Literature DB >> 18639657

Protein identification pipeline for the homology-driven proteomics.

Magno Junqueira1, Victor Spirin, Tiago Santana Balbuena, Henrik Thomas, Ivan Adzhubei, Shamil Sunyaev, Andrej Shevchenko.   

Abstract

Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ Orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download.

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Year:  2008        PMID： 18639657      PMCID： PMC2644553          DOI： 10.1016/j.jprot.2008.07.003

Source DB:  PubMed          Journal:  J Proteomics        ISSN： 1874-3919            Impact factor:   4.044


  31 in total

1.  Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.

Authors:  A Shevchenko; S Sunyaev; A Loboda; A Shevchenko; P Bork; W Ens; K G Standing
Journal:  Anal Chem       Date:  2001-05-01       Impact factor: 6.986

2.  GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model.

Authors:  David L Tabb; Anita Saraf; John R Yates
Journal:  Anal Chem       Date:  2003-12-01       Impact factor: 6.986

3.  High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results.

Authors:  Brian C Searle; Surendra Dasari; Mark Turner; Ashok P Reddy; Dongseok Choi; Phillip A Wilmarth; Ashley L McCormack; Larry L David; Srinivasa R Nagalla
Journal:  Anal Chem       Date:  2004-04-15       Impact factor: 6.986

4.  PepNovo: de novo peptide sequencing via probabilistic network modeling.

Authors:  Ari Frank; Pavel Pevzner
Journal:  Anal Chem       Date:  2005-02-15       Impact factor: 6.986

5.  In-gel digestion for mass spectrometric characterization of proteins and proteomes.

Authors:  Andrej Shevchenko; Henrik Tomas; Jan Havlis; Jesper V Olsen; Matthias Mann
Journal:  Nat Protoc       Date:  2006       Impact factor: 13.491

6.  Purification and mass spectrometry identification of microtubule-binding proteins from Xenopus egg extracts.

Authors:  Vincent Gache; Patrice Waridel; Sylvie Luche; Andrej Shevchenko; Andrei V Popov
Journal:  Methods Mol Med       Date:  2007

7.  Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels.

Authors:  A Shevchenko; M Wilm; O Vorm; M Mann
Journal:  Anal Chem       Date:  1996-03-01       Impact factor: 6.986

8.  Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification.

Authors:  Magno Junqueira; Victor Spirin; Tiago Santana Balbuena; Patrice Waridel; Vineeth Surendranath; Grigoriy Kryukov; Ivan Adzhubei; Henrik Thomas; Shamil Sunyaev; Andrej Shevchenko
Journal:  J Proteome Res       Date:  2008-06-18       Impact factor: 4.466

9.  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

Review 10.  The trypanosomiases.

Authors:  Michael P Barrett; Richard J S Burchmore; August Stich; Julio O Lazzari; Alberto Carlos Frasch; Juan José Cazzulo; Sanjeev Krishna
Journal:  Lancet       Date:  2003-11-01       Impact factor: 79.321
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  17 in total

1.  The effects of chronic treatment with mood stabilizers on the rat hippocampal post-synaptic density proteome.

Authors:  Dhaval Nanavati; Daniel R Austin; Lisa A Catapano; David A Luckenbaugh; Ayse Dosemeci; Husseini K Manji; Guang Chen; Sanford P Markey
Journal:  J Neurochem       Date:  2011-09-21       Impact factor: 5.372

2.  Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry.

Authors:  Mario Looso; Thilo Borchardt; Marcus Krüger; Thomas Braun
Journal:  Mol Cell Proteomics       Date:  2010-02-05       Impact factor: 5.911

3.  Genome-wide association study identifies common genetic variants associated with salivary gland carcinoma and its subtypes.

Authors:  Li Xu; Hongwei Tang; Diane W Chen; Adel K El-Naggar; Peng Wei; Erich M Sturgis
Journal:  Cancer       Date:  2015-03-30       Impact factor: 6.860

Review 4.  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

5.  Biochemical Composition and Assembly of Biosilica-associated Insoluble Organic Matrices from the Diatom Thalassiosira pseudonana.

Authors:  Alexander Kotzsch; Damian Pawolski; Alexander Milentyev; Anna Shevchenko; André Scheffel; Nicole Poulsen; Andrej Shevchenko; Nils Kröger
Journal:  J Biol Chem       Date:  2015-12-28       Impact factor: 5.157

Review 6.  Proteogenomics: concepts, applications and computational strategies.

Authors:  Alexey I Nesvizhskii
Journal:  Nat Methods       Date:  2014-11       Impact factor: 28.547

7.  Preservation of field samples for enzymatic and proteomic characterization: analysis of proteins from the trophallactic fluid of hornets and yellowjackets.

Authors:  Violet A Roskens; James M Carpenter; Kurt M Pickett; Bryan A Ballif
Journal:  J Proteome Res       Date:  2010-10-01       Impact factor: 4.466

Review 8.  Proteogenomics from a bioinformatics angle: A growing field.

Authors:  Gerben Menschaert; David Fenyö
Journal:  Mass Spectrom Rev       Date:  2015-12-15       Impact factor: 10.946

Review 9.  Tools for exploring the proteomosphere.

Authors:  Andrej Shevchenko; Cristina-Maria Valcu; Magno Junqueira
Journal:  J Proteomics       Date:  2009-01-22       Impact factor: 4.044

10.  Analysis of Antimicrobial Peptide Metabolome of Bacterial Endophyte Isolated From Traditionally Used Medicinal Plant Millettia pachycarpa Benth.

Authors:  Ng Ngashangva; Pulok Mukherjee; K Chandradev Sharma; M C Kalita; Sarangthem Indira
Journal:  Front Microbiol       Date:  2021-06-01       Impact factor: 5.640
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