Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis*

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.

[1]  Lars Malmström,et al.  A Computational Tool to Detect and Avoid Redundancy in Selected Reaction Monitoring , 2012, Molecular & Cellular Proteomics.

[2]  C. Tian,et al.  Software for quantitative proteomic analysis using stable isotope labeling and data independent acquisition. , 2011, Analytical chemistry.

[3]  B. Simons,et al.  Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). , 2011, Analytical chemistry.

[4]  R. Aebersold,et al.  mProphet: automated data processing and statistical validation for large-scale SRM experiments , 2011, Nature Methods.

[5]  D. Goodlett,et al.  Faster, quantitative, and accurate precursor acquisition independent from ion count. , 2011, Analytical chemistry.

[6]  M. Mann,et al.  More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. , 2011, Journal of proteome research.

[7]  Ruedi Aebersold,et al.  Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer , 2011, Proceedings of the National Academy of Sciences.

[8]  Matthias Mann,et al.  Mass spectrometry–based proteomics in cell biology , 2010, The Journal of cell biology.

[9]  R. Aebersold,et al.  Increased Selectivity, Analytical Precision, and Throughput in Targeted Proteomics , 2010, Molecular & Cellular Proteomics.

[10]  M. Mann,et al.  Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation , 2010, Molecular & Cellular Proteomics.

[11]  M. Hirai,et al.  MassBank: a public repository for sharing mass spectral data for life sciences. , 2010, Journal of mass spectrometry : JMS.

[12]  Ruedi Aebersold,et al.  Options and considerations when selecting a quantitative proteomics strategy , 2010, Nature Biotechnology.

[13]  S. Blanksby,et al.  Advances in mass spectrometry for lipidomics. , 2010, Annual review of analytical chemistry.

[14]  M. Goshe,et al.  Improving protein and proteome coverage through data-independent multiplexed peptide fragmentation. , 2010, Journal of proteome research.

[15]  S Dresen,et al.  Detection and identification of 700 drugs by multi-target screening with a 3200 Q TRAP® LC-MS/MS system and library searching , 2010, Analytical and bioanalytical chemistry.

[16]  Gennifer E. Merrihew,et al.  Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry. , 2010, Analytical chemistry.

[17]  Susumu Goto,et al.  KEGG for representation and analysis of molecular networks involving diseases and drugs , 2009, Nucleic Acids Res..

[18]  W. Weinmann,et al.  ESI-MS/MS library of 1,253 compounds for application in forensic and clinical toxicology , 2009, Analytical and bioanalytical chemistry.

[19]  Lukas N. Mueller,et al.  Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics , 2009, Cell.

[20]  Jason W. H. Wong,et al.  ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics , 2009, BMC Bioinformatics.

[21]  Samuel I. Miller,et al.  Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. , 2009, Analytical chemistry.

[22]  Christoph H Borchers,et al.  Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma , 2009, Nature Biotechnology.

[23]  M. McKay,et al.  Unique Ion Signature Mass Spectrometry, a Deterministic Method to Assign Peptide Identity , 2009, Molecular & Cellular Proteomics.

[24]  Mark P. Molloy,et al.  How specific is my SRM?: The issue of precursor and product ion redundancy , 2009, Proteomics.

[25]  M. Gorenstein,et al.  The detection, correlation, and comparison of peptide precursor and product ions from data independent LC‐MS with data dependant LC‐MS/MS , 2009, Proteomics.

[26]  A. Yergey,et al.  Quantifying proteins by mass spectrometry: The selectivity of SRM is only part of the problem , 2009, Proteomics.

[27]  Dan Golick,et al.  Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures , 2009, Proteomics.

[28]  Ruedi Aebersold,et al.  Quantitative interaction proteomics using mass spectrometry , 2009, Nature Methods.

[29]  Henry H. N. Lam,et al.  A database of mass spectrometric assays for the yeast proteome , 2008, Nature Methods.

[30]  M. Mann,et al.  Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast , 2008, Nature.

[31]  R. Aebersold,et al.  Selected reaction monitoring for quantitative proteomics: a tutorial , 2008, Molecular systems biology.

[32]  Eugene A. Kapp,et al.  Overview of Tandem Mass Spectrometry (MS/MS) Database Search Algorithms , 2007, Current protocols in protein science.

[33]  Nichole L. King,et al.  Development and validation of a spectral library searching method for peptide identification from MS/MS , 2007, Proteomics.

[34]  William Stafford Noble,et al.  Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. , 2006, Analytical chemistry.

[35]  I. Wilson,et al.  UPLC/MS(E); a new approach for generating molecular fragment information for biomarker structure elucidation. , 2006, Rapid communications in mass spectrometry : RCM.

[36]  R. Beavis,et al.  Using annotated peptide mass spectrum libraries for protein identification. , 2006, Journal of proteome research.

[37]  R. Aebersold,et al.  Mass Spectrometry and Protein Analysis , 2006, Science.

[38]  R. Abagyan,et al.  METLIN: A Metabolite Mass Spectral Database , 2005, Therapeutic drug monitoring.

[39]  Michael J MacCoss,et al.  Quantitative MS for proteomics: teaching a new dog old tricks. , 2005, Analytical chemistry.

[40]  John D. Venable,et al.  Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra , 2004, Nature Methods.

[41]  R. Beavis,et al.  An Improved Model for Prediction of Retention Times of Tryptic Peptides in Ion Pair Reversed-phase HPLC , 2004, Molecular & Cellular Proteomics.

[42]  J. Yates,et al.  A model for random sampling and estimation of relative protein abundance in shotgun proteomics. , 2004, Analytical chemistry.

[43]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[44]  D. Goodlett,et al.  Shotgun collision‐induced dissociation of peptides using a time of flight mass analyzer , 2003, Proteomics.

[45]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[46]  R. Aebersold,et al.  Mass spectrometry in proteomics. , 2001, Chemical reviews.

[47]  D. Wigley,et al.  Teaching a new dog old tricks? , 1998, Structure.

[48]  R. Winchell.  Teaching a new dog old tricks. , 2011, Archives of Surgery.

[49]  Ruedi Aebersold,et al.  High-throughput generation of selected reaction-monitoring assays for proteins and proteomes , 2010, Nature Methods.

[50]  Alexey I Nesvizhskii,et al.  Protein identification by tandem mass spectrometry and sequence database searching. , 2007, Methods in molecular biology.

[51]  Eoin Fahy,et al.  The lipid maps initiative in lipidomics. , 2007, Methods in enzymology.

[52]  Brendan MacLean,et al.  Bioinformatics Applications Note Gene Expression Skyline: an Open Source Document Editor for Creating and Analyzing Targeted Proteomics Experiments , 2022 .

[53]  Tao Xu,et al.  Bioinformatics Applications Note Sequence Analysis Xdia: Improving on the Label-free Data-independent Analysis , 2022 .