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• • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 Emily Kawaler
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 Emily Kawaler
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 Emily Kawaler
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 Emily Kawaler
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 Emily Kawaler
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 Emily Kawaler
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 Emily Kawaler
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 Emily Kawaler
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 Emily Kawaler
  • Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3 Emily Kawaler
• [spctools-discuss] LFQ [email protected]
  • Re: [spctools-discuss] LFQ 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] LFQ Robert Winkler
• [spctools-discuss] Converting Orbitrap Eclipse files to mzML Laura Muehlbauer
  • Re: [spctools-discuss] Converting Orbitrap Eclipse files to mzML 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] Converting Orbitrap Eclipse files to mzML Jason Winget
  • Re: [spctools-discuss] Converting Orbitrap Eclipse files to mzML Laura Muehlbauer
• [spctools-discuss] X!Tandem- Help please [email protected]
  • Re: [spctools-discuss] X!Tandem- Help please Robert Winkler
  • Re: [spctools-discuss] X!Tandem- Help please [email protected]
  • Re: [spctools-discuss] X!Tandem- Help please Robert Winkler
  • Re: [spctools-discuss] X!Tandem- Help please Jimmy Eng
  • Re: [spctools-discuss] X!Tandem- Help please [email protected]
• [spctools-discuss] X!Tandem taking too long [email protected]
  • [spctools-discuss] Re: X!Tandem taking too long [email protected]
  • [spctools-discuss] Re: X!Tandem taking too long [email protected]
• [spctools-discuss] ProtyQuant for comparing TPP samples (.pepXML) Robert
  • Re: [spctools-discuss] ProtyQuant for comparing TPP samples (.pepXML) 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] Crosslink FDR from PeptideProphet Lindsey Ulmer
  • Re: [spctools-discuss] Crosslink FDR from PeptideProphet 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] Crosslink FDR from PeptideProphet Lindsey Ulmer
• [spctools-discuss] Consensus spectral library with split RT Annie Ha
• [spctools-discuss] Comet fixed and variable modifications Francesco Demetrio Lofaro
  • Re: [spctools-discuss] Comet fixed and variable modifications Jimmy Eng
• [spctools-discuss] Unique peptide Francesco Demetrio Lofaro
• [spctools-discuss] Query related to protein abundances in TPP Mehar Un Nissa
  • Re: [spctools-discuss] Query related to protein abundances in TPP Robert Winkler
  • Re: [spctools-discuss] Query related to protein abundances in TPP Mehar Un Nissa
• [spctools-discuss] Query related to PTMprophet results in TPP Mehar Un Nissa
  • Re: [spctools-discuss] Query related to PTMprophet results in TPP 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] how to specify heavy label for oxidised methionine in ASAPRatio 'Alastair Skeffington' via spctools-discuss
  • Re: [spctools-discuss] how to specify heavy label for oxidised methionine in ASAPRatio 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] how to specify heavy label for oxidised methionine in ASAPRatio 'Alastair Skeffington' via spctools-discuss
  • Re: [spctools-discuss] how to specify heavy label for oxidised methionine in ASAPRatio 'Alastair Skeffington' via spctools-discuss
  • Re: [spctools-discuss] how to specify heavy label for oxidised methionine in ASAPRatio 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] how to specify heavy label for oxidised methionine in ASAPRatio 'Alastair Skeffington' via spctools-discuss
  • Re: [spctools-discuss] how to specify heavy label for oxidised methionine in ASAPRatio 'Alastair Skeffington' via spctools-discuss
  • Re: [spctools-discuss] how to specify heavy label for oxidised methionine in ASAPRatio 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] how to specify heavy label for oxidised methionine in ASAPRatio 'Alastair Skeffington' via spctools-discuss
  • Re: [spctools-discuss] how to specify heavy label for oxidised methionine in ASAPRatio 'Alastair Skeffington' via spctools-discuss
• [spctools-discuss] 15N/14N guidence 'Alastair Skeffington' via spctools-discuss
