Literature DB >> 20835799

Mass spectrometric protein identification using the global proteome machine.

David Fenyö1, Jan Eriksson, Ronald Beavis.   

Abstract

Protein identification by mass spectrometry is widely used in biological research. Here, we describe how the global proteome machine (GPM) can be used for protein identification and for validation of the results. We cover identification by searching protein sequence collections and spectral libraries as well as validation of the results using expectation values, rho-diagrams, and spectrum databases.

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Year:  2010        PMID： 20835799      PMCID： PMC3757509          DOI： 10.1007/978-1-60761-842-3_11

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  28 in total

1.  De novo peptide sequencing via tandem mass spectrometry.

Authors:  V Dancík; T A Addona; K R Clauser; J E Vath; P A Pevzner
Journal:  J Comput Biol       Date:  1999 Fall-Winter       Impact factor: 1.479

2.  ProFound: an expert system for protein identification using mass spectrometric peptide mapping information.

Authors:  W Zhang; B T Chait
Journal:  Anal Chem       Date:  2000-06-01       Impact factor: 6.986

3.  RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database.

Authors:  Helen I Field; David Fenyö; Ronald C Beavis
Journal:  Proteomics       Date:  2002-01       Impact factor: 3.984

4.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Authors:  Andrew Keller; Alexey I Nesvizhskii; Eugene Kolker; Ruedi Aebersold
Journal:  Anal Chem       Date:  2002-10-15       Impact factor: 6.986

5.  Open source system for analyzing, validating, and storing protein identification data.

Authors:  Robertson Craig; John P Cortens; Ronald C Beavis
Journal:  J Proteome Res       Date:  2004 Nov-Dec       Impact factor: 4.466

6.  Protein identification in complex mixtures.

Authors:  Jan Eriksson; David Fenyö
Journal:  J Proteome Res       Date:  2005 Mar-Apr       Impact factor: 4.466

7.  Using annotated peptide mass spectrum libraries for protein identification.

Authors:  R Craig; J C Cortens; D Fenyo; R C Beavis
Journal:  J Proteome Res       Date:  2006-08       Impact factor: 4.466

8.  Development and validation of a spectral library searching method for peptide identification from MS/MS.

Authors:  Henry Lam; Eric W Deutsch; James S Eddes; Jimmy K Eng; Nichole King; Stephen E Stein; Ruedi Aebersold
Journal:  Proteomics       Date:  2007-03       Impact factor: 3.984

9.  Identification of the components of simple protein mixtures by high-accuracy peptide mass mapping and database searching.

Authors:  O N Jensen; A V Podtelejnikov; M Mann
Journal:  Anal Chem       Date:  1997-12-01       Impact factor: 6.986

10.  Error-tolerant identification of peptides in sequence databases by peptide sequence tags.

Authors:  M Mann; M Wilm
Journal:  Anal Chem       Date:  1994-12-15       Impact factor: 6.986
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  22 in total

1.  A mass spectrometry proteomics data management platform.

Authors:  Vagisha Sharma; Jimmy K Eng; Michael J Maccoss; Michael Riffle
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2.  Mass spectrometry-based protein identification with accurate statistical significance assignment.

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Journal:  Bioinformatics       Date:  2014-10-31       Impact factor: 6.937

3.  Molecular basis of interactions between SH3 domain-containing proteins and the proline-rich region of the ubiquitin ligase Itch.

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Journal:  J Biol Chem       Date:  2017-02-24       Impact factor: 5.157

4.  Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment.

Authors:  Surendra Dasari; Matthew C Chambers; Misti A Martinez; Kristin L Carpenter; Amy-Joan L Ham; Lorenzo J Vega-Montoto; David L Tabb
Journal:  J Proteome Res       Date:  2012-01-27       Impact factor: 4.466

5.  Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format.

Authors:  Jimmy K Eng; Eric W Deutsch
Journal:  Proteomics       Date:  2020-04-02       Impact factor: 3.984

6.  Biobank resources for future patient care: developments, principles and concepts.

Authors:  Akos Végvári; Charlotte Welinder; Henrik Lindberg; Thomas E Fehniger; György Marko-Varga
Journal:  J Clin Bioinforma       Date:  2011-09-16

7.  The human proteome project: current state and future direction.

Authors:  Pierre Legrain; Ruedi Aebersold; Alexander Archakov; Amos Bairoch; Kumar Bala; Laura Beretta; John Bergeron; Christoph H Borchers; Garry L Corthals; Catherine E Costello; Eric W Deutsch; Bruno Domon; William Hancock; Fuchu He; Denis Hochstrasser; György Marko-Varga; Ghasem Hosseini Salekdeh; Salvatore Sechi; Michael Snyder; Sudhir Srivastava; Mathias Uhlén; Cathy H Wu; Tadashi Yamamoto; Young-Ki Paik; Gilbert S Omenn
Journal:  Mol Cell Proteomics       Date:  2011-07       Impact factor: 5.911

Review 8.  High-throughput analysis of peptide-binding modules.

Authors:  Bernard A Liu; Brett W Engelmann; Piers D Nash
Journal:  Proteomics       Date:  2012-05       Impact factor: 3.984

Review 9.  Systems Proteomics View of the Endogenous Human Claudin Protein Family.

Authors:  Fei Liu; Michael Koval; Shoba Ranganathan; Susan Fanayan; William S Hancock; Emma K Lundberg; Ronald C Beavis; Lydie Lane; Paula Duek; Leon McQuade; Neil L Kelleher; Mark S Baker
Journal:  J Proteome Res       Date:  2016-01-12       Impact factor: 4.466

10.  The state of the human proteome in 2012 as viewed through PeptideAtlas.

Authors:  Terry Farrah; Eric W Deutsch; Michael R Hoopmann; Janice L Hallows; Zhi Sun; Chung-Ying Huang; Robert L Moritz
Journal:  J Proteome Res       Date:  2012-12-05       Impact factor: 4.466
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