Literature DB >> 23294060

The revolution and evolution of shotgun proteomics for large-scale proteome analysis.

John R Yates1.   

Abstract

Mass spectrometry has evolved at an exponential rate over the last 100 years. Innovations in the development of mass spectrometers have created powerful instruments capable of analyzing a wide range of targets, from rare atoms and molecules to very large molecules, such as a proteins, protein complexes, and DNA. These performance gains have been driven by sustaining innovations, punctuated by the occasional disruptive innovation. The use of mass spectrometry for proteome analysis was driven by disruptive innovations that created a capability for large-scale analysis of proteins and modifications.

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Year:  2013        PMID: 23294060      PMCID: PMC3751590          DOI: 10.1021/ja3094313

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  129 in total

1.  Activity-based protein profiling: the serine hydrolases.

Authors:  Y Liu; M P Patricelli; B F Cravatt
Journal:  Proc Natl Acad Sci U S A       Date:  1999-12-21       Impact factor: 11.205

2.  Accurate quantitation of protein expression and site-specific phosphorylation.

Authors:  Y Oda; K Huang; F R Cross; D Cowburn; B T Chait
Journal:  Proc Natl Acad Sci U S A       Date:  1999-06-08       Impact factor: 11.205

3.  Amino acid residue specific stable isotope labeling for quantitative proteomics.

Authors:  Haining Zhu; Songqin Pan; Sheng Gu; E Morton Bradbury; Xian Chen
Journal:  Rapid Commun Mass Spectrom       Date:  2002       Impact factor: 2.419

4.  Shotgun identification of protein modifications from protein complexes and lens tissue.

Authors:  Michael J MacCoss; W Hayes McDonald; Anita Saraf; Rovshan Sadygov; Judy M Clark; Joseph J Tasto; Kathleen L Gould; Dirk Wolters; Michael Washburn; Avery Weiss; John I Clark; John R Yates
Journal:  Proc Natl Acad Sci U S A       Date:  2002-06-11       Impact factor: 11.205

5.  Quantitative mass spectrometry identifies insulin signaling targets in C. elegans.

Authors:  Meng-Qiu Dong; John D Venable; Nora Au; Tao Xu; Sung Kyu Park; Daniel Cociorva; Jeffrey R Johnson; Andrew Dillin; John R Yates
Journal:  Science       Date:  2007-08-03       Impact factor: 47.728

6.  Identification of post-translational modifications by blind search of mass spectra.

Authors:  Dekel Tsur; Stephen Tanner; Ebrahim Zandi; Vineet Bafna; Pavel A Pevzner
Journal:  Nat Biotechnol       Date:  2005-11-27       Impact factor: 54.908

7.  Functional organization of the yeast proteome by systematic analysis of protein complexes.

Authors:  Anne-Claude Gavin; Markus Bösche; Roland Krause; Paola Grandi; Martina Marzioch; Andreas Bauer; Jörg Schultz; Jens M Rick; Anne-Marie Michon; Cristina-Maria Cruciat; Marita Remor; Christian Höfert; Malgorzata Schelder; Miro Brajenovic; Heinz Ruffner; Alejandro Merino; Karin Klein; Manuela Hudak; David Dickson; Tatjana Rudi; Volker Gnau; Angela Bauch; Sonja Bastuck; Bettina Huhse; Christina Leutwein; Marie-Anne Heurtier; Richard R Copley; Angela Edelmann; Erich Querfurth; Vladimir Rybin; Gerard Drewes; Manfred Raida; Tewis Bouwmeester; Peer Bork; Bertrand Seraphin; Bernhard Kuster; Gitte Neubauer; Giulio Superti-Furga
Journal:  Nature       Date:  2002-01-10       Impact factor: 49.962