• [spctools-discuss] New to TPP: finding FDR corresponding to probability RS
  • Re: [spctools-discuss] New to TPP: finding FDR corresponding to probability 'David Shteynberg' via spctools-discuss
• [spctools-discuss] TMT labeling efficiency test Josh Yu
• Re: [spctools-discuss] Are these crapome? Josh Yu
• [spctools-discuss] New at TTP. Problem with PSM validation Carlos Humberto Paván
  • [spctools-discuss] Re: New at TTP. Problem with PSM validation Carlos Humberto Paván
  • Re: [spctools-discuss] New at TTP. Problem with PSM validation 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] New at TTP. Problem with PSM validation Carlos Humberto Paván
  • Re: [spctools-discuss] New at TTP. Problem with PSM validation 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] New at TTP. Problem with PSM validation Carlos Humberto Paván
• [spctools-discuss] QualScore - 0 dtas written Miguel Cosenza
  • [spctools-discuss] Re: QualScore - 0 dtas written Yun-En Chung
• [spctools-discuss] SpectraST: Missing modifications in decoy free library import in ProteomeDiscoverer RS
  • [spctools-discuss] Re: SpectraST: Missing modifications in decoy free library import in ProteomeDiscoverer RS
  • RE: [spctools-discuss] Re: SpectraST: Missing modifications in decoy free library import in ProteomeDiscoverer 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Re: SpectraST: Missing modifications in decoy free library import in ProteomeDiscoverer RS
  • RE: [spctools-discuss] Re: SpectraST: Missing modifications in decoy free library import in ProteomeDiscoverer 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Re: SpectraST: Missing modifications in decoy free library import in ProteomeDiscoverer RS
  • RE: [spctools-discuss] Re: SpectraST: Missing modifications in decoy free library import in ProteomeDiscoverer 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Re: SpectraST: Missing modifications in decoy free library import in ProteomeDiscoverer RS
  • Re: [spctools-discuss] Re: SpectraST: Missing modifications in decoy free library import in ProteomeDiscoverer RS
• [spctools-discuss] Specifying comet param file in batch file Mark Athanason
  • [spctools-discuss] Re: Specifying comet param file in batch file Jimmy Eng
  • RE: [spctools-discuss] Re: Specifying comet param file in batch file Mark Athanason
• [spctools-discuss] Re: Problem with SpectraST [email protected]
• [spctools-discuss] Spectral library generation Srinivas Srikanth
  • RE: [spctools-discuss] Spectral library generation 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Spectral library generation Srinivas Srikanth
  • Re: [spctools-discuss] Spectral library generation Aaron Robinson
• [spctools-discuss] Re: C:/TPP/bin/runsearch' is not recognized as an internal or external command Jimmy Eng
  • [spctools-discuss] Re: C:/TPP/bin/runsearch' is not recognized as an internal or external command Phillip Wilmarth
  • Re: [spctools-discuss] Re: C:/TPP/bin/runsearch' is not recognized as an internal or external command Javan Okendo
  • Re: [spctools-discuss] Re: C:/TPP/bin/runsearch' is not recognized as an internal or external command Phillip Wilmarth
  • RE: [spctools-discuss] Re: C:/TPP/bin/runsearch' is not recognized as an internal or external command 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Re: C:/TPP/bin/runsearch' is not recognized as an internal or external command Javan Okendo
• [spctools-discuss] Percolator Error in TPP Gabrielle H
  • Re: [spctools-discuss] Percolator Error in TPP 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Percolator Error in TPP Gabrielle H
  • Re: [spctools-discuss] Percolator Error in TPP 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Percolator Error in TPP Gabrielle H
  • [spctools-discuss] Re: Percolator Error in TPP Jimmy Eng
  • [spctools-discuss] Re: Percolator Error in TPP Gabrielle H
  • [spctools-discuss] Re: Percolator Error in TPP Gabrielle H
• [spctools-discuss] Trans-Proteomic Pipeline workshop at ASMS Tuesday 10am Central time 'Eric Deutsch' via spctools-discuss
• [spctools-discuss] Spectrast: peptides with modifications are removed when converting NIST .msp formatted library to .splib. Ray
  • [spctools-discuss] Re: Spectrast: peptides with modifications are removed when converting NIST .msp formatted library to .splib. Wenguang
