Literature DB >> 19309175

Software platform for rapidly creating computational tools for mass spectrometry-based proteomics.

Damon May1, Wendy Law, Matt Fitzgibbon, Qiaojun Fang, Martin McIntosh.   

Abstract

We describe and demonstrate the proteomics computational toolkit provided in the open-source msInspect software distribution. The toolkit includes modules written in Java and in the R statistical programming language to aid the rapid development of proteomics software applications. It contains tools for processing and manipulating standard MS data files, including signal processing of LC-MS data and parsing of MS/MS search results, as well as for modeling proteomics data structures, creating charts, and other common tasks. We present this toolkit's capability to rapidly develop new computational tools by presenting an example application, Qurate, a graphical tool for manually curating isotopically labeled peptide quantitative events.

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Year:  2009        PMID： 19309175      PMCID： PMC2696634          DOI： 10.1021/pr900169w

Source DB:  PubMed          Journal:  J Proteome Res        ISSN： 1535-3893            Impact factor:   4.466


  12 in total

1.  Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry.

Authors:  D K Han; J Eng; H Zhou; R Aebersold
Journal:  Nat Biotechnol       Date:  2001-10       Impact factor: 54.908

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 statistical model for identifying proteins by tandem mass spectrometry.

Authors:  Alexey I Nesvizhskii; Andrew Keller; Eugene Kolker; Ruedi Aebersold
Journal:  Anal Chem       Date:  2003-09-01       Impact factor: 6.986

4.  A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.

Authors:  Matthew Bellew; Marc Coram; Matthew Fitzgibbon; Mark Igra; Tim Randolph; Pei Wang; Damon May; Jimmy Eng; Ruihua Fang; Chenwei Lin; Jinzhi Chen; David Goodlett; Jeffrey Whiteaker; Amanda Paulovich; Martin McIntosh
Journal:  Bioinformatics       Date:  2006-06-09       Impact factor: 6.937

5.  General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.

Authors:  Brendan MacLean; Jimmy K Eng; Ronald C Beavis; Martin McIntosh
Journal:  Bioinformatics       Date:  2006-07-28       Impact factor: 6.937

6.  A platform for accurate mass and time analyses of mass spectrometry data.

Authors:  Damon May; Matt Fitzgibbon; Yan Liu; Ted Holzman; Jimmy Eng; C J Kemp; Jeff Whiteaker; Amanda Paulovich; Martin McIntosh
Journal:  J Proteome Res       Date:  2007-06-09       Impact factor: 4.466

7.  Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach.

Authors:  Ruihua Fang; Dwayne A Elias; Matthew E Monroe; Yufeng Shen; Martin McIntosh; Pei Wang; Carrie D Goddard; Stephen J Callister; Ronald J Moore; Yuri A Gorby; Joshua N Adkins; Jim K Fredrickson; Mary S Lipton; Richard D Smith
Journal:  Mol Cell Proteomics       Date:  2006-01-09       Impact factor: 5.911

8.  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

9.  Peptide sequence confidence in accurate mass and time analysis and its use in complex proteomics experiments.

Authors:  Damon May; Yan Liu; Wendy Law; Matt Fitzgibbon; Hong Wang; Samir Hanash; Martin McIntosh
Journal:  J Proteome Res       Date:  2008-12       Impact factor: 4.466

10.  MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.

Authors:  Daniel B Martin; Ted Holzman; Damon May; Amelia Peterson; Ashley Eastham; Jimmy Eng; Martin McIntosh
Journal:  Mol Cell Proteomics       Date:  2008-07-18       Impact factor: 5.911
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  15 in total

1.  A novel alignment method and multiple filters for exclusion of unqualified peptides to enhance label-free quantification using peptide intensity in LC-MS/MS.

Authors:  Xianyin Lai; Lianshui Wang; Haixu Tang; Frank A Witzmann
Journal:  J Proteome Res       Date:  2011-09-21       Impact factor: 4.466

2.  Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

Authors:  Anton A Goloborodko; Lev I Levitsky; Mark V Ivanov; Mikhail V Gorshkov
Journal:  J Am Soc Mass Spectrom       Date:  2013-01-05       Impact factor: 3.109

3.  Protein alterations associated with pancreatic cancer and chronic pancreatitis found in human plasma using global quantitative proteomics profiling.

Authors:  Sheng Pan; Ru Chen; David A Crispin; Damon May; Tyler Stevens; Martin W McIntosh; Mary P Bronner; Argyrios Ziogas; Hoda Anton-Culver; Teresa A Brentnall
Journal:  J Proteome Res       Date:  2011-03-28       Impact factor: 4.466

4.  Novel data analysis tool for semiquantitative LC-MS-MS2 profiling of N-glycans.

Authors:  Hannu Peltoniemi; Suvi Natunen; Ilja Ritamo; Leena Valmu; Jarkko Räbinä
Journal:  Glycoconj J       Date:  2012-06-17       Impact factor: 2.916

5.  Large-scale quantitative glycoproteomics analysis of site-specific glycosylation occupancy.

Authors:  Sheng Pan; Yasuko Tamura; Ru Chen; Damon May; Martin W McIntosh; Teresa A Brentnall
Journal:  Mol Biosyst       Date:  2012-08-14

6.  Identification and accurate quantitation of biological oligosaccharide mixtures.

Authors:  John S Strum; Jaehan Kim; Shuai Wu; Maria Lorna A De Leoz; Kyle Peacock; Rudolf Grimm; J Bruce German; David A Mills; Carlito B Lebrilla
Journal:  Anal Chem       Date:  2012-08-29       Impact factor: 6.986

7.  IsoQuant: a software tool for stable isotope labeling by amino acids in cell culture-based mass spectrometry quantitation.

Authors:  Zhongping Liao; Yunhu Wan; Stefani N Thomas; Austin J Yang
Journal:  Anal Chem       Date:  2012-05-03       Impact factor: 6.986

8.  SVM model for quality assessment of medium resolution mass spectra from 18O-water labeling experiments.

Authors:  Alexey V Nefedov; Miroslaw J Gilski; Rovshan G Sadygov
Journal:  J Proteome Res       Date:  2011-02-23       Impact factor: 4.466

9.  Association of Plasma CD163 Concentration with De Novo-Onset Chronic Graft-versus-Host Disease.

Authors:  Yoshihiro Inamoto; Paul J Martin; Sophie Paczesny; Laura Tabellini; Amin A Momin; Christen L Mumaw; Mary E D Flowers; Stephanie J Lee; Paul A Carpenter; Barry E Storer; Samir Hanash; John A Hansen
Journal:  Biol Blood Marrow Transplant       Date:  2017-04-25       Impact factor: 5.742

10.  WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis.

Authors:  Fan Mo; Qun Mo; Yuanyuan Chen; David R Goodlett; Leroy Hood; Gilbert S Omenn; Song Li; Biaoyang Lin
Journal:  BMC Bioinformatics       Date:  2010-04-29       Impact factor: 3.169
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