Literature DB >> 21075743

Analyzing marginal cases in differential shotgun proteomics.

Paulo C Carvalho1, Juliana S G Fischer, Jonas Perales, John R Yates, Valmir C Barbosa, Elias Bareinboim.   

Abstract

SUMMARY: We present an approach to statistically pinpoint differentially expressed proteins that have quantitation values near the quantitation threshold and are not identified in all replicates (marginal cases). Our method uses a Bayesian strategy to combine parametric statistics with an empirical distribution built from the reproducibility quality of the technical replicates. AVAILABILITY: The software is freely available for academic use at http://pcarvalho.com/patternlab.

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Year:  2010        PMID： 21075743      PMCID： PMC3018820          DOI： 10.1093/bioinformatics/btq632

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


  5 in total

1.  A model for random sampling and estimation of relative protein abundance in shotgun proteomics.

Authors:  Hongbin Liu; Rovshan G Sadygov; John R Yates
Journal:  Anal Chem       Date:  2004-07-15       Impact factor: 6.986

2.  Analyzing shotgun proteomic data with PatternLab for proteomics.

Authors:  Paulo C Carvalho; John R Yates Iii; Valmir C Barbosa
Journal:  Curr Protoc Bioinformatics       Date:  2010-06

3.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology.

Authors:  M P Washburn; D Wolters; J R Yates
Journal:  Nat Biotechnol       Date:  2001-03       Impact factor: 54.908

4.  Dynamic proteomic overview of glioblastoma cells (A172) exposed to perillyl alcohol.

Authors:  Juliana de Saldanha da Gama Fischer; Lujian Liao; Paulo C Carvalho; Valmir C Barbosa; Gilberto B Domont; Maria da Gloria da Costa Carvalho; John R Yates
Journal:  J Proteomics       Date:  2010-01-18       Impact factor: 4.044

5.  PatternLab for proteomics: a tool for differential shotgun proteomics.

Authors:  Paulo C Carvalho; Juliana S G Fischer; Emily I Chen; John R Yates; Valmir C Barbosa
Journal:  BMC Bioinformatics       Date:  2008-07-21       Impact factor: 3.169
  5 in total
  8 in total

1.  Evaluation of normalization methods on GeLC-MS/MS label-free spectral counting data to correct for variation during proteomic workflows.

Authors:  Emine Gokce; Christopher M Shuford; William L Franck; Ralph A Dean; David C Muddiman
Journal:  J Am Soc Mass Spectrom       Date:  2011-09-24       Impact factor: 3.109

2.  Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism.

Authors:  A Y Martinez-Sanguiné; B D'Alessandro; M Langleib; G M Traglia; A Mónaco; R Durán; J A Chabalgoity; L Betancor; L Yim
Journal:  Infect Immun       Date:  2021-02-16       Impact factor: 3.441

3.  Search engine processor: Filtering and organizing peptide spectrum matches.

Authors:  Paulo C Carvalho; Juliana S G Fischer; Tao Xu; Daniel Cociorva; Tiago S Balbuena; Richard H Valente; Jonas Perales; John R Yates; Valmir C Barbosa
Journal:  Proteomics       Date:  2012-04       Impact factor: 3.984

Review 4.  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

Review 5.  Simple, efficient and thorough shotgun proteomic analysis with PatternLab V.

Authors:  Marlon D M Santos; Diogo B Lima; Juliana S G Fischer; Milan A Clasen; Louise U Kurt; Amanda Caroline Camillo-Andrade; Leandro C Monteiro; Priscila F de Aquino; Ana G C Neves-Ferreira; Richard H Valente; Monique R O Trugilho; Giselle V F Brunoro; Tatiana A C B Souza; Renata M Santos; Michel Batista; Fabio C Gozzo; Rosario Durán; John R Yates; Valmir C Barbosa; Paulo C Carvalho
Journal:  Nat Protoc       Date:  2022-04-11       Impact factor: 17.021

6.  The influence of iron on the proteomic profile of Chromobacterium violaceum.

Authors:  Daniel C Lima; Fábio T Duarte; Viviane K S Medeiros; Diogo B Lima; Paulo C Carvalho; Diego Bonatto; Silvia R Batistuzzo de Medeiros
Journal:  BMC Microbiol       Date:  2014-10-20       Impact factor: 3.605

7.  GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide.

Authors:  D C Lima; F T Duarte; V K S Medeiros; P C Carvalho; F C S Nogueira; G D T Araujo; G B Domont; S R Batistuzzo de Medeiros
Journal:  Sci Rep       Date:  2016-06-20       Impact factor: 4.379

8.  Generalisability of vaccine effectiveness estimates: an analysis of cases included in a postlicensure evaluation of 13-valent pneumococcal conjugate vaccine in the USA.

Authors:  Ruth Link-Gelles; Daniel Westreich; Allison E Aiello; Nong Shang; David J Weber; Jennifer B Rosen; Tasneem Motala; Laurene Mascola; Jeffery Eason; Karen Scherzinger; Corinne Holtzman; Arthur L Reingold; Meghan Barnes; Susan Petit; Monica M Farley; Lee H Harrison; Shelley Zansky; Ann Thomas; William Schaffner; Lesley McGee; Cynthia G Whitney; Matthew R Moore
Journal:  BMJ Open       Date:  2017-08-28       Impact factor: 2.692
  8 in total

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