  • [spctools-discuss] Re: Spectrast: peptides with modifications are removed when converting NIST .msp formatted library to .splib. Henry Lam
  • [spctools-discuss] Re: Spectrast: peptides with modifications are removed when converting NIST .msp formatted library to .splib. Henry Lam
• [spctools-discuss] TPP Error Nimai Charan Mahanandia
  • Re: [spctools-discuss] TPP Error Javan Okendo
  • [spctools-discuss] Re: TPP Error felipe velasquez
  • Re: [spctools-discuss] Re: TPP Error Robert Winkler
• [spctools-discuss] Re: ASAPRatio for 15N? Carlo de Oliveira Martins
• [spctools-discuss] SpectrasT can't recognize Protein N-term acetylation modification RayS
  • RE: [spctools-discuss] SpectrasT can't recognize Protein N-term acetylation modification 'Eric Deutsch' via spctools-discuss
• [spctools-discuss] Error while running prophets with the comet results from searchGUI JAVAN OKENDO
  • Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI Jimmy Eng
  • Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI Javan Okendo
  • Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI Jimmy Eng
  • Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI Kate Mostovenko
  • Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI Jimmy Eng
  • Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI Kate Mostovenko
  • Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI Jimmy Eng
  • Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI Jimmy Eng
  • Re: [spctools-discuss] Error while running prophets with the comet results from searchGUI Kate Mostovenko
  • [spctools-discuss] Re: Error while running prophets with the comet results from searchGUI JAVAN OKENDO
  • [spctools-discuss] Re: Error while running prophets with the comet results from searchGUI JAVAN OKENDO
• [spctools-discuss] Help in geneting Sequest and X!Tandem parameter files JAVAN OKENDO
  • Re: [spctools-discuss] Help in geneting Sequest and X!Tandem parameter files Jimmy Eng
  • Re: [spctools-discuss] Help in geneting Sequest and X!Tandem parameter files Javan Okendo
  • Re: [spctools-discuss] Help in geneting Sequest and X!Tandem parameter files Jimmy Eng
• [spctools-discuss] PTMProphet MSFragger modification missing mass Alex Zelter
  • Re: [spctools-discuss] PTMProphet MSFragger modification missing mass 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] PTMProphet MSFragger modification missing mass Alex Zelter
  • Re: [spctools-discuss] PTMProphet MSFragger modification missing mass 'David Shteynberg' via spctools-discuss
• [spctools-discuss] Kojak File not Found Lindsey Ulmer
  • Re: [spctools-discuss] Kojak File not Found 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Kojak File not Found Lindsey Ulmer
  • Re: [spctools-discuss] Kojak File not Found Michael Hoopmann
  • Re: [spctools-discuss] Kojak File not Found Michael Hoopmann
• [spctools-discuss] ProteinProphet error Daniel Geiszler
  • [spctools-discuss] Re: ProteinProphet error Daniel Geiszler
• [spctools-discuss] PTMProphet MSFragger modification mass discrepancy Alex Zelter
  • Re: [spctools-discuss] PTMProphet MSFragger modification mass discrepancy 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] PTMProphet MSFragger modification mass discrepancy Alex Zelter
  • Re: [spctools-discuss] PTMProphet MSFragger modification mass discrepancy 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] PTMProphet MSFragger modification mass discrepancy Alex Zelter
• [spctools-discuss] Problem installing TPP 5.2 on Windows RUI XU
  • Re: [spctools-discuss] Problem installing TPP 5.2 on Windows 'David Shteynberg' via spctools-discuss
• [spctools-discuss] Protein level FDR Tanner Tessier
• [spctools-discuss] TPP 5.2 in Ubuntu 18.04 not showing plots/images in PepProphet nor ProtProphet models Alejandro
  • Re: [spctools-discuss] TPP 5.2 in Ubuntu 18.04 not showing plots/images in PepProphet nor ProtProphet models 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] TPP 5.2 in Ubuntu 18.04 not showing plots/images in PepProphet nor ProtProphet models Alejandro
• [spctools-discuss] No decoys found by IProphet 'Alastair Skeffington' via spctools-discuss
  • [spctools-discuss] Re: No decoys found by IProphet 'Alastair Skeffington' via spctools-discuss
  • Re: [spctools-discuss] No decoys found by IProphet 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] No decoys found by IProphet 'Alastair Skeffington' via spctools-discuss
