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

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Gillet, Ludovic C. Navarro, Pedro Tate, Stephen Röst, Hannes Selevsek, Nathalie Reiter, Lukas Bonner, Ron Aebersold, Ruedi
Description	Country affiliation: Switzerland Author Affiliation: Gillet LC ( Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, 8093 Zürich, Switzerland.)
Abstract	Most proteomic studies use liquid chromatography coupled to tandem mass spectrometry to identify and quantify the peptides generated by the proteolysis of a biological sample. However, with the current methods it remains challenging to rapidly, consistently, reproducibly, accurately, and sensitively detect and quantify large fractions of proteomes across multiple samples. Here we present a new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest. It consists of using the information available in fragment ion spectral libraries to mine the complete fragment ion maps generated using a data-independent acquisition method. For this study, the data were acquired on a fast, high resolution quadrupole-quadrupole time-of-flight (TOF) instrument by repeatedly cycling through 32 consecutive 25-Da precursor isolation windows (swaths). This SWATH MS acquisition setup generates, in a single sample injection, time-resolved fragment ion spectra for all the analytes detectable within the 400-1200 m/z precursor range and the user-defined retention time window. We show that suitable combinations of fragment ions extracted from these data sets are sufficiently specific to confidently identify query peptides over a dynamic range of 4 orders of magnitude, even if the precursors of the queried peptides are not detectable in the survey scans. We also show that queried peptides are quantified with a consistency and accuracy comparable with that of selected reaction monitoring, the gold standard proteomic quantification method. Moreover, targeted data extraction enables ad libitum quantification refinement and dynamic extension of protein probing by iterative re-mining of the once-and-forever acquired data sets. This combination of unbiased, broad range precursor ion fragmentation and targeted data extraction alleviates most constraints of present proteomic methods and should be equally applicable to the comprehensive analysis of other classes of analytes, beyond proteomics.
File Format	HTM / HTML
ISSN	15359476
e-ISSN	15359484
DOI	10.1074/mcp.O111.016717
Journal	Molecular & Cellular Proteomics
Issue Number	6
Volume Number	11
Language	English
Publisher	American Society for Biochemistry and Molecular Biology
Publisher Date	2012-06-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Proteomics Data Mining Peptide Mapping Proteome Chemistry Tandem Mass Spectrometry Amino Acid Sequence Chromatography, Liquid Computer Simulation Data Interpretation, Statistical Limit Of Detection Mitochondria Enzymology Molecular Sequence Data Peptide Fragments Protein Processing, Post-translational Metabolism Reference Standards Saccharomyces Cerevisiae Saccharomyces Cerevisiae Proteins Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Medicine Analytical Chemistry Molecular Biology Biochemistry

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