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• • Re: [spctools-discuss] TPP installation failure in RHEL 7.4 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] TPP installation failure in RHEL 7.4 Jai Ganesh
  • Re: [spctools-discuss] TPP installation failure in RHEL 7.4 'David Shteynberg' via spctools-discuss
• RE: [spctools-discuss] Questions about spectral library generation different search engines and shared peptides Eric Deutsch
  • Re: [spctools-discuss] Questions about spectral library generation different search engines and shared peptides Nikita Boeren
• [spctools-discuss] Combination of consensus libraries and import in MRM format via spectraST Kristina Plate
  • RE: [spctools-discuss] Combination of consensus libraries and import in MRM format via spectraST Eric Deutsch
  • Re: [spctools-discuss] Combination of consensus libraries and import in MRM format via spectraST Kristina Plate
  • RE: [spctools-discuss] Combination of consensus libraries and import in MRM format via spectraST Eric Deutsch
  • Re: [spctools-discuss] Combination of consensus libraries and import in MRM format via spectraST Kristina Plate
  • RE: [spctools-discuss] Combination of consensus libraries and import in MRM format via spectraST Eric Deutsch
  • Re: [spctools-discuss] Combination of consensus libraries and import in MRM format via spectraST Kristina Plate
• [spctools-discuss] Kojak + PeptideProphet FDR cutoff Thomas Gossenreiter
  • Re: [spctools-discuss] Kojak + PeptideProphet FDR cutoff 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] Kojak + PeptideProphet FDR cutoff Thomas Gossenreiter
  • Re: [spctools-discuss] Kojak + PeptideProphet FDR cutoff Thomas Gossenreiter
  • Re: [spctools-discuss] Kojak + PeptideProphet FDR cutoff 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] Kojak + PeptideProphet FDR cutoff Thomas Gossenreiter
• [spctools-discuss] Best itraq quantification method using Fusion Lifu Sheng
  • [spctools-discuss] Re: Best itraq quantification method using Fusion Phillip Wilmarth
• Re: [spctools-discuss] PeptideProphet - Kojak 1.5.5 vs. 1.6.1 David Shteynberg
  • Re: [spctools-discuss] PeptideProphet - Kojak 1.5.5 vs. 1.6.1 Thomas Gossenreiter
  • Re: [spctools-discuss] PeptideProphet - Kojak 1.5.5 vs. 1.6.1 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] PeptideProphet - Kojak 1.5.5 vs. 1.6.1 Thomas Gossenreiter
  • Re: [spctools-discuss] PeptideProphet - Kojak 1.5.5 vs. 1.6.1 'Michael Hoopmann' via spctools-discuss
  • Re: [spctools-discuss] PeptideProphet - Kojak 1.5.5 vs. 1.6.1 'David Shteynberg' via spctools-discuss
  • Re: [spctools-discuss] PeptideProphet - Kojak 1.5.5 vs. 1.6.1 Thomas Gossenreiter
• [spctools-discuss] Double or sequential digest using Kojak in combination with PeptideProphet nzsuzsanna
  • Re: [spctools-discuss] Double or sequential digest using Kojak in combination with PeptideProphet Michael Hoopmann
  • Re: [spctools-discuss] Double or sequential digest using Kojak in combination with PeptideProphet nzsuzsanna
• [spctools-discuss] What happens during consensus building? Kristina Plate
  • [spctools-discuss] Re: What happens during consensus building? Kristina Plate
• [spctools-discuss] How to quantify proteins using St Peter? Debangana Chakravorty
  • [spctools-discuss] How to quantify proteins using St Peter? Jason Winget
• [spctools-discuss] problem installing TPP 5.2 on CentOS Linux release 7.3.1611 smdb
  • Re: [spctools-discuss] problem installing TPP 5.2 on CentOS Linux release 7.3.1611 David Shteynberg