• [spctools-discuss] Query related to Lorikeet viewer PTMprophet results in TPP Mehar Un Nissa
  • [spctools-discuss] Re: Query related to Lorikeet viewer PTMprophet results in TPP Mehar Un Nissa
  • Re: [spctools-discuss] Re: Query related to Lorikeet viewer PTMprophet results in TPP 'Luis Mendoza' via spctools-discuss
  • Re: [spctools-discuss] Re: Query related to Lorikeet viewer PTMprophet results in TPP 'David Shteynberg' via spctools-discuss
• [spctools-discuss] irt issue Srinivas Srikanth
  • RE: [spctools-discuss] irt issue 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] irt issue Srinivas Srikanth
• [spctools-discuss] QualScore input format Sebastien Leblanc
• [spctools-discuss] Failed, error code 256 when I want to run LIBRA with TPP Cindy Dieryckx
  • Re: [spctools-discuss] Failed, error code 256 when I want to run LIBRA with TPP 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] Failed, error code 256 when I want to run LIBRA with TPP Cindy Dieryckx
  • Re: [spctools-discuss] Failed, error code 256 when I want to run LIBRA with TPP 'Luis Mendoza' via spctools-discuss
• [spctools-discuss] mzIDentML [email protected]
  • RE: [spctools-discuss] mzIDentML 'Michael Hoopmann' via spctools-discuss
  • Re: [spctools-discuss] mzIDentML [email protected]
• [spctools-discuss] all Kojak identified unlinked PSMs assigned a probability of 0 TPP/Kojak Alex Zelter
  • Re: [spctools-discuss] all Kojak identified unlinked PSMs assigned a probability of 0 TPP/Kojak 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] all Kojak identified unlinked PSMs assigned a probability of 0 TPP/Kojak Alex Zelter
• [spctools-discuss] nan detected in NonParametricDistribution ... TPP Kojak Alex Zelter
  • Re: [spctools-discuss] nan detected in NonParametricDistribution ... TPP Kojak 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] nan detected in NonParametricDistribution ... TPP Kojak 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] nan detected in NonParametricDistribution ... TPP Kojak Alex Zelter
• [spctools-discuss] Query related to filtering PTMprophet results in TPP Mehar Un Nissa
  • Re: [spctools-discuss] Query related to filtering PTMprophet results in TPP 'David Shteynberg' via spctools-discuss
• [spctools-discuss] Installation Error Xavier Alexander M
• [spctools-discuss] Query related to PTMprophet tool in TPP Mehar Un Nissa
  • Re: [spctools-discuss] Query related to PTMprophet tool in TPP 'David Shteynberg' via spctools-discuss
• [spctools-discuss] Spectra indexing for Waters DDA data David Schmidt
• [spctools-discuss] Interpretation of stats from pepXML viewer 'Alastair Skeffington' via spctools-discuss
  • RE: [spctools-discuss] Interpretation of stats from pepXML viewer 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Interpretation of stats from pepXML viewer Jimmy Eng
  • RE: [spctools-discuss] Interpretation of stats from pepXML viewer 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Interpretation of stats from pepXML viewer 'Alastair Skeffington' via spctools-discuss
• [spctools-discuss] Perl library errors: Centos 7 Shagun Gupta
  • RE: [spctools-discuss] Perl library errors: Centos 7 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Perl library errors: Centos 7 Shagun Gupta
  • RE: [spctools-discuss] Perl library errors: Centos 7 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Perl library errors: Centos 7 Shagun Gupta
  • RE: [spctools-discuss] Perl library errors: Centos 7 'Eric Deutsch' via spctools-discuss
  • Re: [spctools-discuss] Perl library errors: Centos 7 Shagun Gupta
  • RE: [spctools-discuss] Perl library errors: Centos 7 'Eric Deutsch' via spctools-discuss
• [spctools-discuss] Question: mzML parsing issue SpectraST 5.0 (stand alone, Linux, MacOS) Oliver Alka
  • [spctools-discuss] Re: Question: mzML parsing issue SpectraST 5.0 (stand alone, Linux, MacOS) oliveralka
  • RE: [spctools-discuss] Re: Question: mzML parsing issue SpectraST 5.0 (stand alone, Linux, MacOS) 'Eric Deutsch' via spctools-discuss
• [spctools-discuss] New to TPP: trouble understanding search parameters Tanner Tessier
• [spctools-discuss] Peptideprophet/iprophet/proteinprophet to combine MaxQuant output? Jesse
• [spctools-discuss] TPP installation failure in RHEL 7.4 arun kumar

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