Literature DB >> 22543378

Toward objective evaluation of proteomic algorithms.

John R Yates1, Sung Kyu Robin Park, Claire M Delahunty, Tao Xu, Jeffrey N Savas, Daniel Cociorva, Paulo Costa Carvalho.   

Abstract

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Year:  2012        PMID： 22543378      PMCID： PMC3509209          DOI： 10.1038/nmeth.1983

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  17 in total

1.  A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases.

Authors:  Rovshan G Sadygov; John R Yates
Journal:  Anal Chem       Date:  2003-08-01       Impact factor: 6.986

2.  A correlation algorithm for the automated quantitative analysis of shotgun proteomics data.

Authors:  Michael J MacCoss; Christine C Wu; Hongbin Liu; Rovshan Sadygov; John R Yates
Journal:  Anal Chem       Date:  2003-12-15       Impact factor: 6.986

3.  TANDEM: matching proteins with tandem mass spectra.

Authors:  Robertson Craig; Ronald C Beavis
Journal:  Bioinformatics       Date:  2004-02-19       Impact factor: 6.937

4.  Open mass spectrometry search algorithm.

Authors:  Lewis Y Geer; Sanford P Markey; Jeffrey A Kowalak; Lukas Wagner; Ming Xu; Dawn M Maynard; Xiaoyu Yang; Wenyao Shi; Stephen H Bryant
Journal:  J Proteome Res       Date:  2004 Sep-Oct       Impact factor: 4.466

5.  Can the false-discovery rate be misleading?

Authors:  Rodrigo Barboza; Daniel Cociorva; Tao Xu; Valmir C Barbosa; Jonas Perales; Richard H Valente; Felipe M G França; John R Yates; Paulo C Carvalho
Journal:  Proteomics       Date:  2011-09-06       Impact factor: 3.984

6.  A probability-based approach for high-throughput protein phosphorylation analysis and site localization.

Authors:  Sean A Beausoleil; Judit Villén; Scott A Gerber; John Rush; Steven P Gygi
Journal:  Nat Biotechnol       Date:  2006-09-10       Impact factor: 54.908

7.  Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy.

Authors:  Brian M Balgley; Tom Laudeman; Li Yang; Tao Song; Cheng S Lee
Journal:  Mol Cell Proteomics       Date:  2007-05-28       Impact factor: 5.911

8.  Generalized method for probability-based peptide and protein identification from tandem mass spectrometry data and sequence database searching.

Authors:  Antonio Ramos-Fernández; Alberto Paradela; Rosana Navajas; Juan Pablo Albar
Journal:  Mol Cell Proteomics       Date:  2008-05-31       Impact factor: 5.911

9.  Probabilistic consensus scoring improves tandem mass spectrometry peptide identification.

Authors:  Sven Nahnsen; Andreas Bertsch; Jörg Rahnenführer; Alfred Nordheim; Oliver Kohlbacher
Journal:  J Proteome Res       Date:  2011-06-23       Impact factor: 4.466

10.  A case study on the comparison of different software tools for automated quantification of peptides.

Authors:  Niklaas Colaert; Joël Vandekerckhove; Lennart Martens; Kris Gevaert
Journal:  Methods Mol Biol       Date:  2011
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  18 in total

1.  Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.

Authors:  Robert J Chalkley; Nuno Bandeira; Matthew C Chambers; Karl R Clauser; John S Cottrell; Eric W Deutsch; Eugene A Kapp; Henry H N Lam; W Hayes McDonald; Thomas A Neubert; Rui-Xiang Sun
Journal:  Mol Cell Proteomics       Date:  2013-10-31       Impact factor: 5.911

2.  Mass Spectral Analysis of Synthetic Peptides: Implications in Proteomics.

Authors:  Medicharala Venkata Jagannadham; Pratap Gayatri; Taniya Mary Binny; Bathisaran Raman; Duvvuri Butchi Kameshwari; Ramakrishnan Nagaraj
Journal:  J Biomol Tech       Date:  2021-04

3.  A non-parametric cutout index for robust evaluation of identified proteins.

Authors:  Oliver Serang; Joao Paulo; Hanno Steen; Judith A Steen
Journal:  Mol Cell Proteomics       Date:  2013-01-04       Impact factor: 5.911

Review 4.  Protein analysis by shotgun/bottom-up proteomics.

Authors:  Yaoyang Zhang; Bryan R Fonslow; Bing Shan; Moon-Chang Baek; John R Yates
Journal:  Chem Rev       Date:  2013-02-26       Impact factor: 60.622

5.  Ecto-Fc MS identifies ligand-receptor interactions through extracellular domain Fc fusion protein baits and shotgun proteomic analysis.

Authors:  Jeffrey N Savas; Joris De Wit; Davide Comoletti; Roland Zemla; Anirvan Ghosh; John R Yates
Journal:  Nat Protoc       Date:  2014-08-07       Impact factor: 13.491

6.  PepExplorer: a similarity-driven tool for analyzing de novo sequencing results.

Authors:  Felipe V Leprevost; Richard H Valente; Diogo B Lima; Jonas Perales; Rafael Melani; John R Yates; Valmir C Barbosa; Magno Junqueira; Paulo C Carvalho
Journal:  Mol Cell Proteomics       Date:  2014-05-30       Impact factor: 5.911

7.  The ribosome assembly factor Nop53 controls association of the RNA exosome with pre-60S particles in yeast.

Authors:  Leidy Paola P Cepeda; Felipe F M Bagatelli; Renata M Santos; Marlon D M Santos; Fabio C S Nogueira; Carla C Oliveira
Journal:  J Biol Chem       Date:  2019-10-29       Impact factor: 5.157

Review 8.  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

9.  Proteomic analysis reveals a role for Bcl2-associated athanogene 3 and major vault protein in resistance to apoptosis in senescent cells by regulating ERK1/2 activation.

Authors:  Martina P Pasillas; Sarah Shields; Rebecca Reilly; Jan Strnadel; Christian Behl; Robin Park; John R Yates; Richard Klemke; Steven L Gonias; Judith A Coppinger
Journal:  Mol Cell Proteomics       Date:  2014-07-05       Impact factor: 5.911

10.  A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis.

Authors:  Faviel F Gonzalez-Galarza; Craig Lawless; Simon J Hubbard; Jun Fan; Conrad Bessant; Henning Hermjakob; Andrew R Jones
Journal:  OMICS       Date:  2012-07-17
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