  • Re: [spctools-discuss] problem installing TPP 5.2 on CentOS Linux release 7.3.1611 smdb
  • Re: [spctools-discuss] problem installing TPP 5.2 on CentOS Linux release 7.3.1611 smdb
  • Re: [spctools-discuss] problem installing TPP 5.2 on CentOS Linux release 7.3.1611 Shagun Gupta
  • [spctools-discuss] Re: problem installing TPP 5.2 on CentOS Linux release 7.3.1611 smdb
• [spctools-discuss] xinteract exited with non-zero exit code: 139 [stuck on PeptideProphetParser command] sangramjit basu
  • Re: [spctools-discuss] xinteract exited with non-zero exit code: 139 [stuck on PeptideProphetParser command] David Shteynberg
• [spctools-discuss] Comet2018+PTMProphet Janel
  • Re: [spctools-discuss] Comet2018+PTMProphet David Shteynberg
  • Re: [spctools-discuss] Comet2018+PTMProphet Janel Beckley
  • Re: [spctools-discuss] Comet2018+PTMProphet David Shteynberg
  • Re: [spctools-discuss] Comet2018+PTMProphet Janel Beckley
• [spctools-discuss] Problems installing TPP 5.2.0 sangramjit basu
• [spctools-discuss] iRT calculation in existing library via import Kristina Plate
• [spctools-discuss] Problem installing TPP 5.2.0 in Fedora (Red Hat Enterprise Linux Server 7.6) sangramjit basu
  • [spctools-discuss] Re: Problem installing TPP 5.2.0 in Fedora (Red Hat Enterprise Linux Server 7.6) Jimmy Eng
  • [spctools-discuss] Re: Problem installing TPP 5.2.0 in Fedora (Red Hat Enterprise Linux Server 7.6) sangramjit basu
• [spctools-discuss] X!Tandem search failed in TPP v5.0.0 sudip ghosh
• [spctools-discuss] X!Tandem search fails in TPP 5.0.0 sudip ghosh
  • Re: [spctools-discuss] X!Tandem search fails in TPP 5.0.0 David Shteynberg
  • Re: [spctools-discuss] X!Tandem search fails in TPP 5.0.0 sudip ghosh
• Re: [spctools-discuss] TPP SpectraST Failed to open input file David Shteynberg
• [spctools-discuss] problem to install TPP 5.2.0 Virginie Imbault
  • RE: [spctools-discuss] problem to install TPP 5.2.0 Eric Deutsch
  • [spctools-discuss] Re: problem to install TPP 5.2.0 'Lars Brinkmann' via spctools-discuss
• [spctools-discuss] Upcoming Trans-Proteomic Pipeline (TPP) courses Eric Deutsch
  • [spctools-discuss] Upcoming Trans-Proteomic Pipeline (TPP) courses 'Eric Deutsch' via spctools-discuss
• [spctools-discuss] Whether PeptideProphet tool can be used to validate the PSM identified with different algorithm other than SEQUEST, TANDEM, COMET etc.. Sangeetha R
• Re: [spctools-discuss] RefreshParser within xinteract unable to find all proteins corresponding to identified peptides Jimmy Eng
  • Re: [spctools-discuss] RefreshParser within xinteract unable to find all proteins corresponding to identified peptides Vidya Venkatraman
  • Re: [spctools-discuss] RefreshParser within xinteract unable to find all proteins corresponding to identified peptides Jimmy Eng
  • Re: [spctools-discuss] RefreshParser within xinteract unable to find all proteins corresponding to identified peptides Vidya Venkatraman
• [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 Alejandro
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 David Shteynberg
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 Alejandro
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 David Shteynberg
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 David Shteynberg
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 David Shteynberg
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 David Shteynberg
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 Alejandro
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 David Shteynberg
