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Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques
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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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“Therefore, DIA results in the identification of nearly all detectable peptides within a selected mass range, allowing for comprehensive and accurate quantification of identified proteins in the sample with minimal missing values [81, 82].”
From Systems-based proteomics to resolve the biology of Alzheimer’s disease beyond amyloid and tau (2021) · cites this paper as [81]
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Metadata
- Authors
- Meyer, J. G., & Schilling, B.
- Affiliations
- Buck Institute for Research on Aging (US)
- Corresponding author
- Schilling, Birgit
- Venue
- Expert Review of Proteomics
- Publisher
- Informa UK Limited
- Published
- 2017-05-04
- Volume
- 14
- Issue
- 5
- Pages
- 419-429
- ISSN
- 1478-9450 (ISSN-L)
- 1744-8387
- PMC
- PMC5671767
- OpenAlex
- W2610156696
- Cited by
- 151
- References
- 80
- Citations by year
- 2026: 6 · 2025: 13 · 2024: 20 · 2023: 15 · 2022: 24 · 2021: 17 · 2020: 28 · 2019: 18 · 2018: 7 · 2017: 3
- FWCI
- 1.76
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Expert Review of Proteomics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of Diabetes and Digestive and Kidney Diseases (R24DK085610)
- NIH (S10 OD016281)
- NIH T32 (T32G000266)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- quantitative proteomics, data-independent acquisition, multiple reaction monitoring, parallel reaction monitoring, SWATH, biomarker discovery, clinical proteomics, high-resolution mass spectrometry, bioinformatics pipeline, disease pathways
- MeSH terms
- Humans, Biomarkers, Molecular Diagnostic Techniques, Proteomics
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