8.  A protein complex network of Drosophila melanogaster.

Authors:  K G Guruharsha; Jean-François Rual; Bo Zhai; Julian Mintseris; Pujita Vaidya; Namita Vaidya; Chapman Beekman; Christina Wong; David Y Rhee; Odise Cenaj; Emily McKillip; Saumini Shah; Mark Stapleton; Kenneth H Wan; Charles Yu; Bayan Parsa; Joseph W Carlson; Xiao Chen; Bhaveen Kapadia; K VijayRaghavan; Steven P Gygi; Susan E Celniker; Robert A Obar; Spyros Artavanis-Tsakonas
Journal:  Cell       Date:  2011-10-28       Impact factor: 41.582

9.  Analysis of quantitative proteomic data generated via multidimensional protein identification technology.

Authors:  Michael P Washburn; Ryan Ulaszek; Cosmin Deciu; David M Schieltz; John R Yates
Journal:  Anal Chem       Date:  2002-04-01       Impact factor: 6.986

10.  Mixture analysis by triple-quadrupole mass spectrometry: metabolic profiling of urinary carboxylic acids.

Authors:  D F Hunt; A B Giordani; G Rhodes; D A Herold
Journal:  Clin Chem       Date:  1982-12       Impact factor: 8.327

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  22 in total

1.  Nuclear LC3 Associates with Slowly Diffusing Complexes that Survey the Nucleolus.

Authors:  Lewis J Kraft; Pallavi Manral; Jacob Dowler; Anne K Kenworthy
Journal:  Traffic       Date:  2016-02-18       Impact factor: 6.215

2.  Dodecyl maltopyranoside enabled purification of active human GABA type A receptors for deep and direct proteomic sequencing.

Authors:  Xi Zhang; Keith W Miller
Journal:  Mol Cell Proteomics       Date:  2014-12-03       Impact factor: 5.911

Review 3.  Post-genomics nanotechnology is gaining momentum: nanoproteomics and applications in life sciences.

Authors:  Firas H Kobeissy; Basri Gulbakan; Ali Alawieh; Pierre Karam; Zhiqun Zhang; Joy D Guingab-Cagmat; Stefania Mondello; Weihong Tan; John Anagli; Kevin Wang
Journal:  OMICS       Date:  2014-01-10

4.  IMTBX and Grppr: Software for Top-Down Proteomics Utilizing Ion Mobility-Mass Spectrometry.

Authors:  Dmitry M Avtonomov; Daniel A Polasky; Brandon T Ruotolo; Alexey I Nesvizhskii
Journal:  Anal Chem       Date:  2018-01-16       Impact factor: 6.986

Review 5.  New-generation mass spectrometry expands the toolbox of cell and developmental biology.

Authors:  Camille Lombard-Banek; Erika P Portero; Rosemary M Onjiko; Peter Nemes
Journal:  Genesis       Date:  2017-01       Impact factor: 2.487

6.  Fixed-Charge Trimethyl Pyrilium Modification for Enabling Enhanced Top-Down Mass Spectrometry Sequencing of Intact Protein Complexes.

Authors:  Daniel A Polasky; Frederik Lermyte; Michael Nshanian; Frank Sobott; Phillip C Andrews; Joseph A Loo; Brandon T Ruotolo
Journal:  Anal Chem       Date:  2018-02-02       Impact factor: 6.986

Review 7.  Recent trends of capillary electrophoresis-mass spectrometry in proteomics research.

Authors:  Fabio P Gomes; John R Yates
Journal:  Mass Spectrom Rev       Date:  2019-08-12       Impact factor: 10.946

8.  Mass spectrometric analysis of the cell surface N-glycoproteome by combining metabolic labeling and click chemistry.

Authors:  Johanna M Smeekens; Weixuan Chen; Ronghu Wu
Journal:  J Am Soc Mass Spectrom       Date:  2014-11-26       Impact factor: 3.109

9.  Proteomic approaches for cancer epigenetics research.

Authors:  Dylan M Marchione; Benjamin A Garcia; John Wojcik
Journal:  Expert Rev Proteomics       Date:  2018-11-27       Impact factor: 3.940

Review 10.  Ion Activation Methods for Peptides and Proteins.

Authors:  Jennifer S Brodbelt
Journal:  Anal Chem       Date:  2015-12-11       Impact factor: 6.986

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