Literature DB >> 21552256

Combining quantitative proteomics data processing workflows for greater sensitivity.

Niklaas Colaert1, Christophe Van Huele, Sven Degroeve, An Staes, Joël Vandekerckhove, Kris Gevaert, Lennart Martens.   

Abstract

We here describe a normalization method to combine quantitative proteomics data. By merging the output of two popular quantification software packages, we obtained a 20% increase (on average) in the number of quantified human proteins without suffering from a loss of quality. Our integrative workflow is freely available through our user-friendly, open-source Rover software (http://compomics-rover.googlecode.com/).

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Year:  2011        PMID： 21552256     DOI： 10.1038/nmeth.1604

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


  15 in total

1.  Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.

Authors:  Yee Hwa Yang; Sandrine Dudoit; Percy Luu; David M Lin; Vivian Peng; John Ngai; Terence P Speed
Journal:  Nucleic Acids Res       Date:  2002-02-15       Impact factor: 16.971

Review 2.  Mass spectrometry and protein analysis.

Authors:  Bruno Domon; Ruedi Aebersold
Journal:  Science       Date:  2006-04-14       Impact factor: 47.728

3.  Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies.

Authors:  Brian C Searle; Mark Turner; Alexey I Nesvizhskii
Journal:  J Proteome Res       Date:  2008-01       Impact factor: 4.466

Review 4.  An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data.

Authors:  Lukas N Mueller; Mi-Youn Brusniak; D R Mani; Ruedi Aebersold
Journal:  J Proteome Res       Date:  2008-01-04       Impact factor: 4.466

5.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

Authors:  Jürgen Cox; Matthias Mann
Journal:  Nat Biotechnol       Date:  2008-11-30       Impact factor: 54.908

6.  Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines.

Authors:  Wen Yu; J Alex Taylor; Michael T Davis; Leo E Bonilla; Kimberly A Lee; Paul L Auger; Chris C Farnsworth; Andrew A Welcher; Scott D Patterson
Journal:  Proteomics       Date:  2010-03       Impact factor: 3.984

Review 7.  Peptide and protein quantification: a map of the minefield.

Authors:  Marc Vaudel; Albert Sickmann; Lennart Martens
Journal:  Proteomics       Date:  2010-02       Impact factor: 3.984

8.  Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins.

Authors:  Kris Gevaert; Jozef Van Damme; Marc Goethals; Grégoire R Thomas; Bart Hoorelbeke; Hans Demol; Lennart Martens; Magda Puype; An Staes; Joël Vandekerckhove
Journal:  Mol Cell Proteomics       Date:  2002-11       Impact factor: 5.911

9.  Rover: a tool to visualize and validate quantitative proteomics data from different sources.

Authors:  Niklaas Colaert; Kenny Helsens; Francis Impens; Joël Vandekerckhove; Kris Gevaert
Journal:  Proteomics       Date:  2010-03       Impact factor: 3.984

10.  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
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  6 in total

1.  An adaptive alignment algorithm for quality-controlled label-free LC-MS.

Authors:  Marianne Sandin; Ashfaq Ali; Karin Hansson; Olle Månsson; Erik Andreasson; Svante Resjö; Fredrik Levander
Journal:  Mol Cell Proteomics       Date:  2013-01-09       Impact factor: 5.911

2.  T-2 toxin induced Salmonella Typhimurium intoxication results in decreased Salmonella numbers in the cecum contents of pigs, despite marked effects on Salmonella-host cell interactions.

Authors:  Elin Verbrugghe; Virginie Vandenbroucke; Maarten Dhaenens; Neil Shearer; Joline Goossens; Sarah De Saeger; Mia Eeckhout; Katharina D'Herde; Arthur Thompson; Dieter Deforce; Filip Boyen; Bregje Leyman; Alexander Van Parys; Patrick De Backer; Freddy Haesebrouck; Siska Croubels; Frank Pasmans
Journal:  Vet Res       Date:  2012-03-22       Impact factor: 3.683

3.  Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.

Authors:  Federico Abascal; Iakes Ezkurdia; Juan Rodriguez-Rivas; Jose Manuel Rodriguez; Angela del Pozo; Jesús Vázquez; Alfonso Valencia; Michael L Tress
Journal:  PLoS Comput Biol       Date:  2015-06-10       Impact factor: 4.475

Review 4.  Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

Authors:  Yasset Perez-Riverol; Rui Wang; Henning Hermjakob; Markus Müller; Vladimir Vesada; Juan Antonio Vizcaíno
Journal:  Biochim Biophys Acta       Date:  2013-03-01

5.  Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes.

Authors:  Iakes Ezkurdia; David Juan; Jose Manuel Rodriguez; Adam Frankish; Mark Diekhans; Jennifer Harrow; Jesus Vazquez; Alfonso Valencia; Michael L Tress
Journal:  Hum Mol Genet       Date:  2014-06-16       Impact factor: 6.150

6.  The potential clinical impact of the release of two drafts of the human proteome.

Authors:  Iakes Ezkurdia; Enrique Calvo; Angela Del Pozo; Jesús Vázquez; Alfonso Valencia; Michael L Tress
Journal:  Expert Rev Proteomics       Date:  2015-10-23       Impact factor: 3.940
  6 in total

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