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Updated: Jan 26, 2026

An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome
Published on: September 20, 2022
Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition
Jesse G Meyer1, Birgit Schilling1
1a Mass Spectrometry Core , Buck Institute for Research on Aging , Novato , CA , USA.
Introduction:
While selected/multiple-reaction monitoring (SRM or MRM) is considered the gold standard for quantitative protein measurement, emerging data-independent acquisition (DIA) using high-resolution scans have opened a new dimension of high-throughput, comprehensive quantitative proteomics. These newer methodologies are particularly well suited for discovery of biomarker candidates from human disease samples, and for investigating and understanding human disease pathways. Areas covered: This article reviews the current state of targeted and untargeted DIA mass spectrometry-based proteomic workflows, including SRM, parallel-reaction monitoring (PRM) and untargeted DIA (e.g., SWATH). Corresponding bioinformatics strategies, as well as application in biological and clinical studies are presented. Expert commentary: Nascent application of highly-multiplexed untargeted DIA, such as SWATH, for accurate protein quantification from clinically relevant and disease-related samples shows great potential to comprehensively investigate biomarker candidates and understand disease.
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