Literature DB >> 20521246

Analyzing shotgun proteomic data with PatternLab for proteomics.

Paulo C Carvalho1, John R Yates Iii, Valmir C Barbosa.   

Abstract

PatternLab for proteomics is a one-stop shop computational environment for analyzing shotgun proteomic data. Its modules provide means to pinpoint proteins/peptides that are differentially expressed and those that are unique to a state. It can also cluster the ones that share similar expression profiles in time-course experiments, as well as help in interpreting results according to Gene Ontology. PatternLab is user-friendly, simple, and provides a graphical user interface. (c) 2010 by John Wiley & Sons, Inc.

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Year:  2010        PMID： 20521246      PMCID： PMC2933420          DOI： 10.1002/0471250953.bi1313s30

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  11 in total

1.  Probability-based protein identification by searching sequence databases using mass spectrometry data.

Authors:  D N Perkins; D J Pappin; D M Creasy; J S Cottrell
Journal:  Electrophoresis       Date:  1999-12       Impact factor: 3.535

2.  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

3.  A quantitative analysis software tool for mass spectrometry-based proteomics.

Authors:  Sung Kyu Park; John D Venable; Tao Xu; John R Yates
Journal:  Nat Methods       Date:  2008-03-16       Impact factor: 28.547

4.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.

Authors:  J K Eng; A L McCormack; J R Yates
Journal:  J Am Soc Mass Spectrom       Date:  1994-11       Impact factor: 3.109

5.  Identifying differences in protein expression levels by spectral counting and feature selection.

Authors:  P C Carvalho; J Hewel; V C Barbosa; J R Yates
Journal:  Genet Mol Res       Date:  2008-04-15

6.  Validation of tandem mass spectrometry database search results using DTASelect.

Authors:  Daniel Cociorva; David L Tabb; John R Yates
Journal:  Curr Protoc Bioinformatics       Date:  2007-01

7.  Analysis of quantitative proteomic data generated via multidimensional protein identification technology.

Authors:  Michael P Washburn; Ryan Ulaszek; Cosmin Deciu; David M Schieltz; John R Yates
Journal:  Anal Chem       Date:  2002-04-01       Impact factor: 6.986

8.  Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.

Authors:  Shao-En Ong; Blagoy Blagoev; Irina Kratchmarova; Dan Bach Kristensen; Hanno Steen; Akhilesh Pandey; Matthias Mann
Journal:  Mol Cell Proteomics       Date:  2002-05       Impact factor: 5.911

9.  GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data.

Authors:  Paulo C Carvalho; Juliana Sg Fischer; Emily I Chen; Gilberto B Domont; Maria Gc Carvalho; Wim M Degrave; John R Yates; Valmir C Barbosa
Journal:  Proteome Sci       Date:  2009-02-24       Impact factor: 2.480

10.  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
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  12 in total

1.  Improving the TFold test for differential shotgun proteomics.

Authors:  Paulo C Carvalho; John R Yates; Valmir C Barbosa
Journal:  Bioinformatics       Date:  2012-04-26       Impact factor: 6.937

2.  Analyzing marginal cases in differential shotgun proteomics.

Authors:  Paulo C Carvalho; Juliana S G Fischer; Jonas Perales; John R Yates; Valmir C Barbosa; Elias Bareinboim
Journal:  Bioinformatics       Date:  2010-11-11       Impact factor: 6.937

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

4.  Type I signal peptidase and protein secretion in Staphylococcus aureus.

Authors:  Mark A Schallenberger; Sherry Niessen; Changxia Shao; Bruce J Fowler; Floyd E Romesberg
Journal:  J Bacteriol       Date:  2012-03-23       Impact factor: 3.490

5.  Proteomic profiling of the influence of iron availability on Cryptococcus gattii.

Authors:  Juliana Crestani; Paulo Costa Carvalho; Xuemei Han; Adriana Seixas; Leonardo Broetto; Juliana de Saldanha da Gama Fischer; Charley Christian Staats; Augusto Schrank; John R Yates; Marilene Henning Vainstein
Journal:  J Proteome Res       Date:  2011-10-26       Impact factor: 4.466

6.  Protein S-glutathionylation in malaria parasites.

Authors:  Sebastian Kehr; Esther Jortzik; Claire Delahunty; John R Yates; Stefan Rahlfs; Katja Becker
Journal:  Antioxid Redox Signal       Date:  2011-07-07       Impact factor: 8.401

7.  Large-scale proteome comparative analysis of developing rhizomes of the ancient vascular plant equisetum hyemale.

Authors:  Tiago Santana Balbuena; Ruifeng He; Fernanda Salvato; David R Gang; Jay J Thelen
Journal:  Front Plant Sci       Date:  2012-06-26       Impact factor: 5.753

8.  In-depth characterization of trypsin-like serine peptidases in the midgut of the sugar fed Culex quinquefasciatus.

Authors:  André Borges-Veloso; Leonardo Saboia-Vahia; Geovane Dias-Lopes; Gilberto B Domont; Constança Britto; Patricia Cuervo; Jose B De Jesus
Journal:  Parasit Vectors       Date:  2015-07-16       Impact factor: 3.876

9.  Expression of active trypsin-like serine peptidases in the midgut of sugar-feeding female Anopheles aquasalis.

Authors:  Geovane Dias-Lopes; Andre Borges-Veloso; Leonardo Saboia-Vahia; Gilberto B Domont; Constança Britto; Patricia Cuervo; Jose Batista De Jesus
Journal:  Parasit Vectors       Date:  2015-05-29       Impact factor: 3.876

10.  Expression of the mevalonate pathway enzymes in the Lutzomyia longipalpis (Diptera: Psychodidae) sex pheromone gland demonstrated by an integrated proteomic approach.

Authors:  Natalia González-Caballero; Andrés Rodríguez-Vega; Geovane Dias-Lopes; Jesus G Valenzuela; Jose M C Ribeiro; Paulo Costa Carvalho; Richard H Valente; Reginaldo P Brazil; Patricia Cuervo
Journal:  J Proteomics       Date:  2013-11-01       Impact factor: 4.044
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