spctools-discuss

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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 Deutsch4

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

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 Mendoza2

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

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 Shteynberg4

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

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 Mendoza4

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 Shteynberg3

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 Midha4

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.org2

10/25/22

Hi Caroline, There are several options available for you. The first option is to link original RAMP.

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Hi Caroline, There are several options available for you. The first option is to link original RAMP.

10/25/22

Will Comstock, Luis Mendoza2

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

10/12/22

Hi guys is there any information or publication about qtofpeakpicker? I would like to understand how

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Hi guys is there any information or publication about qtofpeakpicker? I would like to understand how

10/12/22

Aarthie Senathirajah, … Eric Deutsch4

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 Mendoza9

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 Deutsch4

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 Eng2

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 Mendoza2

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 Deutsch6

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 Mendoza2

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

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 Mendoza2

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 Shteynberg11

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 Mendoza6

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 Mendoza3

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 Shteynberg6

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 Shteynberg5

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 Shteynberg5

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 Deutsch7

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

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

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