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 Alejandro
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 David Shteynberg
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 Alejandro
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 David Shteynberg
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 Alejandro
  • Re: [spctools-discuss] iProphet failing when combining Comet and MSGF in TPP 5.2 using Ubuntu 18.04 David Shteynberg
• [spctools-discuss] TPP @ ASMS 2019 -- booth #118 + Tuesday Workshop Luis Mendoza
• [spctools-discuss] Libra qunatification error in window version 10 Syed Azmal Ali
• [spctools-discuss] TPP 5.2 compile error Ubuntu 18.04 Alejandro
  • RE: [spctools-discuss] TPP 5.2 compile error Ubuntu 18.04 Eric Deutsch
  • Re: [spctools-discuss] TPP 5.2 compile error Ubuntu 18.04 Alejandro
  • Re: [spctools-discuss] TPP 5.2 compile error Ubuntu 18.04 Alejandro
• [spctools-discuss] update iRT in an existing .splib library Matthew Russell
  • [spctools-discuss] Re: update iRT in an existing .splib library Henry Lam
  • Re: [spctools-discuss] Re: update iRT in an existing .splib library Matthew Russell
  • Re: [spctools-discuss] Re: update iRT in an existing .splib library Henry Lam
  • Re: [spctools-discuss] Re: update iRT in an existing .splib library Matthew Russell
  • Re: [spctools-discuss] Re: update iRT in an existing .splib library Matthew Russell
• [spctools-discuss] Error spectrast create mode Lei Wang
  • [spctools-discuss] Re: Error spectrast create mode smdb
  • [spctools-discuss] Re: Error spectrast create mode smdb
• [spctools-discuss] Comet search for two constant modification on one amino acid Kamal Mandal
• [spctools-discuss] Xtandem searches crash and unable to kill command Valdemir Melechco Carvalho
  • [spctools-discuss] Re: Xtandem searches crash and unable to kill command Valdemir Melechco Carvalho
• [spctools-discuss] TPP 5.2 Compile Error Dean
  • Re: [spctools-discuss] TPP 5.2 Compile Error David Shteynberg
  • Re: [spctools-discuss] TPP 5.2 Compile Error Dean
• [spctools-discuss] Processing an Output from StPeter in MSstats Dmytro Morderer
• [spctools-discuss] Combining the DIA Umpire results by iProphet Ankit Balhara
  • [spctools-discuss] Re: Combining the DIA Umpire results by iProphet Felipe da Veiga Leprevost
  • Re: [spctools-discuss] Re: Combining the DIA Umpire results by iProphet Ankit Balhara
  • Re: [spctools-discuss] Re: Combining the DIA Umpire results by iProphet David Shteynberg
  • RE: [EXT] Re: [spctools-discuss] Re: Combining the DIA Umpire results by iProphet Noel Carter
  • Re: [spctools-discuss] Re: Combining the DIA Umpire results by iProphet Ankit Balhara
  • Re: [spctools-discuss] Re: Combining the DIA Umpire results by iProphet ilya gertsman
  • RE: [spctools-discuss] Re: Combining the DIA Umpire results by iProphet Eric Deutsch
  • Re: [spctools-discuss] Re: Combining the DIA Umpire results by iProphet Alexey Nesvizhskii
• [spctools-discuss] xinteract TPP v5.2.0 - exited with non-zero exit code: 139 Elva Liu
• [spctools-discuss] StPeter SIn displays all --n/a-- in protXML viewer (TPP v. 5.2.0) Jason Winget
  • [spctools-discuss] Re: StPeter SIn displays all --n/a-- in protXML viewer (TPP v. 5.2.0) Jason Winget
  • RE: [spctools-discuss] Re: StPeter SIn displays all --n/a-- in protXML viewer (TPP v. 5.2.0) Eric Deutsch
  • Re: [spctools-discuss] Re: StPeter SIn displays all --n/a-- in protXML viewer (TPP v. 5.2.0) Jason
  • Re: [spctools-discuss] Re: StPeter SIn displays all --n/a-- in protXML viewer (TPP v. 5.2.0) Luis Mendoza
