Literature DB >> 20622826

PeptideClassifier for protein inference and targeted quantitative proteomics.

Ermir Qeli, Christian H Ahrens.   

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Year:  2010        PMID： 20622826     DOI： 10.1038/nbt0710-647

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  15 in total

1.  The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data.

Authors:  Steven Carr; Ruedi Aebersold; Michael Baldwin; Al Burlingame; Karl Clauser; Alexey Nesvizhskii
Journal:  Mol Cell Proteomics       Date:  2004-04-09       Impact factor: 5.911

2.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.

Authors:  Joshua E Elias; Steven P Gygi
Journal:  Nat Methods       Date:  2007-03       Impact factor: 28.547

Review 3.  Analysis and validation of proteomic data generated by tandem mass spectrometry.

Authors:  Alexey I Nesvizhskii; Olga Vitek; Ruedi Aebersold
Journal:  Nat Methods       Date:  2007-10       Impact factor: 28.547

4.  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 5.  A human proteome detection and quantitation project.

Authors:  N Leigh Anderson; Norman G Anderson; Terry W Pearson; Christoph H Borchers; Amanda G Paulovich; Scott D Patterson; Michael Gillette; Ruedi Aebersold; Steven A Carr
Journal:  Mol Cell Proteomics       Date:  2009-01-07       Impact factor: 5.911

6.  Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast.

Authors:  Lyris M F de Godoy; Jesper V Olsen; Jürgen Cox; Michael L Nielsen; Nina C Hubner; Florian Fröhlich; Tobias C Walther; Matthias Mann
Journal:  Nature       Date:  2008-09-28       Impact factor: 49.962

7.  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

8.  False discovery rates of protein identifications: a strike against the two-peptide rule.

Authors:  Nitin Gupta; Pavel A Pevzner
Journal:  J Proteome Res       Date:  2009-09       Impact factor: 4.466

9.  A high-quality catalog of the Drosophila melanogaster proteome.

Authors:  Erich Brunner; Christian H Ahrens; Sonali Mohanty; Hansruedi Baetschmann; Sandra Loevenich; Frank Potthast; Eric W Deutsch; Christian Panse; Ulrik de Lichtenberg; Oliver Rinner; Hookeun Lee; Patrick G A Pedrioli; Johan Malmstrom; Katja Koehler; Sabine Schrimpf; Jeroen Krijgsveld; Floyd Kregenow; Albert J R Heck; Ernst Hafen; Ralph Schlapbach; Ruedi Aebersold
Journal:  Nat Biotechnol       Date:  2007-04-22       Impact factor: 54.908

10.  IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.

Authors:  Ze-Qiang Ma; Surendra Dasari; Matthew C Chambers; Michael D Litton; Scott M Sobecki; Lisa J Zimmerman; Patrick J Halvey; Birgit Schilling; Penelope M Drake; Bradford W Gibson; David L Tabb
Journal:  J Proteome Res       Date:  2009-08       Impact factor: 4.466
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  32 in total

1.  Hierarchical clustering of shotgun proteomics data.

Authors:  Ville R Koskinen; Patrick A Emery; David M Creasy; John S Cottrell
Journal:  Mol Cell Proteomics       Date:  2011-03-29       Impact factor: 5.911

2.  σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111.

Authors:  Martina Lardi; Claudio Aguilar; Alessandro Pedrioli; Ulrich Omasits; Angela Suppiger; Gerardo Cárcamo-Oyarce; Nadine Schmid; Christian H Ahrens; Leo Eberl; Gabriella Pessi
Journal:  Appl Environ Microbiol       Date:  2015-04-03       Impact factor: 4.792

3.  gpGrouper: A Peptide Grouping Algorithm for Gene-Centric Inference and Quantitation of Bottom-Up Proteomics Data.

Authors:  Alexander B Saltzman; Mei Leng; Bhoomi Bhatt; Purba Singh; Doug W Chan; Lacey Dobrolecki; Hamssika Chandrasekaran; Jong M Choi; Antrix Jain; Sung Y Jung; Michael T Lewis; Matthew J Ellis; Anna Malovannaya
Journal:  Mol Cell Proteomics       Date:  2018-08-09       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.  Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii.

Authors:  Tabea Mettler; Timo Mühlhaus; Dorothea Hemme; Mark-Aurel Schöttler; Jens Rupprecht; Adam Idoine; Daniel Veyel; Sunil Kumar Pal; Liliya Yaneva-Roder; Flavia Vischi Winck; Frederik Sommer; Daniel Vosloh; Bettina Seiwert; Alexander Erban; Asdrubal Burgos; Samuel Arvidsson; Stephanie Schönfelder; Anne Arnold; Manuela Günther; Ursula Krause; Marc Lohse; Joachim Kopka; Zoran Nikoloski; Bernd Mueller-Roeber; Lothar Willmitzer; Ralph Bock; Michael Schroda; Mark Stitt
Journal:  Plant Cell       Date:  2014-06-03       Impact factor: 11.277

Review 6.  A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics.

Authors:  Alexey I Nesvizhskii
Journal:  J Proteomics       Date:  2010-09-08       Impact factor: 4.044

7.  A Peptidomimetic Antibiotic Targets Outer Membrane Proteins and Disrupts Selectively the Outer Membrane in Escherichia coli.

Authors:  Matthias Urfer; Jasmina Bogdanovic; Fabio Lo Monte; Kerstin Moehle; Katja Zerbe; Ulrich Omasits; Christian H Ahrens; Gabriella Pessi; Leo Eberl; John A Robinson
Journal:  J Biol Chem       Date:  2015-12-01       Impact factor: 5.157

8.  A link between arabinose utilization and oxalotrophy in Bradyrhizobium japonicum.

Authors:  Marion Koch; Nathanaël Delmotte; Christian H Ahrens; Ulrich Omasits; Kathrin Schneider; Francesco Danza; Barnali Padhi; Valérie Murset; Olivier Braissant; Julia A Vorholt; Hauke Hennecke; Gabriella Pessi
Journal:  Appl Environ Microbiol       Date:  2014-01-24       Impact factor: 4.792

9.  Nitrogen-Sparing Mechanisms in Chlamydomonas Affect the Transcriptome, the Proteome, and Photosynthetic Metabolism.

Authors:  Stefan Schmollinger; Timo Mühlhaus; Nanette R Boyle; Ian K Blaby; David Casero; Tabea Mettler; Jeffrey L Moseley; Janette Kropat; Frederik Sommer; Daniela Strenkert; Dorothea Hemme; Matteo Pellegrini; Arthur R Grossman; Mark Stitt; Michael Schroda; Sabeeha S Merchant
Journal:  Plant Cell       Date:  2014-04-18       Impact factor: 11.277

Review 10.  Application of targeted mass spectrometry in bottom-up proteomics for systems biology research.

Authors:  Nathan P Manes; Aleksandra Nita-Lazar
Journal:  J Proteomics       Date:  2018-02-13       Impact factor: 4.044
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