Literature DB >> 17545182

VIPER: an advanced software package to support high-throughput LC-MS peptide identification.

Matthew E Monroe1, Nikola Tolić, Navdeep Jaitly, Jason L Shaw, Joshua N Adkins, Richard D Smith.   

Abstract

SUMMARY: The accurate mass and time (AMT) tag approach is used for analysis of large scale experiments by combining information generated over multiple datasets and instrument types. The VIPER software package is one of the key components of the data processing pipeline and implements automated algorithms to discover LC-MS features, align and match these LC-MS features to a database of peptides previously identified in LC-MS/MS analyses, and identify and quantify pairs of isotopically labeled peptides. AVAILABILITY: VIPER may be downloaded free of charge at http://ncrr.pnl.gov/software/

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Year:  2007        PMID： 17545182     DOI： 10.1093/bioinformatics/btm281

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


  114 in total

1.  Proteomic analysis of bronchoalveolar lavage fluid proteins from mice infected with Francisella tularensis ssp. novicida.

Authors:  Susan M Varnum; Bobbie-Jo M Webb-Robertson; Joel G Pounds; Ronald J Moore; Richard D Smith; Charles W Frevert; Shawn J Skerrett; David Wunschel
Journal:  J Proteome Res       Date:  2012-06-22       Impact factor: 4.466

2.  BPDA - a Bayesian peptide detection algorithm for mass spectrometry.

Authors:  Youting Sun; Jianqiu Zhang; Ulisses Braga-Neto; Edward R Dougherty
Journal:  BMC Bioinformatics       Date:  2010-09-29       Impact factor: 3.169

3.  BPDA2d--a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry.

Authors:  Youting Sun; Jianqiu Zhang; Ulisses Braga-Neto; Edward R Dougherty
Journal:  Bioinformatics       Date:  2011-12-06       Impact factor: 6.937

4.  Machine learning based prediction for peptide drift times in ion mobility spectrometry.

Authors:  Anuj R Shah; Khushbu Agarwal; Erin S Baker; Mudita Singhal; Anoop M Mayampurath; Yehia M Ibrahim; Lars J Kangas; Matthew E Monroe; Rui Zhao; Mikhail E Belov; Gordon A Anderson; Richard D Smith
Journal:  Bioinformatics       Date:  2010-05-21       Impact factor: 6.937

5.  Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size.

Authors:  Haizhen Zhang; Kristin E Burnum; Maria L Luna; Brianne O Petritis; Jong-Seo Kim; Wei-Jun Qian; Ronald J Moore; Alejandro Heredia-Langner; Bobbie-Jo M Webb-Robertson; Brian D Thrall; David G Camp; Richard D Smith; Joel G Pounds; Tao Liu
Journal:  Proteomics       Date:  2011-11-04       Impact factor: 3.984

6.  Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content.

Authors:  Vladislav A Petyuk; Navdeep Jaitly; Ronald J Moore; Jie Ding; Thomas O Metz; Keqi Tang; Matthew E Monroe; Aleksey V Tolmachev; Joshua N Adkins; Mikhail E Belov; Alan R Dabney; Wei-Jun Qian; David G Camp; Richard D Smith
Journal:  Anal Chem       Date:  2007-12-29       Impact factor: 6.986

7.  The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates.

Authors:  Lily Khadempour; Kristin E Burnum-Johnson; Erin S Baker; Carrie D Nicora; Bobbie-Jo M Webb-Robertson; Richard A White; Matthew E Monroe; Eric L Huang; Richard D Smith; Cameron R Currie
Journal:  Mol Ecol       Date:  2016-10-26       Impact factor: 6.185

8.  Sources of technical variability in quantitative LC-MS proteomics: human brain tissue sample analysis.

Authors:  Paul D Piehowski; Vladislav A Petyuk; Daniel J Orton; Fang Xie; Ronald J Moore; Manuel Ramirez-Restrepo; Anzhelika Engel; Andrew P Lieberman; Roger L Albin; David G Camp; Richard D Smith; Amanda J Myers
Journal:  J Proteome Res       Date:  2013-04-10       Impact factor: 4.466

9.  Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments.

Authors:  Aleksey V Tolmachev; Matthew E Monroe; Samuel O Purvine; Ronald J Moore; Navdeep Jaitly; Joshua N Adkins; Gordon A Anderson; Richard D Smith
Journal:  Anal Chem       Date:  2008-10-15       Impact factor: 6.986

10.  Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions.

Authors:  Nathan P Manes; Ryan D Estep; Heather M Mottaz; Ronald J Moore; Therese R W Clauss; Matthew E Monroe; Xiuxia Du; Joshua N Adkins; Scott W Wong; Richard D Smith
Journal:  J Proteome Res       Date:  2008-01-19       Impact factor: 4.466
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