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• • Re: [spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization Longping Fu
  • Re: [spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization David Shteynberg
  • Re: [spctools-discuss] Assistance Needed with Warning Messages in PTMProphet for TPP 6.3.3 PTM Localization Longping Fu
• [spctools-discuss] I need help with silac search using a a combined file from xtandem and comet sudarshan kumar
  • [spctools-discuss] Re: I need help with silac search using a a combined file from xtandem and comet sudarshan kumar
• [spctools-discuss] XPRESS peak intensity value Iryna Abramchuk
  • Re: [spctools-discuss] XPRESS peak intensity value Jimmy Eng
  • Re: [spctools-discuss] XPRESS peak intensity value Iryna Abramchuk
  • Re: [spctools-discuss] XPRESS peak intensity value Jimmy Eng
  • Re: [spctools-discuss] XPRESS peak intensity value Iryna Abramchuk
  • Re: [spctools-discuss] XPRESS peak intensity value Jimmy Eng
  • Re: [spctools-discuss] XPRESS peak intensity value Iryna Abramchuk
  • Re: [spctools-discuss] XPRESS peak intensity value sudarshan kumar
  • Re: [spctools-discuss] XPRESS peak intensity value 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] XPRESS peak intensity value Iryna Abramchuk
• [spctools-discuss] workflow for SILAC analysis sudarshan kumar
• [spctools-discuss] Optimal hardware for TPP server? Will Comstock
  • RE: [spctools-discuss] Optimal hardware for TPP server? 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Optimal hardware for TPP server? Will Comstock
• [spctools-discuss] Feature request for LIBRA Debojyoti Pal
  • RE: [spctools-discuss] Feature request for LIBRA 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Feature request for LIBRA Debojyoti Pal
• [spctools-discuss] I need to acquisition settings for running silac samples (only heavy lysine (13 C6 and 15N2 and no argininge) sudarshan kumar
• [spctools-discuss] MASH explorer Sanclayver Araújo
• [spctools-discuss] StPeter error - Could not read spectra Jason Winget
  • [spctools-discuss] Re: StPeter error - Could not read spectra David Shteynberg
• [spctools-discuss] Stpeter negative SIn value? sudarshan kumar
  • [spctools-discuss] Re: Stpeter negative SIn value? [email protected]
  • [spctools-discuss] Re: Stpeter negative SIn value? sudarshan kumar
  • Re: [spctools-discuss] Re: Stpeter negative SIn value? sudarshan kumar
  • Re: [spctools-discuss] Re: Stpeter negative SIn value? [email protected]
  • Re: [spctools-discuss] Re: Stpeter negative SIn value? sudarshan kumar
• [spctools-discuss] Stpeter sudarshan kumar
  • [spctools-discuss] Re: Stpeter [email protected]
• [spctools-discuss] Regarding protein prophet input - what difference does it make if I use PTM prophet file or not Debojyoti Pal
  • [spctools-discuss] Re: Regarding protein prophet input - what difference does it make if I use PTM prophet file or not Debojyoti Pal
• Re: [spctools-discuss] Navigating peptideSieve Tips/Tricks? sophie culos
  • Re: [spctools-discuss] Navigating peptideSieve Tips/Tricks? 'David Shteynberg' via spctools-discuss
• [spctools-discuss] Regarding total intensity normalization in LIBRA Debojyoti Pal
  • [spctools-discuss] Re: Regarding total intensity normalization in LIBRA Debojyoti Pal
• [spctools-discuss] Variable mod query in COMET Debojyoti Pal
  • Re: [spctools-discuss] Variable mod query in COMET 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Variable mod query in COMET Debojyoti Pal
  • Re: [spctools-discuss] Variable mod query in COMET 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Variable mod query in COMET Debojyoti Pal
• [spctools-discuss] Access to Mascot file results Carlo de Oliveira Martins
  • Re: [spctools-discuss] Access to Mascot file results 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Access to Mascot file results Carlo de Oliveira Martins
• [spctools-discuss] Problem with PeptideProphet Tanmay Singh
  • Re: [spctools-discuss] Problem with PeptideProphet 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] converting prot.xml to tsv/something else Emma Whittington
  • Re: [spctools-discuss] converting prot.xml to tsv/something else 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] converting prot.xml to tsv/something else Emma Whittington
• Re: [spctools-discuss] Upcoming Trans-Proteomic Pipeline (TPP) course Luis
• [spctools-discuss] Re: Upcoming Trans-Proteomic Pipeline (TPP) course Emma Whittington
  • Re: [spctools-discuss] Re: Upcoming Trans-Proteomic Pipeline (TPP) course Manuela Piazzi
  • Re: [spctools-discuss] Re: Upcoming Trans-Proteomic Pipeline (TPP) course 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Re: Upcoming Trans-Proteomic Pipeline (TPP) course Aparna Agarwal
  • Re: [spctools-discuss] Re: Upcoming Trans-Proteomic Pipeline (TPP) course 'Luis Mendoza' via spctools-discuss
• Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides [email protected]
  • Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides Hampton, Brian
  • Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides Emma Whittington
  • Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides Hampton, Brian
  • Re: [spctools-discuss] ProteinProphet output number of unique peptides vs total number of peptides 'David Shteynberg' via spctools-discuss
• [spctools-discuss] TPP Tandem input files Emma Whittington
