Literature DB >> 24336358

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics.

Ute Distler1, Jörg Kuharev2, Pedro Navarro3, Yishai Levin4, Hansjörg Schild3, Stefan Tenzer3.   

Abstract

We present a data-independent acquisition mass spectrometry method, ultradefinition (UD) MS(E). This approach utilizes ion mobility drift time-specific collision-energy profiles to enhance precursor fragmentation efficiency over current MS(E) and high-definition (HD) MS(E) data-independent acquisition techniques. UDMS(E) provided high reproducibility and substantially improved proteome coverage of the HeLa cell proteome compared to previous implementations of MS(E), and it also outperformed a state-of-the-art data-dependent acquisition workflow. Additionally, we report a software tool, ISOQuant, for processing label-free quantitative UDMS(E) data.

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Year:  2013        PMID： 24336358     DOI： 10.1038/nmeth.2767

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


  26 in total

1.  Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.

Authors:  Ludovic C Gillet; Pedro Navarro; Stephen Tate; Hannes Röst; Nathalie Selevsek; Lukas Reiter; Ron Bonner; Ruedi Aebersold
Journal:  Mol Cell Proteomics       Date:  2012-01-18       Impact factor: 5.911

2.  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

3.  Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures.

Authors:  Guo-Zhong Li; Johannes P C Vissers; Jeffrey C Silva; Dan Golick; Marc V Gorenstein; Scott J Geromanos
Journal:  Proteomics       Date:  2009-03       Impact factor: 3.984

4.  Retention time alignment algorithms for LC/MS data must consider non-linear shifts.

Authors:  Katharina Podwojski; Arno Fritsch; Daniel C Chamrad; Wolfgang Paul; Barbara Sitek; Kai Stühler; Petra Mutzel; Christian Stephan; Helmut E Meyer; Wolfgang Urfer; Katja Ickstadt; Jörg Rahnenführer
Journal:  Bioinformatics       Date:  2009-01-28       Impact factor: 6.937

5.  More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS.

Authors:  Annette Michalski; Juergen Cox; Matthias Mann
Journal:  J Proteome Res       Date:  2011-02-28       Impact factor: 4.466

6.  Nanoparticle size is a critical physicochemical determinant of the human blood plasma corona: a comprehensive quantitative proteomic analysis.

Authors:  Stefan Tenzer; Dominic Docter; Susanne Rosfa; Alexandra Wlodarski; Jörg Kuharev; Alexander Rekik; Shirley K Knauer; Christoph Bantz; Thomas Nawroth; Carolin Bier; Jarinratn Sirirattanapan; Wolf Mann; Lennart Treuel; Reinhard Zellner; Michael Maskos; Hansjörg Schild; Roland H Stauber
Journal:  ACS Nano       Date:  2011-08-25       Impact factor: 15.881

7.  Using ion mobility data to improve peptide identification: intrinsic amino acid size parameters.

Authors:  Stephen J Valentine; Michael A Ewing; Jonathan M Dilger; Matthew S Glover; Scott Geromanos; Chris Hughes; David E Clemmer
Journal:  J Proteome Res       Date:  2011-04-01       Impact factor: 4.466

8.  The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS.

Authors:  Scott J Geromanos; Johannes P C Vissers; Jeffrey C Silva; Craig A Dorschel; Guo-Zhong Li; Marc V Gorenstein; Robert H Bateman; James I Langridge
Journal:  Proteomics       Date:  2009-03       Impact factor: 3.984

9.  Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation.

Authors:  Tamar Geiger; Juergen Cox; Matthias Mann
Journal:  Mol Cell Proteomics       Date:  2010-07-07       Impact factor: 5.911

10.  The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.

Authors:  Juan Antonio Vizcaíno; Richard G Côté; Attila Csordas; José A Dianes; Antonio Fabregat; Joseph M Foster; Johannes Griss; Emanuele Alpi; Melih Birim; Javier Contell; Gavin O'Kelly; Andreas Schoenegger; David Ovelleiro; Yasset Pérez-Riverol; Florian Reisinger; Daniel Ríos; Rui Wang; Henning Hermjakob
Journal:  Nucleic Acids Res       Date:  2012-11-29       Impact factor: 16.971
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  154 in total

1.  Proteomic Analysis of the Pseudomonas aeruginosa Iron Starvation Response Reveals PrrF Small Regulatory RNA-Dependent Iron Regulation of Twitching Motility, Amino Acid Metabolism, and Zinc Homeostasis Proteins.

