Comprehensive Tandem-Mass-Spectrometry Coverage of Complex Samples Enabled by Data-Set-Dependent Acquisition

Analytical Chemistry
Corey D BroecklingJessica E Prenni

Abstract

Tandem mass spectrometry (MS/MS) is an invaluable experimental tool for providing analytical data supporting the identification of small molecules and peptides in mass-spectrometry-based "omics" experiments. Data-dependent MS/MS (DDA) is a real-time MS/MS-acquisition strategy that is responsive to the signals detected in a given sample. However, in analysis of even moderately complex samples with state-of-the-art instrumentation, the speed of MS/MS acquisition is insufficient to offer comprehensive MS/MS coverage of all detected molecules. Data-independent approaches (DIA) offer greater MS/MS coverage, typically at the expense of selectivity or sensitivity. This report describes data-set-dependent MS/MS (DsDA), a novel integration of MS1-data processing and target prioritization to enable comprehensive MS/MS sampling during the initial MS-level experiment. This approach is guided by the premise that in omics experiments, individual injections are typically made as part of a larger set of samples, and feedback between data processing and data acquisition can allow approximately real-time optimization of MS/MS-acquisition parameters and nearly complete MS/MS-sampling coverage. Using a combination of R, Proteowizard, XCMS, and WRE...Continue Reading

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Citations

Mar 19, 2019·Annual Review of Analytical Chemistry·María Eugenia MongeFacundo M Fernández
Apr 1, 2021·Analytical Chemistry·Vinny DaviesSimon Rogers
Jun 20, 2021·Mass Spectrometry Reviews·Emmanuel DefossezGaétan Glauser
Jul 13, 2019·Analytical Chemistry·Paul D HutchinsJoshua J Coon

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