  • Re: [spctools-discuss] TPP Tandem input files 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] Next proteomics informatics course? [email protected]
  • [spctools-discuss] Re: Next proteomics informatics course? Jimmy Eng
  • [spctools-discuss] Re: Next proteomics informatics course? Reza Assalkhou
  • RE: [spctools-discuss] Re: Next proteomics informatics course? 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Re: Next proteomics informatics course? don johann
  • Re: [spctools-discuss] Re: Next proteomics informatics course? 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Re: Next proteomics informatics course? don johann
  • Re: [spctools-discuss] Re: Next proteomics informatics course? 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] TPP @ ASMS 2023 -- Posters, Tuesday Workshop, and Bioinformatics Hub 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] Proteome discoverer users guide Sanclayver Araújo
  • [spctools-discuss] Re: Proteome discoverer users guide Phillip Wilmarth
  • Re: [spctools-discuss] Proteome discoverer users guide Jimmy Eng
  • Re: [spctools-discuss] Proteome discoverer users guide Sanclayver Araújo
• [spctools-discuss] Installer for TPP 6.3.0 does not recognize existence of MS VC++ 2015-2022 Scott Starry
  • Re: [spctools-discuss] Installer for TPP 6.3.0 does not recognize existence of MS VC++ 2015-2022 'David Shteynberg' via spctools-discuss
• [spctools-discuss] TPP 6.3.0 Release is now available 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] protein validation felipe velasquez
  • Re: [spctools-discuss] protein validation 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] protein validation felipe velasquez
  • Re: [spctools-discuss] protein validation Jimmy Eng
  • Re: [spctools-discuss] protein validation felipe velasquez
• [spctools-discuss] Problem with PTMprophet felipe velasquez
  • Re: [spctools-discuss] Problem with PTMprophet 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Problem with PTMprophet felipe velasquez
  • Re: [spctools-discuss] Problem with PTMprophet 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Problem with PTMprophet felipe velasquez
• [spctools-discuss] SILAC quantification with targeted SIM Will Comstock
  • Re: [spctools-discuss] SILAC quantification with targeted SIM Jimmy Eng
  • Re: [spctools-discuss] SILAC quantification with targeted SIM Will Comstock
  • Re: [spctools-discuss] SILAC quantification with targeted SIM Will Comstock
  • Re: [spctools-discuss] SILAC quantification with targeted SIM 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] Re: Output sequence coverage info Yasir Ahmed
  • [spctools-discuss] Re: Output sequence coverage info Yasir Ahmed
  • Re: [spctools-discuss] Re: Output sequence coverage info 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Re: Output sequence coverage info Yasir Ahmed
  • Re: [spctools-discuss] Re: Output sequence coverage info 'Luis Mendoza' via spctools-discuss
• RE: [spctools-discuss] SSL problem 'Eric Deutsch' via spctools-discuss
• [spctools-discuss] How does RT train work? Aarthie Senathirajah
• [spctools-discuss] MSFragger param Priti Panchal
  • RE: [spctools-discuss] MSFragger param 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] MSFragger param Priti Panchal
  • Re: [spctools-discuss] MSFragger param 'Eric Deutsch' via spctools-discuss
• [spctools-discuss] TPP 6.2.0 Release is now available 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] Analyzing Metaproteomic Data Aarthie Senathirajah
  • Re: [spctools-discuss] Analyzing Metaproteomic Data 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] not getting significant hits while analyzing .raw file reeju
• [spctools-discuss] protein prophet failing on Eclipse searches [email protected]
  • Re: [spctools-discuss] protein prophet failing on Eclipse searches 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] protein prophet failing on Eclipse searches 'David Shteynberg' via spctools-discuss
  • [spctools-discuss] Re: protein prophet failing on Eclipse searches [email protected]
• [spctools-discuss] Libra results for individual peptides in ProteinProphet results page Debojyoti Pal
• [spctools-discuss] Error running xinteract on Kojak results using latest Docker image Michael Riffle
  • Re: [spctools-discuss] Error running xinteract on Kojak results using latest Docker image 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] Error running xinteract on Kojak results using latest Docker image Michael Riffle
• [spctools-discuss] RAMP Caroline Lennartsson
  • [spctools-discuss] Re: RAMP [email protected]
• [spctools-discuss] Support for Skyline-built spectral libraries in DIALib-QC tool Jakub Červenka
  • Re: [spctools-discuss] Support for Skyline-built spectral libraries in DIALib-QC tool 'Charu Midha' via spctools-discuss
  • Re: [spctools-discuss] Support for Skyline-built spectral libraries in DIALib-QC tool Jakub Červenka
  • Re: [spctools-discuss] Support for Skyline-built spectral libraries in DIALib-QC tool 'Charu Midha' via spctools-discuss
• [spctools-discuss] Xpress ratio in pepXML do not match those in XPressPeptideUpdateParser.cgi [email protected]
  • Re: [spctools-discuss] Xpress ratio in pepXML do not match those in XPressPeptideUpdateParser.cgi 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Xpress ratio in pepXML do not match those in XPressPeptideUpdateParser.cgi [email protected]
