Literature DB >> 18805798

MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis.

Daehee Hwang1, Ning Zhang, Hookeun Lee, Eugene Yi, Hui Zhang, Inyoul Y Lee, Leroy Hood, Ruedi Aebersold.   

Abstract

UNLABELLED: MS-BID (MS Biomarker Discovery Platform) is an integrative computational pipeline for biomarker discovery using LC-MS-based comparative proteomic analysis. This platform consists of several computational tools for: (i) detecting peptides in the collected patterns; (ii) matching detected peptides across a number of LC-MS datasets and (iii) selecting discriminatory peptides between classes of samples. AVAILABILITY: MS-BID source codes, binaries and documentations are freely available under LGPL from http://tools.proteomecenter.org/msBID.php.

Mesh：

Year:  2008        PMID： 18805798      PMCID： PMC2579714          DOI： 10.1093/bioinformatics/btn491

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


  5 in total

Review 1.  Mass spectrometry-based proteomics.

Authors:  Ruedi Aebersold; Matthias Mann
Journal:  Nature       Date:  2003-03-13       Impact factor: 49.962

2.  The human plasma proteome: a nonredundant list developed by combination of four separate sources.

Authors:  N Leigh Anderson; Malu Polanski; Rembert Pieper; Tina Gatlin; Radhakrishna S Tirumalai; Thomas P Conrads; Timothy D Veenstra; Joshua N Adkins; Joel G Pounds; Richard Fagan; Anna Lobley
Journal:  Mol Cell Proteomics       Date:  2004-01-12       Impact factor: 5.911

3.  A data integration methodology for systems biology.

Authors:  Daehee Hwang; Alistair G Rust; Stephen Ramsey; Jennifer J Smith; Deena M Leslie; Andrea D Weston; Pedro de Atauri; John D Aitchison; Leroy Hood; Andrew F Siegel; Hamid Bolouri
Journal:  Proc Natl Acad Sci U S A       Date:  2005-11-21       Impact factor: 11.205

4.  SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling.

Authors:  Lukas N Mueller; Oliver Rinner; Alexander Schmidt; Simon Letarte; Bernd Bodenmiller; Mi-Youn Brusniak; Olga Vitek; Ruedi Aebersold; Markus Müller
Journal:  Proteomics       Date:  2007-10       Impact factor: 3.984

5.  A common open representation of mass spectrometry data and its application to proteomics research.

Authors:  Patrick G A Pedrioli; Jimmy K Eng; Robert Hubley; Mathijs Vogelzang; Eric W Deutsch; Brian Raught; Brian Pratt; Erik Nilsson; Ruth H Angeletti; Rolf Apweiler; Kei Cheung; Catherine E Costello; Henning Hermjakob; Sequin Huang; Randall K Julian; Eugene Kapp; Mark E McComb; Stephen G Oliver; Gilbert Omenn; Norman W Paton; Richard Simpson; Richard Smith; Chris F Taylor; Weimin Zhu; Ruedi Aebersold
Journal:  Nat Biotechnol       Date:  2004-11       Impact factor: 54.908
  5 in total
  7 in total

1.  msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies.

Authors:  Berend Hoekman; Rainer Breitling; Frank Suits; Rainer Bischoff; Peter Horvatovich
Journal:  Mol Cell Proteomics       Date:  2012-02-07       Impact factor: 5.911

2.  Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data.

Authors:  Kang Ning; Damian Fermin; Alexey I Nesvizhskii
Journal:  J Proteome Res       Date:  2012-02-29       Impact factor: 4.466

Review 3.  Challenges and Opportunities for Bayesian Statistics in Proteomics.

Authors:  Oliver M Crook; Chun-Wa Chung; Charlotte M Deane
Journal:  J Proteome Res       Date:  2022-03-08       Impact factor: 4.466

4.  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

5.  Bioinformatics Tools for Mass Spectrometry-Based High-Throughput Quantitative Proteomics Platforms.

Authors:  Alexey V Nefedov; Miroslaw J Gilski; Rovshan G Sadygov
Journal:  Curr Proteomics       Date:  2011-07       Impact factor: 0.837

6.  VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

Authors:  Elena S Peterson; Lee Ann McCue; Alexandra C Schrimpe-Rutledge; Jeffrey L Jensen; Hyunjoo Walker; Markus A Kobold; Samantha R Webb; Samuel H Payne; Charles Ansong; Joshua N Adkins; William R Cannon; Bobbie-Jo M Webb-Robertson
Journal:  BMC Genomics       Date:  2012-04-05       Impact factor: 3.969

7.  PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use.

Authors:  Heidi Vähämaa; Ville R Koskinen; Waltteri Hosia; Robert Moulder; Olli S Nevalainen; Riitta Lahesmaa; Tero Aittokallio; Jussi Salmi
Journal:  Int J Proteomics       Date:  2011-04-19
  7 in total

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