spctools-discuss  

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• • Re: [spctools-discuss] Libra condition.xml syntax Luis Mendoza
  • [spctools-discuss] Re: Libra condition.xml syntax Konstantinos Vougas
• [spctools-discuss] Semi-empirical spectra generation: single aa substitution Jelena Chuklina
• [spctools-discuss] Sequest search question David Zhao
• [spctools-discuss] Should I use discriminant score or expect value for PTM modeling for comet search results David Zhao
• [spctools-discuss] Re: Multiple lysine modifications and quantification Jesse
• [spctools-discuss] Export to .xls from command line Adam Oberstein
  • Re: [spctools-discuss] Export to .xls from command line 钟传奇
  • Re: [spctools-discuss] Export to .xls from command line Luis Mendoza
  • Re: [spctools-discuss] Export to .xls from command line 钟传奇
  • Re: [spctools-discuss] Export to .xls from command line 钟传奇
  • [spctools-discuss] Re: Export to .xls from command line Jason Winget
  • [spctools-discuss] Re: Export to .xls from command line Adam Oberstein
  • [spctools-discuss] Re: Export to .xls from command line Adam Oberstein
  • [spctools-discuss] Re: Export to .xls from command line Adam Oberstein
  • Re: [spctools-discuss] Export to .xls from command line 钟传奇
• [spctools-discuss] TPP 4.7 error when performing data search (following tutorial) Jelena Chuklina
• [spctools-discuss] How to fix message NOCMDFILE Marianne Brannon
  • [spctools-discuss] Re: How to fix message NOCMDFILE Marianne Brannon
• [spctools-discuss] How to set iprobility value cutoff input for proteinprophet? 钟传奇
• [spctools-discuss] X!Tandem searches take too long Marianne Brannon
  • Re: [spctools-discuss] X!Tandem searches take too long Joseph Slagel
  • Re: [spctools-discuss] X!Tandem searches take too long Marianne Brannon
  • Re: [spctools-discuss] X!Tandem searches take too long Joseph Slagel
• [spctools-discuss] Attempted to access forbidden directory SURUCHI AGGARWAL
• [spctools-discuss] Possible Bug in TPP 4.7.1 dsimpson3
  • [spctools-discuss] Re: Possible Bug in TPP 4.7.1 dsimpson3
  • [spctools-discuss] Re: Possible Bug in TPP 4.7.1 [email protected]
• [spctools-discuss] ASAPRatio Problem Shadab Ahmad
  • [spctools-discuss] Re: ASAPRatio Problem Xabier Martinez De Morentin
  • Re: [spctools-discuss] Re: ASAPRatio Problem David Shteynberg
• [spctools-discuss] Base peak intensity values not reported in pepxml files Brian Hampton
  • [spctools-discuss] Re: Base peak intensity values not reported in pepxml files Jason Winget
  • Re: [spctools-discuss] Re: Base peak intensity values not reported in pepxml files Brian Hampton
  • Re: [spctools-discuss] Re: Base peak intensity values not reported in pepxml files Jimmy Eng
  • Re: [spctools-discuss] Re: Base peak intensity values not reported in pepxml files Brian Hampton
• [spctools-discuss] Tandem2XML problem (RETURN CODE:768) zeyu sun
  • Re: [spctools-discuss] Tandem2XML problem (RETURN CODE:768) Luis Mendoza
• [spctools-discuss] ProteinProphet crashes by an unknown reason Lee, Joungmin
• [spctools-discuss] ProteinProphet crashes Lee, Joungmin
• [spctools-discuss] ASAPRatio problem update - is fixed in TPP 4.7.1 ! Brian Hampton
• [spctools-discuss] ASAPRatio, not using massdiff properly for chemical isotopic labeling? Brian Hampton
  • Re: [spctools-discuss] ASAPRatio, not using massdiff properly for chemical isotopic labeling? David Shteynberg
• [spctools-discuss] HOW to get the "Specify Tandem Parameters File"?~~~help~~~ jason cao
  • Re: [spctools-discuss] HOW to get the "Specify Tandem Parameters File"?~~~help~~~ 钟传奇
  • Re: [spctools-discuss] HOW to get the "Specify Tandem Parameters File"?~~~help~~~ jason cao
• [spctools-discuss] what is "Specify Tandem Parameters File"!!!! jason cao
• [spctools-discuss] how to creat a " Specify Tandem Parameters File "!!!!!!!! hurry~~~help jason cao
