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Aarthie Senathirajah
Mar 23
How does RT train work?
Hi I was wondering if there was a tutorial on how to use RT Train? I'm not sure what kind of
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How does RT train work?
Hi I was wondering if there was a tutorial on how to use RT Train? I'm not sure what kind of
Mar 23
Priti Panchal
,
Eric Deutsch
4
Feb 22
MSFragger param
ah, I see, okay, sure, I put one here: http://www.tppms.org/tmp/msfragger.params On Tue, Feb 21, 2023
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MSFragger param
ah, I see, okay, sure, I put one here: http://www.tppms.org/tmp/msfragger.params On Tue, Feb 21, 2023
Feb 22
Luis Mendoza
Feb 17
TPP 6.2.0 Release is now available
Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.2.0 "Nacreous" We are
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TPP 6.2.0 Release is now available
Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.2.0 "Nacreous" We are
Feb 17
Aarthie Senathirajah
,
Luis Mendoza
2
Feb 14
Analyzing Metaproteomic Data
Hello, The version of msconvert that is shipped with TPP is a couple of years old and does not know
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Analyzing Metaproteomic Data
Hello, The version of msconvert that is shipped with TPP is a couple of years old and does not know
Feb 14
reeju
Jan 27
not getting significant hits while analyzing .raw file
Hi all, I have been trying to analyze .raw file generated on waters synapt of standard protein BSA
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not getting significant hits while analyzing .raw file
Hi all, I have been trying to analyze .raw file generated on waters synapt of standard protein BSA
Jan 27
cabarnes...@gmail.com
, …
David Shteynberg
4
11/30/22
protein prophet failing on Eclipse searches
Hi all. Thanks for resolving this error. To everyone else, this was user error on my part. On Tuesday
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protein prophet failing on Eclipse searches
Hi all. Thanks for resolving this error. To everyone else, this was user error on my part. On Tuesday
11/30/22
Debojyoti Pal
11/27/22
Libra results for individual peptides in ProteinProphet results page
Hello everyone I would like to suggest a feature that I feel would be immensely helpful. I am running
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Libra results for individual peptides in ProteinProphet results page
Hello everyone I would like to suggest a feature that I feel would be immensely helpful. I am running
11/27/22
2kl...@gmail.com
,
Luis Mendoza
4
11/16/22
Xpress ratio in pepXML do not match those in XPressPeptideUpdateParser.cgi
Dear Luis, Apologies for the delay. How can I send you the file/s? Thanks On Wednesday, November 2,
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Xpress ratio in pepXML do not match those in XPressPeptideUpdateParser.cgi
Dear Luis, Apologies for the delay. How can I send you the file/s? Thanks On Wednesday, November 2,
11/16/22
Michael Riffle
,
David Shteynberg
3
11/14/22
Error running xinteract on Kojak results using latest Docker image
Worked like a charm, thanks David! Mike On Monday, November 14, 2022 at 5:32:29 PM UTC-8 David
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Error running xinteract on Kojak results using latest Docker image
Worked like a charm, thanks David! Mike On Monday, November 14, 2022 at 5:32:29 PM UTC-8 David
11/14/22
Jakub Červenka
,
Charu Midha
4
10/31/22
Support for Skyline-built spectral libraries in DIALib-QC tool
Hi Jakub, DIALib-QC currently supports assessing spectronaut/peakview/openswath/prosite (exported in
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Support for Skyline-built spectral libraries in DIALib-QC tool
Hi Jakub, DIALib-QC currently supports assessing spectronaut/peakview/openswath/prosite (exported in
10/31/22
Caroline Lennartsson
,
mhoo...@systemsbiology.org
2
10/25/22
RAMP
Hi Caroline, There are several options available for you. The first option is to link original RAMP.
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RAMP
Hi Caroline, There are several options available for you. The first option is to link original RAMP.
10/25/22
Will Comstock
,
Luis Mendoza
2
10/13/22
Windows 11 Compatibility
Hi Will, We tested it on Windows 11 a few months ago and noticed no issues. Please do let us know if
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Windows 11 Compatibility
Hi Will, We tested it on Windows 11 a few months ago and noticed no issues. Please do let us know if
10/13/22
Adrian Brun
10/12/22
qtofpeakpicker
Hi guys is there any information or publication about qtofpeakpicker? I would like to understand how
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qtofpeakpicker
Hi guys is there any information or publication about qtofpeakpicker? I would like to understand how
10/12/22
Aarthie Senathirajah
, …
Eric Deutsch
4
9/27/22
TMT pro-16plex Libra Condition file
Upgrading to TPP 6.1.0 is definitely recommended, however, as there are many additional benefits to
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TMT pro-16plex Libra Condition file
Upgrading to TPP 6.1.0 is definitely recommended, however, as there are many additional benefits to
9/27/22
Yasir Ahmed
, …
Luis Mendoza
9
9/9/22
Libra quantification on TMT 16-plex returns zeros only
Great, glad that it is now working for you! We will remove references to that deprecated parameter
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Libra quantification on TMT 16-plex returns zeros only
Great, glad that it is now working for you! We will remove references to that deprecated parameter
9/9/22
Will Comstock
,
Eric Deutsch
4
9/8/22
Install without reboot?
