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A Review on Quantitative Multiplexed Proteomics
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Over the last few decades, mass spectrometry‐based proteomics has become an increasingly powerful tool that is now able to routinely detect and quantify thousands of proteins. A major advance for global protein quantification was the introduction of isobaric tags, which, in a single experiment, enabled the global quantification of proteins across multiple samples. Herein, these methods are referred to as multiplexed proteomics. The principles, advantages, and drawbacks of various multiplexed proteomics techniques are discussed and compared with alternative approaches. We also discuss how the emerging combination of multiplexing with targeted proteomics might enable the reliable and high‐quality quantification of very low abundance proteins across multiple conditions. Lastly, we suggest that fusing multiplexed proteomics with data‐independent acquisition approaches might enable the comparison of hundreds of different samples without missing values, while maintaining the superb measurement precision and accuracy obtainable with isobaric tag quantification.
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“Major developments in mass spectrometry-based, antibody-based and aptamer-based proteomics over the past decade have enabled the robust quantification of thousands of proteins in single samples87–90.”
From Measuring biological age using omics data (2022) · cites this paper as [87]
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Ding, L., Lin, H., Huang, C., Vallanadu, V., Ashley, K., Pitts, S. R., Mutlu, A. S., Zhou, Y., Ma, X., Choi, J. M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.10.06.757189
Comparative Proteomic Quantification Reveals Novel Longevity Regulators
Ding, L., Lin, H., Huang, C., Vallanadu, V., Ashley, K., Pitts, S. R., Mutlu, A. S., Zhou, Y., Ma, X., Choi, J. M., et al. (2026) · PROTEOMICS · doi:10.1002/pmic.70195
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Quantitative Top‐Down Proteomics: A Review
Cupp‐Sutton, K. A., Atallah, M. A., Zhao, Z., Anjum, S., Chowdhury, T., Sunny, A. T., Szamweber, P., & Wu, S. (2026) · Mass Spectrometry Reviews · doi:10.1002/mas.70051
Metadata
- Authors
- Pappireddi, N., Martin, L., & Wühr, M.
- Affiliations
- Princeton University (US)
- Corresponding author
- Wühr, Martin
- ORCID
- Wühr, Martin
- Venue
- ChemBioChem
- Publisher
- Wiley
- Published
- 2019-04-18
- Volume
- 20
- Issue
- 10
- Pages
- 1210-1224
- ISSN
- 1439-4227 (ISSN-L)
- 1439-7633
- PMC
- PMC6520187
- OpenAlex
- W2908241150
- Cited by
- 299
- References
- 106
- Citations by year
- 2026: 20 · 2025: 32 · 2024: 44 · 2023: 53 · 2022: 56 · 2021: 53 · 2020: 34 · 2019: 6
- FWCI
- 3.84
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- ChemBioChem (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- National Institute of General Medical Sciences (1R35GM128813, T32GM007388)
- U.S. Department of Energy (DE-SC0018420, DE-SC0018260)
- 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 › Advanced Biosensing Techniques and Applications
- Keywords
- multiplexed proteomics, quantitative proteomics, isobaric tags, targeted proteomics, low-abundance proteins, data-independent acquisition, mass spectrometry
- MeSH terms
- Humans, Isotope Labeling, Proteins, Proteome, Proteomics, Tandem Mass Spectrometry
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