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

By Ludovic C. Gillet, Pedro Navarro, S. Tate, Hannes L. Röst, N. Selevsek, Lukas Reiter, R. Bonner, R. Aebersold. Molecular & Cellular Proteomics, 2012

2,509 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/af36e48b2a87d8d7b669bf0f05084f152167e245

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Citations in the corpus

Untargeted metabolomics strategies – Challenges and Emerging Directions (2016, methodology): “A second untargeted metabolomics approach is based on data independent acquisition (DIA), where workflows integrate full MS1 with MS/MS fragmentation for all precursor ions either simultaneously (MS [8]) or in finite mass ranges (SWATH [9]).”
OpenMS: a flexible open-source software platform for mass spectrometry data analysis (2016, methodology): “For maximal sensitivity, the authors chose a targeted analysis strategy for SWATH-MS data 40 that had been developed previously using the OpenMS software library.”
Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues (2015, methodology): “This reduces the cycle time (3.5 s) by a factor of 1.7 as compared with the previously used MS1/AIF (All Ion Fragmentation) method for DIA3, while matching the cycle time of the original SWATH-MS acquisition method (19).”
Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients (2018, background): “In addition, it may also be helpful to usemore sensitive protein MS techniques; for instance, data-independent acquisition MS (Gillet et al., 2012).”