Hi Will, excellent, thanks for posting the final tested solution! Eric From: spctools-discuss@
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Install without reboot?
Hi Will, excellent, thanks for posting the final tested solution! Eric From: spctools-discuss@
9/8/22
Aparna Agarwal
,
Jimmy Eng
2
8/23/22
Load spectra: Warning - no spectra searched : Comet
Hi. There could be a few reasons why would report a "Warning - no spectra searched" message
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Load spectra: Warning - no spectra searched : Comet
Hi. There could be a few reasons why would report a "Warning - no spectra searched" message
8/23/22
Priti Panchal
,
Luis Mendoza
2
8/4/22
Tandem Analysis
Hello Priti, You can specify non-enzymatic cleavage by setting the protein, cleavage site parameter
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Tandem Analysis
Hello Priti, You can specify non-enzymatic cleavage by setting the protein, cleavage site parameter
8/4/22
Anju Nagpal
, …
Eric Deutsch
6
7/26/22
Comet parameters
I'm not certain I understand your question. If you're looking for a template X!Tandem params
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Comet parameters
I'm not certain I understand your question. If you're looking for a template X!Tandem params
7/26/22
Aarthie Senathirajah
,
Luis Mendoza
2
7/19/22
Comet Params file for MS2 and MS3 TMT11-plex, comet won't load any spectra when mslevel=3
Hello, It seems that your issue may be caused by this parameter: ms_level = 2-3 # MS level to analyze
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Comet Params file for MS2 and MS3 TMT11-plex, comet won't load any spectra when mslevel=3
Hello, It seems that your issue may be caused by this parameter: ms_level = 2-3 # MS level to analyze
7/19/22
MT S
7/12/22
SpectraST iRT normalization problem
Hello, I'm trying to generate a spectral library using SpectraST, and all worked well except the
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SpectraST iRT normalization problem
Hello, I'm trying to generate a spectral library using SpectraST, and all worked well except the
7/12/22
Malcolm Cook
,
Luis Mendoza
2
6/14/22
account management
Hi Malcolm, Yes, those instructions for adding new accounts are still valid; I find it simplest to
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account management
Hi Malcolm, Yes, those instructions for adding new accounts are still valid; I find it simplest to
6/14/22
Malcolm Cook
,
David Shteynberg
11
6/11/22
tpp2mzid: error 4: Syntax error parsing XML
Apologies, my notes are published at Installing Trans Proteomic Pipeline (TPP) on CentOS 7 tl;dr: do
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tpp2mzid: error 4: Syntax error parsing XML
Apologies, my notes are published at Installing Trans Proteomic Pipeline (TPP) on CentOS 7 tl;dr: do
6/11/22
Wenhao
, …
Luis Mendoza
6
6/11/22
TPP 5.2.0 installation error CentOS 7.8
Very nice, thank you! On Fri, Jun 10, 2022 at 4:18 PM Malcolm Cook <malcol...@gmail.com>
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TPP 5.2.0 installation error CentOS 7.8
Very nice, thank you! On Fri, Jun 10, 2022 at 4:18 PM Malcolm Cook <malcol...@gmail.com>
6/11/22
Malcolm Cook
,
Luis Mendoza
3
6/10/22
Job runner completion confusion
Hi Luis, Yeah, I quickly got used to it but thought it worth pointing out. It only had me confused
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Job runner completion confusion
Hi Luis, Yeah, I quickly got used to it but thought it worth pointing out. It only had me confused
6/10/22
Malcolm Cook
,
David Shteynberg
6
6/8/22
getting 403/Forbidden on new install at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
Great! Thank you for keep and sharing your useful notes in this process. Let us know if you encounter
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getting 403/Forbidden on new install at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl
Great! Thank you for keep and sharing your useful notes in this process. Let us know if you encounter
6/8/22
Malcolm Cook
,
David Shteynberg
5
6/8/22
stuck with problem making tpp
I agree with you re using -k. I only did it after make was terminating with an error in order to try
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stuck with problem making tpp
I agree with you re using -k. I only did it after make was terminating with an error in order to try
6/8/22
Farshad Abdollah-Nia
,
David Shteynberg
5
6/8/22
Tandem2XML all-15N issue
Hi David, Thank you for updating the code and sorry for my late reply. This solves the problem for
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Tandem2XML all-15N issue
Hi David, Thank you for updating the code and sorry for my late reply. This solves the problem for
6/8/22
Luis Mendoza
, …
Eric Deutsch
7
6/7/22
TPP 6.1.0 Release is now available
Hi Malcolm, thank you for the corrections, the page is now updated. Let me know if you find any other
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TPP 6.1.0 Release is now available
Hi Malcolm, thank you for the corrections, the page is now updated. Let me know if you find any other
6/7/22
malcook
6/7/22
svn checkout errors and a workaround
While executing svn checkout http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline I
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svn checkout errors and a workaround
While executing svn checkout http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline I
6/7/22