• [spctools-discuss] [PeptideProphet] limitation of input file size? User
  • Re: [spctools-discuss] [PeptideProphet] limitation of input file size? Joseph Slagel
  • Re: [spctools-discuss] [PeptideProphet] limitation of input file size? User
  • Re: [spctools-discuss] [PeptideProphet] limitation of input file size? Joseph Slagel
  • Re: [spctools-discuss] [PeptideProphet] limitation of input file size? User
• [spctools-discuss] [PeptideProphet_Mascot] Runtime to terminate it in an unusual way. User
• [spctools-discuss] PTM prophet and DiMethylation Oded
  • Re: [spctools-discuss] PTM prophet and DiMethylation David Shteynberg
  • Re: [spctools-discuss] PTM prophet and DiMethylation [email protected]
  • Re: [spctools-discuss] PTM prophet and DiMethylation Jesse Meyer
  • Re: [spctools-discuss] PTM prophet and DiMethylation David Shteynberg
  • Re: [spctools-discuss] PTM prophet and DiMethylation Jesse Meyer
  • Re: [spctools-discuss] PTM prophet and DiMethylation David Shteynberg
  • Re: [spctools-discuss] PTM prophet and DiMethylation David Shteynberg
  • Re: [spctools-discuss] PTM prophet and DiMethylation [email protected]
  • Re: [spctools-discuss] PTM prophet and DiMethylation Jesse
  • Re: [spctools-discuss] PTM prophet and DiMethylation David Shteynberg
  • Re: [spctools-discuss] PTM prophet and DiMethylation Jesse
  • Re: [spctools-discuss] PTM prophet and DiMethylation David Shteynberg
  • Re: [spctools-discuss] PTM prophet and DiMethylation Jesse
  • Re: [spctools-discuss] PTM prophet and DiMethylation David Shteynberg
• [spctools-discuss] TPP translation code is wrong. Rachel
  • Re: [spctools-discuss] TPP translation code is wrong. Luis Mendoza
  • Re: [spctools-discuss] TPP translation code is wrong. Jimmy Eng
  • [spctools-discuss] Re: TPP translation code is wrong. Rachel
• [spctools-discuss] PeptideProphet Libra analysis return code 65280 Chloe Chien
  • Re: [spctools-discuss] PeptideProphet Libra analysis return code 65280 Luis Mendoza
• [spctools-discuss] Generation of mzIdentML from TPP results Robert
  • Re: [spctools-discuss] Generation of mzIdentML from TPP results Joseph Slagel
  • Re: [spctools-discuss] Generation of mzIdentML from TPP results Robert Winkler
  • Re: [spctools-discuss] Generation of mzIdentML from TPP results Joseph Slagel
• [spctools-discuss] peptide prophet "read in no data" Delphine
  • Re: [spctools-discuss] peptide prophet "read in no data" David Shteynberg
  • Re: [spctools-discuss] peptide prophet "read in no data" David Shteynberg
  • Re: [spctools-discuss] peptide prophet "read in no data" delphine wood
  • RE: [spctools-discuss] peptide prophet "read in no data" Eric Deutsch
  • Re: [spctools-discuss] peptide prophet "read in no data" David Shteynberg
• [spctools-discuss] TPP @ ASMS -- booth # 5 Luis Mendoza
• [spctools-discuss] Thermo fusion data process zhangchengpu0203
  • Fwd: [spctools-discuss] Thermo fusion data process Hannes Röst
  • Re: Fwd: [spctools-discuss] Thermo fusion data process Chambers, Matthew
• [spctools-discuss] core dumped running PeptideProphet, TPP 4.7.1 AMI Krystalle S. Diaz
  • Re: [spctools-discuss] core dumped running PeptideProphet, TPP 4.7.1 AMI David Shteynberg
  • Re: [spctools-discuss] core dumped running PeptideProphet, TPP 4.7.1 AMI Krystalle S. Diaz
  • Re: [spctools-discuss] core dumped running PeptideProphet, TPP 4.7.1 AMI David Shteynberg
  • Re: [spctools-discuss] core dumped running PeptideProphet, TPP 4.7.1 AMI Krystalle S. Diaz
• [spctools-discuss] How to do Differential protein expression (DPE) analysis using Spectral counts (PSMs) for the whole bacterial proteome? Margarita Andreevskaya
• [spctools-discuss] Unknown data type when running Peptide Analysis Jorey Dong
• [spctools-discuss] Spectrast Tier-Wise Scoring Chris
  • [spctools-discuss] Re: Spectrast Tier-Wise Scoring Henry Lam