Authors:  Cassandra E Nelson; Weiliang Huang; Luke K Brewer; Angela T Nguyen; Maureen A Kane; Angela Wilks; Amanda G Oglesby-Sherrouse
Journal:  J Bacteriol       Date:  2019-05-22       Impact factor: 3.490

2.  Affinity-Based Selectivity Profiling of an In-Class Selective Competitive Inhibitor of Acyl Protein Thioesterase 2.

Authors:  Sang Joon Won; Joseph D Eschweiler; Jaimeen D Majmudar; Fei San Chong; Sin Ye Hwang; Brandon T Ruotolo; Brent R Martin
Journal:  ACS Med Chem Lett       Date:  2016-12-09       Impact factor: 4.345

3.  diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition.

Authors:  Florian Meier; Andreas-David Brunner; Max Frank; Annie Ha; Isabell Bludau; Eugenia Voytik; Stephanie Kaspar-Schoenefeld; Markus Lubeck; Oliver Raether; Nicolai Bache; Ruedi Aebersold; Ben C Collins; Hannes L Röst; Matthias Mann
Journal:  Nat Methods       Date:  2020-11-30       Impact factor: 28.547

4.  Variable-Velocity Traveling-Wave Ion Mobility Separation Enhancing Peak Capacity for Data-Independent Acquisition Proteomics.

Authors:  Sarah E Haynes; Daniel A Polasky; Sugyan M Dixit; Jaimeen D Majmudar; Kieran Neeson; Brandon T Ruotolo; Brent R Martin
Journal:  Anal Chem       Date:  2017-05-09       Impact factor: 6.986

5.  Optimized Workflow for Selecting Peptides for HDX-MS Data Analyses.

Authors:  Lars Sørensen; Rune Salbo
Journal:  J Am Soc Mass Spectrom       Date:  2018-08-31       Impact factor: 3.109

6.  Systematic evaluation of data-independent acquisition for sensitive and reproducible proteomics-a prototype design for a single injection assay.

Authors:  Michael R Heaven; Adam J Funk; Archie L Cobbs; Wendy D Haffey; Jeremy L Norris; Robert E McCullumsmith; Kenneth D Greis
Journal:  J Mass Spectrom       Date:  2016-01       Impact factor: 1.982

7.  Rho-A prenylation and signaling link epithelial homeostasis to intestinal inflammation.

Authors:  Rocío López-Posadas; Christoph Becker; Claudia Günther; Stefan Tenzer; Kerstin Amann; Ulrike Billmeier; Raja Atreya; Gionata Fiorino; Stefania Vetrano; Silvio Danese; Arif B Ekici; Stefan Wirtz; Veronika Thonn; Alastair J M Watson; Cord Brakebusch; Martin Bergö; Markus F Neurath; Imke Atreya
Journal:  J Clin Invest       Date:  2016-01-11       Impact factor: 14.808

8.  Comparative proteomic analysis of SLC13A5 knockdown reveals elevated ketogenesis and enhanced cellular toxic response to chemotherapeutic agents in HepG2 cells.

Authors:  Tao Hu; Weiliang Huang; Zhihui Li; Maureen A Kane; Lei Zhang; Shiew-Mei Huang; Hongbing Wang
Journal:  Toxicol Appl Pharmacol       Date:  2020-07-04       Impact factor: 4.219

9.  The Abundant Tegument Protein pUL25 of Human Cytomegalovirus Prevents Proteasomal Degradation of pUL26 and Supports Its Suppression of ISGylation.

Authors:  Christine Zimmermann; Nicole Büscher; Steffi Krauter; Nadine Krämer; Uwe Wolfrum; Elisabeth Sehn; Stefan Tenzer; Bodo Plachter
Journal:  J Virol       Date:  2018-11-27       Impact factor: 5.103

10.  Hydrogen Sulfide and Reactive Sulfur Species Impact Proteome S-Sulfhydration and Global Virulence Regulation in Staphylococcus aureus.

Authors:  Hui Peng; Yixiang Zhang; Lauren D Palmer; Thomas E Kehl-Fie; Eric P Skaar; Jonathan C Trinidad; David P Giedroc
Journal:  ACS Infect Dis       Date:  2017-09-06       Impact factor: 5.084
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