Literature DB >> 25346941

M2Lite: An Open-source, Light-weight, Pluggable and Fast Proteome Discoverer MSF to mzIdentML Tool.

Paul Aiyetan1, Bai Zhang1, Lily Chen1, Zhen Zhang1, Hui Zhang1.   

Abstract

Proteome Discoverer is one of many tools used for protein database search and peptide to spectrum assignment in mass spectrometry-based proteomics. However, the inadequacy of conversion tools makes it challenging to compare and integrate its results to those of other analytical tools. Here we present M2Lite, an open-source, light-weight, easily pluggable and fast conversion tool. M2Lite converts proteome discoverer derived MSF files to the proteomics community defined standard - the mzIdentML file format. M2Lite's source code is available as open-source at https://bitbucket.org/paiyetan/m2lite/src and its compiled binaries and documentation can be freely downloaded at https://bitbucket.org/paiyetan/m2lite/downloads.

Entities:  

Keywords:  Bioinformatics; IDPicker; MSF; Peptide identification; Proteome Discoverer; Proteomics; mzIdentML; pepXML

Year:  2014        PMID： 25346941      PMCID： PMC4206089     

Source DB:  PubMed          Journal:  J Bioinform        ISSN： 2373-0196


  12 in total

1.  Probability-based protein identification by searching sequence databases using mass spectrometry data.

Authors:  D N Perkins; D J Pappin; D M Creasy; J S Cottrell
Journal:  Electrophoresis       Date:  1999-12       Impact factor: 3.535

2.  MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis.

Authors:  David L Tabb; Christopher G Fernando; Matthew C Chambers
Journal:  J Proteome Res       Date:  2007-02       Impact factor: 4.466

3.  mzML: a single, unifying data format for mass spectrometer output.

Authors:  Eric Deutsch
Journal:  Proteomics       Date:  2008-07       Impact factor: 3.984

Review 4.  Protein analysis by shotgun/bottom-up proteomics.

Authors:  Yaoyang Zhang; Bryan R Fonslow; Bing Shan; Moon-Chang Baek; John R Yates
Journal:  Chem Rev       Date:  2013-02-26       Impact factor: 60.622

5.  ProteoWizard: open source software for rapid proteomics tools development.

Authors:  Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick
Journal:  Bioinformatics       Date:  2008-07-07       Impact factor: 6.937

6.  The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Authors:  Gerhard Mayer; Luisa Montecchi-Palazzi; David Ovelleiro; Andrew R Jones; Pierre-Alain Binz; Eric W Deutsch; Matthew Chambers; Marius Kallhardt; Fredrik Levander; James Shofstahl; Sandra Orchard; Juan Antonio Vizcaíno; Henning Hermjakob; Christian Stephan; Helmut E Meyer; Martin Eisenacher
Journal:  Database (Oxford)       Date:  2013-03-12       Impact factor: 3.451

7.  IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.

Authors:  Ze-Qiang Ma; Surendra Dasari; Matthew C Chambers; Michael D Litton; Scott M Sobecki; Lisa J Zimmerman; Patrick J Halvey; Birgit Schilling; Penelope M Drake; Bradford W Gibson; David L Tabb
Journal:  J Proteome Res       Date:  2009-08       Impact factor: 4.466

8.  mzML--a community standard for mass spectrometry data.

Authors:  Lennart Martens; Matthew Chambers; Marc Sturm; Darren Kessner; Fredrik Levander; Jim Shofstahl; Wilfred H Tang; Andreas Römpp; Steffen Neumann; Angel D Pizarro; Luisa Montecchi-Palazzi; Natalie Tasman; Mike Coleman; Florian Reisinger; Puneet Souda; Henning Hermjakob; Pierre-Alain Binz; Eric W Deutsch
Journal:  Mol Cell Proteomics       Date:  2010-08-17       Impact factor: 5.911

9.  The mzIdentML data standard for mass spectrometry-based proteomics results.

Authors:  Andrew R Jones; Martin Eisenacher; Gerhard Mayer; Oliver Kohlbacher; Jennifer Siepen; Simon J Hubbard; Julian N Selley; Brian C Searle; James Shofstahl; Sean L Seymour; Randall Julian; Pierre-Alain Binz; Eric W Deutsch; Henning Hermjakob; Florian Reisinger; Johannes Griss; Juan Antonio Vizcaíno; Matthew Chambers; Angel Pizarro; David Creasy
Journal:  Mol Cell Proteomics       Date:  2012-02-27       Impact factor: 5.911

10.  A uniform proteomics MS/MS analysis platform utilizing open XML file formats.

Authors:  Andrew Keller; Jimmy Eng; Ning Zhang; Xiao-jun Li; Ruedi Aebersold
Journal:  Mol Syst Biol       Date:  2005-08-02       Impact factor: 11.429
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  2 in total

1.  XGlycScan: An Open-source Software For N-linked Glycosite Assignment, Quantification and Quality Assessment of Data from Mass Spectrometry-based Glycoproteomic Analysis.

Authors:  Paul Aiyetan; Bai Zhang; Zhen Zhang; Hui Zhang
Journal:  MOJ Proteom Bioinform       Date:  2014

Review 2.  Proteome Discoverer-A Community Enhanced Data Processing Suite for Protein Informatics.

Authors:  Benjamin C Orsburn
Journal:  Proteomes       Date:  2021-03-23
  2 in total

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