• [spctools-discuss] New tool to convert Proteome Discoverer (1.3 and above) MSF file(s) to the mzIdentML 1.1.0, pepXML and tabs-delimited-text format file(s) Paul Aiyetan
  • [spctools-discuss] Re: New tool to convert Proteome Discoverer (1.3 and above) MSF file(s) to the mzIdentML 1.1.0, pepXML and tabs-delimited-text format file(s) Delphine
  • [spctools-discuss] Re: New tool to convert Proteome Discoverer (1.3 and above) MSF file(s) to the mzIdentML 1.1.0, pepXML and tabs-delimited-text format file(s) apauls
• [spctools-discuss] PTMProphet workflow Chris
  • Re: [spctools-discuss] PTMProphet workflow David Shteynberg
  • Re: [spctools-discuss] PTMProphet workflow Chris
  • Re: [spctools-discuss] PTMProphet workflow David Shteynberg
• [spctools-discuss] Parallel InterProphet versus Combined InterProphet Chris
  • Re: [spctools-discuss] Parallel InterProphet versus Combined InterProphet David Shteynberg
  • Re: [spctools-discuss] Parallel InterProphet versus Combined InterProphet Chris
• [spctools-discuss] Client management in TPP Sebastian Wiese
  • Re: [spctools-discuss] Client management in TPP Brian Hampton
• [spctools-discuss] SpectraST Krishan Kumar
  • Re: [spctools-discuss] SpectraST Hannes Röst
  • [spctools-discuss] SpectraST Genet
  • [spctools-discuss] SpectraST [email protected]
• [spctools-discuss] Re: How to use the TPP pipline with sequest searched results in html format Aprajita Gupta
  • Re: [spctools-discuss] Re: How to use the TPP pipline with sequest searched results in html format Goran Mitulović
• [spctools-discuss] Next TPP course Sep 30 - Oct 3 in Madrid, Spain: pre-registration is open! Eric Deutsch
• [spctools-discuss] A question about Mayu. 钟传奇
  • Re: [spctools-discuss] A question about Mayu. David Shteynberg
  • Re: [spctools-discuss] A question about Mayu. 钟传奇
  • Re: [spctools-discuss] A question about Mayu. David Shteynberg
• [spctools-discuss] TTP Libra for iTRAQ quantification Bo
  • Re: [spctools-discuss] TTP Libra for iTRAQ quantification Luis Mendoza
  • Re: [spctools-discuss] TTP Libra for iTRAQ quantification Bo
  • Re: [spctools-discuss] TTP Libra for iTRAQ quantification SS
  • Re: [spctools-discuss] TTP Libra for iTRAQ quantification Luis Mendoza
  • Re: [spctools-discuss] TTP Libra for iTRAQ quantification SS
• [spctools-discuss] TPP 4.7.1 Release is now available Joseph Slagel
• [spctools-discuss] qualscore Philipp Lange
• [spctools-discuss] TPP 4.7.0 installation problems on Ubuntu 14.04 Will Fondrie
  • Re: [spctools-discuss] TPP 4.7.0 installation problems on Ubuntu 14.04 Joseph Slagel
  • Re: [spctools-discuss] TPP 4.7.0 installation problems on Ubuntu 14.04 Will Fondrie
  • Re: [spctools-discuss] TPP 4.7.0 installation problems on Ubuntu 14.04 Will Fondrie
  • [spctools-discuss] Re: TPP 4.7.0 installation problems on Ubuntu 14.04 ChargedPeptide
  • [spctools-discuss] Re: TPP 4.7.0 installation problems on Ubuntu 14.04 Robert
  • Re: [spctools-discuss] Re: TPP 4.7.0 installation problems on Ubuntu 14.04 Joseph Slagel
  • Re: [spctools-discuss] Re: TPP 4.7.0 installation problems on Ubuntu 14.04 Robert Winkler
  • Re: [spctools-discuss] Re: TPP 4.7.0 installation problems on Ubuntu 14.04 Joseph Slagel
  • Re: [spctools-discuss] Re: TPP 4.7.0 installation problems on Ubuntu 14.04 Brian Hampton
  • [spctools-discuss] Re: TPP 4.7.0 installation problems on Ubuntu 14.04 MD
• Re: [spctools-discuss] idconverter (prot/pepxml to mzid): Problems with TPP George Rosenberger
  • Re: [spctools-discuss] idconverter (prot/pepxml to mzid): Problems with TPP wlstraube
• [spctools-discuss] Constructing a synthetic 13C or 15N SpetraST library. Vadim Patsalo
• [spctools-discuss] Definition of the N-glyco model Ruby
  • Re: [spctools-discuss] Definition of the N-glyco model David Shteynberg
• [spctools-discuss] Tandem2XML warning message - WARNING: Multiple variable modifications on Q for scan 6605. wlstraube
• [spctools-discuss] TPP translation code Rachel
