter will do things a little differently. It’s hard to
say which is better. I think we did some tests a while back and the SCIEX
conversion of 5600 DDA data
Hi Elkan, every converter will do things a little differently. It’s hard to
say which is better. I think we did some tests a while back and the SCIEX
conversion of 5600 DDA data yielded slightly more IDs than with msconvert
converter, but they were pretty similar. For most datasets, it should not
still work?
3. These are "MaxQuant compatible CR". I have removed those but without any
change in result. Unfortunately.
Hannes
On Friday, October 20, 2017 at 5:57:45 PM UTC-4, Eric Deutsch wrote:
Hi Hannes, I had a quick peek at your file and while I didn’t do any
testing a few th
Greater than symbol should be first on the line. Instead of:
sp>|Q13547|HDAC1_HUMAN
must be:
>sp|Q13547|HDAC1_HUMAN
Eric
*From:* spctools-discuss@googlegroups.com [mailto:
spctools-discuss@googlegroups.com] *On Behalf Of *Adam R
*Sent:* Thursday, September 28, 2017 8:41 PM
*To:*
Hi everyone, I would like to let you know about various TPP course related
events:
There is still room to register attend the TPP course here at ISB July
19-21. This was originally designed as an advanced course, but we have
altered it to be more of an introductory course due to various
Hi Jianqiao, although I am not 100% certain, I do not recall any SpectraST
feature where it will try to match a spectrum to a library entry outside
the normal tolerance window, but corrected for an alternate charge state.
This is an interesting idea for a feature, I hadn’t thought about this
Hi Jamie, thanks for letting us know about the problem. It was a different
problem than before. It is back up now.
Although we do plan to upgrade the Wiki software, so it will have to go
down again for maintenance sometime soon, but not scheduled yet.
*From:*
Hi, our MySQL back-end to the wiki was acting up yesterday at the time your
email was sent (although your email just landed in my inbox now). This was
fixed yesterday and should all be fine now. You might find this page of
guides useful:
wser give
me another confussion,if a signal modification is enough, how should the
libra program to differentiate the proteins for quantification later.
在 2017年4月7日星期五 UTC+8上午10:53:51，Eric Deutsch写道：
Hi, I don’t think that will get you anything useful, although you could try
it to see if you
Hi, I don’t think that will get you anything useful, although you could try
it to see if you get anything that way. All you want is a single
modification on n-term and K as in the other thread.
I’m guessing what happens is that the reporter ions like to hold the charge
and most peptides will
It might be no problem. The installation instructions say:
If it compiles and you get an error about being unable to find HomePath
then you're fine. However, if you get an error not being able to find a
module, then go back to cpan and install it.
*From:*
There’s no trivial solution, I think. But here are some non-trivial
possibilities:
1) Search the whole dataset with variable heavy label
2) Create a spectral library with the heavy labeled peptides and merge that
library with a normal human library and search with SpectraST
3) Replace all the
:* Eric Deutsch <edeut...@systemsbiology.org>
*Subject:* Re: [spctools-discuss] Re: tandem.exe command line parameters
(other than the input.xml file)
Hi Eric,
Thanks for the reply. Actually, the OpenMS wrapper seems to let me change
the parameters at it's command line...so I think we'r
Hi Mike, nothing has changed, this is still the current state. We are not
the authors of this tool, we just bundle it and use it. I think it is
unlikely that the original author would change this, and I don’t think we
will ever change it.
*From:* spctools-discuss@googlegroups.com [mailto:
, January 24, 2017 10:42 AM
*To:* Eric Deutsch
*Subject:* Re: [spctools-discuss] Error while conversion of files
One more thing, the .mzML file after the conversion from .Wiff was of
nearly 18 GB.
On Wed, Jan 25, 2017 at 12:01 AM, Joel Christie <joel.jo.chris...@gmail.com>
wrote:
Hi,
Comet search is not over. I don't know whether it should take this
much of time?
On Saturday, 21 January 2017 00:25:08 UTC+5:30, Eric Deutsch wrote:
Hi Joel, the problem is a space in your folder names. Some tools are
confused by this. If you rename “Joel Data” to “JoelData” (without the
space
Hi Joel, the problem is a space in your folder names. Some tools are
confused by this. If you rename “Joel Data” to “JoelData” (without the
space) and remove any other spaces in file name and folder names, things
should work a lot better.
Regards,
Eric
*From:*
I cannot recall any other report like this and have never experienced
anything like this myself that I can recall. Can you describe in more
detail exactly what the origin and version of this executable is?
Is it true that other executables like Comet or X!Tandem do not suffer from
this huge
Hi, although SpectraST has a few multi-threaded features, I don’t think the
msp conversion is multithreaded, so that is just one thread only. This
conversion is actually not very CPU intensive at all, but rather I/O bound,
i.e. the speed of your disks probably matters most. I’m guessing that on
ions. I thought that I might be able to
increase identification by accepting hits with lower thresholds. I do
understand what you mentioned here.
Thanks again,
Ali
On Tuesday, January 3, 2017 at 1:57:38 PM UTC-5, Eric Deutsch wrote:
In the ideal case where the PeptideProphet and iProp
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