Multiplexed MS/MS for improved data-independent acquisition
Jarrett D. Egertson,Andreas Kuehn,Gennifer E. Merrihew,Nicholas W. Bateman,Brendan MacLean,Ying S. Ting,Jesse D. Canterbury,Donald M Marsh,Markus Kellmann,Vlad Zabrouskov,Christine C. Wu,Michael J. MacCoss +11 more
TLDR
A multiplexing strategy is demonstrated for DIA analysis that increases precursor selectivity fivefold and can be used for data-dependent acquisition or selected reaction monitoring.Abstract:
In mass spectrometry-based proteomics, data-independent acquisition (DIA) strategies can acquire a single data set useful for both identification and quantification of detectable peptides in a complex mixture. However, DIA data are noisy owing to a typical five- to tenfold reduction in precursor selectivity compared to data obtained with data-dependent acquisition or selected reaction monitoring. We demonstrate a multiplexing strategy, MSX, for DIA analysis that increases precursor selectivity fivefold.read more
Citations
More filters
“Bioinformatics” 특집을 내면서
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Journal ArticleDOI
MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis.
Hiroshi Tsugawa,Tomas Cajka,Tobias Kind,Yan Ma,Brendan T. Higgins,Kazutaka Ikeda,Mitsuhiro Kanazawa,Jean S. VanderGheynst,Oliver Fiehn,Masanori Arita +9 more
TL;DR: For a reversed-phase LC-MS/MS analysis of nine algal strains, MS-DIAL using an enriched LipidBlast library identified 1,023 lipid compounds, highlighting the chemotaxonomic relationships between theAlgal strains.
Journal ArticleDOI
Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues
Roland Bruderer,Oliver M. Bernhardt,Tejas Gandhi,Saša M. Miladinović,Lin-Yang Cheng,Simon Messner,Tobias Ehrenberger,Vito R T Zanotelli,Yulia Butscheid,Claudia Escher,Olga Vitek,Oliver Rinner,Lukas Reiter +12 more
TL;DR: It is shown that HRM outperformed shotgun proteomics both in the number of consistently identified peptides across multiple measurements and quantification of differentially abundant proteins, implying that DIA should be the preferred method for quantitative protein profiling.
Journal ArticleDOI
Data‐independent acquisition‐based SWATH ‐ MS for quantitative proteomics: a tutorial
Christina Ludwig,Ludovic C Gillet,George Rosenberger,George Rosenberger,Sabine Amon,Ben C. Collins,Ruedi Aebersold,Ruedi Aebersold +7 more
TL;DR: This tutorial provides guidelines on how to set up and plan a SWATH‐MS experiment, how to perform the mass spectrometric measurement and how to analyse SWath‐MS data using peptide‐centric scoring.
Journal ArticleDOI
DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics
Chih-Chiang Tsou,Dmitry M. Avtonomov,Brett Larsen,Monika Tucholska,Hyungwon Choi,Anne-Claude Gingras,Alexey I. Nesvizhskii +6 more
TL;DR: DIA-Umpire enables targeted extraction of quantitative information based on peptides initially identified in only a subset of the samples, resulting in more consistent quantification across multiple samples.
References
More filters
“Bioinformatics” 특집을 내면서
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Journal ArticleDOI
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
Brendan MacLean,Daniela M. Tomazela,Nicholas J. Shulman,Matthew C. Chambers,Gregory L. Finney,Barbara Frewen,Randall Kern,David L. Tabb,Daniel C. Liebler,Michael J. MacCoss +9 more
TL;DR: The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM).
Journal ArticleDOI
A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics
TL;DR: A linear dynamic range over 2 orders of magnitude is demonstrated by using the number of spectra (spectral sampling) acquired for each protein by the data-dependent acquisition of peptides eluting into the mass spectrometer.
Journal ArticleDOI
A cross-platform toolkit for mass spectrometry and proteomics
Matthew C. Chambers,Brendan MacLean,Robert Burke,Dario Amodei,Daniel Ruderman,Steffen Neumann,Laurent Gatto,Bernd Fischer,Brian S. Pratt,Jarrett D. Egertson,Katherine Hoff,Darren Kessner,Natalie Tasman,Nicholas J. Shulman,Barbara Frewen,Tahmina A Baker,Mi-Youn Brusniak,Christopher Paulse,David M. Creasy,Lisa Flashner,Kian Kani,Chris Moulding,Sean L. Seymour,Lydia M. Nuwaysir,Brent Lefebvre,Frank E. Kuhlmann,Joe Roark,Paape Rainer,Suckau Detlev,Tina Hemenway,Andreas Huhmer,James I. Langridge,Brian Connolly,Trey Chadick,Krisztina Holly,Josh Eckels,Eric W. Deutsch,Robert L. Moritz,Jonathan E. Katz,David B. Agus,Michael J. MacCoss,David L. Tabb,Parag Mallick,Parag Mallick +43 more
TL;DR: The ProteoWizard Toolkit is developed, a robust set of open-source, software libraries and applications designed to facilitate proteomics research that implements the first-ever, non-commercial, unified data access interface for proteomics, bridging field-standard open formats and all common vendor formats.
Journal ArticleDOI
Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis
Ludovic C Gillet,Pedro Navarro,Stephen Tate,Hannes L. Röst,Nathalie Selevsek,Lukas Reiter,Ron Bonner,Ruedi Aebersold,Ruedi Aebersold +8 more
TL;DR: A new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest is presented, using the information available in fragment ion spectral libraries to mine the complete fragment ion maps generated using a data-independent acquisition method.