Literature DB >> 19129212

Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data.

Nils Gehlenborg1, Wei Yan, Inyoul Y Lee, Hyuntae Yoo, Kay Nieselt, Daehee Hwang, Ruedi Aebersold, Leroy Hood.   

Abstract

SUMMARY: We describe an integrative software platform, Prequips, for comparative proteomics-based systems biology analysis that: (i) integrates all information generated from mass spectrometry (MS)-based proteomics as well as from basic proteomics data analysis tools, (ii) visualizes such information for various proteomic analyses via graphical interfaces and (iii) links peptide and protein abundances to external tools often used in systems biology studies. AVAILABILITY: http://prequips.sourceforge.net

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Year:  2009        PMID： 19129212      PMCID： PMC2720692          DOI： 10.1093/bioinformatics/btp005

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  6 in total

1.  TM4: a free, open-source system for microarray data management and analysis.

Authors:  A I Saeed; V Sharov; J White; J Li; W Liang; N Bhagabati; J Braisted; M Klapa; T Currier; M Thiagarajan; A Sturn; M Snuffin; A Rezantsev; D Popov; A Ryltsov; E Kostukovich; I Borisovsky; Z Liu; A Vinsavich; V Trush; J Quackenbush
Journal:  Biotechniques       Date:  2003-02       Impact factor: 1.993

2.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Authors:  Andrew Keller; Alexey I Nesvizhskii; Eugene Kolker; Ruedi Aebersold
Journal:  Anal Chem       Date:  2002-10-15       Impact factor: 6.986

3.  A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry.

Authors:  Xiao-jun Li; Patrick G A Pedrioli; Jimmy Eng; Dan Martin; Eugene C Yi; Hookeun Lee; Ruedi Aebersold
Journal:  Anal Chem       Date:  2004-07-01       Impact factor: 6.986

4.  An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures.

Authors:  Alexander Schmidt; Nils Gehlenborg; Bernd Bodenmiller; Lukas N Mueller; Dave Campbell; Markus Mueller; Ruedi Aebersold; Bruno Domon
Journal:  Mol Cell Proteomics       Date:  2008-05-29       Impact factor: 5.911

5.  The Gaggle: an open-source software system for integrating bioinformatics software and data sources.

Authors:  Paul T Shannon; David J Reiss; Richard Bonneau; Nitin S Baliga
Journal:  BMC Bioinformatics       Date:  2006-03-28       Impact factor: 3.169

6.  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
  6 in total
  4 in total

1.  GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data.

Authors:  Kristoffer T G Rigbolt; Jens T Vanselow; Blagoy Blagoev
Journal:  Mol Cell Proteomics       Date:  2011-05-20       Impact factor: 5.911

2.  The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases.

Authors:  Nils Gehlenborg; Daehee Hwang; Inyoul Y Lee; Hyuntae Yoo; David Baxter; Brianne Petritis; Rose Pitstick; Bruz Marzolf; Stephen J Dearmond; George A Carlson; Leroy Hood
Journal:  Database (Oxford)       Date:  2009-09-17       Impact factor: 3.451

3.  MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data.

Authors:  Tomás Pluskal; Sandra Castillo; Alejandro Villar-Briones; Matej Oresic
Journal:  BMC Bioinformatics       Date:  2010-07-23       Impact factor: 3.169

4.  ePlant and the 3D data display initiative: integrative systems biology on the world wide web.

Authors:  Geoffrey Fucile; David Di Biase; Hardeep Nahal; Garon La; Shokoufeh Khodabandeh; Yani Chen; Kante Easley; Dinesh Christendat; Lawrence Kelley; Nicholas J Provart
Journal:  PLoS One       Date:  2011-01-10       Impact factor: 3.240
  4 in total

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