  • Re: [spctools-discuss] TPP translation code Hannes Röst
  • Re: [spctools-discuss] TPP translation code Jimmy Eng
• [spctools-discuss] Extract UV data Eva B
• [spctools-discuss] ROC figure problem Bo
  • Re: [spctools-discuss] ROC figure problem David Shteynberg
  • Re: [spctools-discuss] ROC figure problem Bo
  • Re: [spctools-discuss] ROC figure problem Bo
• [spctools-discuss] Can XInteract export XML result with FDR at unique peptide level? 李桂林
• [spctools-discuss] FDR calculation in TPP Bo
  • Re: [spctools-discuss] FDR calculation in TPP Hannes Röst
  • [spctools-discuss] Re: FDR calculation in TPP Bjorn
  • Re: [spctools-discuss] Re: FDR calculation in TPP David Shteynberg
  • Re: [spctools-discuss] Re: FDR calculation in TPP Bo
  • [spctools-discuss] Re: FDR calculation in TPP Bo
• [spctools-discuss] label-free quantification Rachel
  • Re: [spctools-discuss] label-free quantification Punit Kadimi
  • Re: [spctools-discuss] label-free quantification Hannes Röst
• [spctools-discuss] X!Tandem search using Petunia in Windows Will Fondrie
  • Re: [spctools-discuss] X!Tandem search using Petunia in Windows David Shteynberg
  • Re: [spctools-discuss] X!Tandem search using Petunia in Windows Will Fondrie
• [spctools-discuss] Peptides identified without the fixed modification C57 - carbamidomethylation Ruby
  • Re: [spctools-discuss] Peptides identified without the fixed modification C57 - carbamidomethylation David Shteynberg
• [spctools-discuss] Can fval value produced by Prophet be used to calculate FDR? liguilin223
• [spctools-discuss] Sqt2XML error Will Fondrie
  • Re: [spctools-discuss] Sqt2XML error David Shteynberg
  • Re: [spctools-discuss] Sqt2XML error Will Fondrie
  • Re: [spctools-discuss] Sqt2XML error David Shteynberg
  • Re: [spctools-discuss] Sqt2XML error Will Fondrie
  • Re: [spctools-discuss] Sqt2XML error Jimmy Eng
  • Re: [spctools-discuss] Sqt2XML error David Shteynberg
  • Re: [spctools-discuss] Sqt2XML error Jimmy Eng
  • [spctools-discuss] Re: Sqt2XML error tonikoller
  • [spctools-discuss] Re: Sqt2XML error Will Fondrie
  • [spctools-discuss] Re: Sqt2XML error tonikoller
• [spctools-discuss] TPP 4.7 and ASAPRatio problem Brian Hampton
  • Re: [spctools-discuss] TPP 4.7 and ASAPRatio problem David Shteynberg
• [spctools-discuss] TPP funding from NIGMS Eric Deutsch
  • Re: [spctools-discuss] TPP funding from NIGMS Robert Winkler
  • Re: [spctools-discuss] TPP funding from NIGMS Rebekah Dawson
• [spctools-discuss] Using new version of Comet with TPP Brian Hampton
  • Re: [spctools-discuss] Using new version of Comet with TPP Joseph Slagel
  • Re: [spctools-discuss] Using new version of Comet with TPP Luis Mendoza
  • Re: [spctools-discuss] Using new version of Comet with TPP Brian Hampton
• [spctools-discuss] Error combining multiple pepXML files with ProteinProphet command v4.7.0 GATTACA
  • Re: [spctools-discuss] Error combining multiple pepXML files with ProteinProphet command v4.7.0 David Shteynberg
  • Re: [spctools-discuss] Error combining multiple pepXML files with ProteinProphet command v4.7.0 Damian
  • Re: [spctools-discuss] Error combining multiple pepXML files with ProteinProphet command v4.7.0 Ruby
• [spctools-discuss] Can PeptideProphet and iProphet succeed with few matched decoys? Vadim Patsalo
  • Re: [spctools-discuss] Can PeptideProphet and iProphet succeed with few matched decoys? Hannes Röst
  • Re: [spctools-discuss] Can PeptideProphet and iProphet succeed with few matched decoys? Vadim Patsalo
  • Re: [spctools-discuss] Can PeptideProphet and iProphet succeed with few matched decoys? Hannes Röst
  • RE: [spctools-discuss] Can PeptideProphet and iProphet succeed with few matched decoys? Eric Deutsch
  • Re: [spctools-discuss] Can PeptideProphet and iProphet succeed with few matched decoys? Hannes Röst

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