  • Re: [spctools-discuss] Re: StPeter SIn displays all --n/a-- in protXML viewer (TPP v. 5.2.0) Luis Mendoza
  • Re: [spctools-discuss] Re: StPeter SIn displays all --n/a-- in protXML viewer (TPP v. 5.2.0) Jason
• [spctools-discuss] PeptideProphet scores Felipe da Veiga Leprevost
  • Re: [spctools-discuss] PeptideProphet scores David Shteynberg
• [spctools-discuss] PTMProphet 5.2.0. error Felipe da Veiga Leprevost
  • Re: [spctools-discuss] PTMProphet 5.2.0. error David Shteynberg
  • Re: [spctools-discuss] PTMProphet 5.2.0. error Felipe da Veiga Leprevost
  • Re: [spctools-discuss] PTMProphet 5.2.0. error David Shteynberg
  • Re: [spctools-discuss] PTMProphet 5.2.0. error Felipe da Veiga Leprevost
  • Re: [spctools-discuss] PTMProphet 5.2.0. error Felipe da Veiga Leprevost
  • Re: [spctools-discuss] PTMProphet 5.2.0. error David Shteynberg
  • Re: [spctools-discuss] PTMProphet 5.2.0. error Felipe da Veiga Leprevost
• [spctools-discuss] Combining the data on two tissues in one library Ankit Balhara
  • RE: [spctools-discuss] Combining the data on two tissues in one library Eric Deutsch
  • Re: [spctools-discuss] Combining the data on two tissues in one library Ankit Balhara
• [spctools-discuss] TPP 5.2.0 Release is now available Luis Mendoza
• [spctools-discuss] Re: TPP Comet Peptide Prophet Error [email protected]
• [spctools-discuss] TPP 5.1.0 installation and Perl Amit Yadav
• [spctools-discuss] peptideprophet does not produce valid pepXML, but iprophet does Michael Riffle
  • Re: [spctools-discuss] peptideprophet does not produce valid pepXML, but iprophet does David Shteynberg
  • Re: [spctools-discuss] peptideprophet does not produce valid pepXML, but iprophet does Michael Riffle
  • Re: [spctools-discuss] peptideprophet does not produce valid pepXML, but iprophet does David Shteynberg
• RE: [spctools-discuss] StPeter ERROR: Unknown modification: C[158] Michael Hoopmann
  • Re: [spctools-discuss] StPeter ERROR: Unknown modification: C[158] Goutham Vasam
  • Re: [spctools-discuss] StPeter ERROR: Unknown modification: C[158] Luis Mendoza
• [spctools-discuss] Warning message during the peptideprophet analysis Ankit Balhara
  • Re: [spctools-discuss] Warning message during the peptideprophet analysis Jesse Meyer
  • Re: [spctools-discuss] Warning message during the peptideprophet analysis Ankit Balhara
  • Re: [spctools-discuss] Warning message during the peptideprophet analysis Jesse Meyer
  • Re: [spctools-discuss] Warning message during the peptideprophet analysis Ankit Balhara
• [spctools-discuss] mzXML - peak encoding/decoding jeffreyavansanten
  • RE: [spctools-discuss] mzXML - peak encoding/decoding Eric Deutsch
• [spctools-discuss] Quantic vs St. Peter Hampton, Brian
• [spctools-discuss] RefreshParser reports number of unmapped entries - why are there unmapped entries? Hampton, Brian
  • Re: [spctools-discuss] RefreshParser reports number of unmapped entries - why are there unmapped entries? David Shteynberg
  • Re: [spctools-discuss] RefreshParser reports number of unmapped entries - why are there unmapped entries? Hampton, Brian
  • Re: [spctools-discuss] RefreshParser reports number of unmapped entries - why are there unmapped entries? David Shteynberg
  • Re: [spctools-discuss] RefreshParser reports number of unmapped entries - why are there unmapped entries? Hampton, Brian
• [spctools-discuss] Problem during spectrast library generation Ankit Balhara
  • RE: [spctools-discuss] Problem during spectrast library generation Eric Deutsch
  • Re: [spctools-discuss] Problem during spectrast library generation Ankit Balhara