  • Re: [spctools-discuss] Xpress ratio in pepXML do not match those in XPressPeptideUpdateParser.cgi [email protected]
• [spctools-discuss] Windows 11 Compatibility Will Comstock
  • Re: [spctools-discuss] Windows 11 Compatibility 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] qtofpeakpicker Adrian Brun
• [spctools-discuss] TMT pro-16plex Libra Condition file Aarthie Senathirajah
  • Re: [spctools-discuss] TMT pro-16plex Libra Condition file Yasir Ahmed
  • Re: [spctools-discuss] TMT pro-16plex Libra Condition file Aarthie Senathirajah
  • RE: [spctools-discuss] TMT pro-16plex Libra Condition file 'Eric Deutsch' via spctools-discuss
• [spctools-discuss] Libra quantification on TMT 16-plex returns zeros only Yasir Ahmed
  • Re: [spctools-discuss] Libra quantification on TMT 16-plex returns zeros only 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Libra quantification on TMT 16-plex returns zeros only Yasir Ahmed
  • Re: [spctools-discuss] Libra quantification on TMT 16-plex returns zeros only 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] Install without reboot? Will Comstock
  • RE: [spctools-discuss] Install without reboot? 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Install without reboot? Will Comstock
  • RE: [spctools-discuss] Install without reboot? 'Eric Deutsch' via spctools-discuss
• [spctools-discuss] Load spectra: Warning - no spectra searched : Comet Aparna Agarwal
  • [spctools-discuss] Re: Load spectra: Warning - no spectra searched : Comet Jimmy Eng
• [spctools-discuss] Tandem Analysis Priti Panchal
  • Re: [spctools-discuss] Tandem Analysis 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] Comet parameters Anju Nagpal
  • RE: [spctools-discuss] Comet parameters 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Comet parameters Anju Nagpal
  • RE: [spctools-discuss] Comet parameters 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Comet parameters Anju Nagpal
  • RE: [spctools-discuss] Comet parameters Eric Deutsch
• [spctools-discuss] WGS data analysis costs Tohid Ghasemnejad
• [spctools-discuss] Comet Params file for MS2 and MS3 TMT11-plex, comet won't load any spectra when mslevel=3 Aarthie Senathirajah
  • 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
• [spctools-discuss] SpectraST iRT normalization problem MT S
• [spctools-discuss] account management Malcolm Cook
  • Re: [spctools-discuss] account management 'Luis Mendoza' via spctools-discuss
• Re: [spctools-discuss] Job runner completion confusion Malcolm Cook
• [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML Malcolm Cook
  • Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML Malcolm Cook
  • Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML Malcolm Cook
  • Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML Malcolm Cook
  • Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML Malcolm Cook
  • Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML Malcolm Cook
  • Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] tpp2mzid: error 4: Syntax error parsing XML Malcolm Cook
• [spctools-discuss] getting 403/Forbidden on new install at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl Malcolm Cook
  • Re: [spctools-discuss] getting 403/Forbidden on new install at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] getting 403/Forbidden on new install at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl Malcolm Cook
  • Re: [spctools-discuss] getting 403/Forbidden on new install at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl Malcolm Cook
  • Re: [spctools-discuss] getting 403/Forbidden on new install at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl Malcolm Cook
  • Re: [spctools-discuss] getting 403/Forbidden on new install at http://localhost:10401/tpp/cgi-bin/tpp_gui.pl 'David Shteynberg' via spctools-discuss
• [spctools-discuss] stuck with problem making tpp Malcolm Cook
  • Re: [spctools-discuss] stuck with problem making tpp 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] stuck with problem making tpp Malcolm Cook
  • Re: [spctools-discuss] stuck with problem making tpp 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] stuck with problem making tpp Malcolm Cook
• [spctools-discuss] svn checkout errors and a workaround malcook
• [spctools-discuss] TPP @ ASMS 2022 -- Posters and Monday Workshop 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] TPP 6.1.0 Release is now available 'Luis Mendoza' via spctools-discuss
  • [spctools-discuss] Re: TPP 6.1.0 Release is now available malcook
  • Re: [spctools-discuss] Re: TPP 6.1.0 Release is now available 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Re: TPP 6.1.0 Release is now available Malcolm Cook
  • Re: [spctools-discuss] Re: TPP 6.1.0 Release is now available 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] Re: TPP 6.1.0 Release is now available Malcolm Cook
  • RE: [spctools-discuss] Re: TPP 6.1.0 Release is now available Eric Deutsch
• [spctools-discuss] TPP 6.1.0 rc9 Missing module in Perl installation Juergen Bartel
  • Re: [spctools-discuss] TPP 6.1.0 rc9 Missing module in Perl installation 'David Shteynberg' via spctools-discuss
• [spctools-discuss] Error in converting .raw file to .mzml file Jingyi Hu

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