  • RE: [spctools-discuss] Problem during spectrast library generation Eric Deutsch
  • [spctools-discuss] Re: Problem during spectrast library generation Ankit Balhara
• [spctools-discuss] A question about the Mayu Ankit Balhara
• [spctools-discuss] Problem analyzing MS-GF+ data using peptideprophet tool of TPP GUI- Petunia Ankit Balhara
  • [spctools-discuss] Re: Problem analyzing MS-GF+ data using peptideprophet tool of TPP GUI- Petunia Alejandro
  • Re: [spctools-discuss] Re: Problem analyzing MS-GF+ data using peptideprophet tool of TPP GUI- Petunia Ankit Balhara
• [spctools-discuss] Anlaysis of MS-GF+ data using Peptideprophet tool of TPP GUI "Petunia" Ankit Balhara
• [spctools-discuss] xsl file not being created Bronson Petterson
  • [spctools-discuss] Re: xsl file not being created Jimmy Eng
• [spctools-discuss] Re: A question about ProteinProphet Le ZHENG
• [spctools-discuss] Libra quantification for TMT 11-plex Rachel Nadeau
  • Re: [spctools-discuss] Libra quantification for TMT 11-plex Luis Mendoza
• [spctools-discuss] some questions: model failure, parametric vs semi-parametric, same search engine but different parameters, function of scripts alastair.skeffington via spctools-discuss
  • Re: [spctools-discuss] some questions: model failure, parametric vs semi-parametric, same search engine but different parameters, function of scripts David Shteynberg
• [spctools-discuss] Re: External Tools Export mzIdentML [email protected]
  • RE: [spctools-discuss] Re: External Tools Export mzIdentML Eric Deutsch
• [spctools-discuss] Failed in running ASAPRatio Ruifeng Hu
  • Re: [spctools-discuss] Failed in running ASAPRatio Ruifeng Hu
  • Re: [spctools-discuss] Failed in running ASAPRatio David Shteynberg
  • Re: [spctools-discuss] Failed in running ASAPRatio David Shteynberg
• [spctools-discuss] root in TPP docker image 16899d782bad on Win 10? Robert
  • RE: [spctools-discuss] root in TPP docker image 16899d782bad on Win 10? Eric Deutsch
• [spctools-discuss] simple text editor for TPP 5.2 docker? Robert
  • RE: [spctools-discuss] simple text editor for TPP 5.2 docker? Eric Deutsch
• [spctools-discuss] working with replicate data and 15N labelled proteins Gunjan Pandey
• [spctools-discuss] How to set number of cores/threads/RAM in TPP Gunjan Pandey
  • RE: [spctools-discuss] How to set number of cores/threads/RAM in TPP Eric Deutsch
  • Re: [spctools-discuss] How to set number of cores/threads/RAM in TPP Gunjan Pandey
• [spctools-discuss] TPP 5.2 ProteinProphet WARNING: Trying to compute mass of non-residue: Robert
  • RE: [spctools-discuss] TPP 5.2 ProteinProphet WARNING: Trying to compute mass of non-residue: Eric Deutsch
  • Re: [spctools-discuss] TPP 5.2 ProteinProphet WARNING: Trying to compute mass of non-residue: Robert Winkler
  • Re: [spctools-discuss] TPP 5.2 ProteinProphet WARNING: Trying to compute mass of non-residue: David Shteynberg
  • Re: [spctools-discuss] TPP 5.2 ProteinProphet WARNING: Trying to compute mass of non-residue: Robert
  • Re: [spctools-discuss] TPP 5.2 ProteinProphet WARNING: Trying to compute mass of non-residue: Robert
• [spctools-discuss] Linux version of TPP Kamal Mandal
  • RE: [spctools-discuss] Linux version of TPP Eric Deutsch
  • Re: [spctools-discuss] Linux version of TPP Kamal Mandal
  • RE: [spctools-discuss] Linux version of TPP Eric Deutsch
  • Re: [spctools-discuss] Linux version of TPP Kamal Mandal
  • Re: [spctools-discuss] Linux version of TPP Kamal Mandal

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