Increasing the Multiplexing Capacity of TMTs Using Reporter Ion Isotopologues with Isobaric Masses
Open accessAbstract
Quantitative mass spectrometry methods offer near-comprehensive proteome coverage; however, these methods still suffer with regards to sample throughput. Multiplex quantitation via isobaric chemical tags (e.g., TMT and iTRAQ) provides an avenue for mass spectrometry-based proteome quantitation experiments to move away from simple binary comparisons and toward greater parallelization. Herein, we demonstrate a straightforward method for immediately expanding the throughput of the TMT isobaric reagents from 6-plex to 8-plex. This method is based upon our ability to resolve the isotopic shift that results from substituting a (15)N for a (13)C. In an accommodation to the preferred fragmentation pathways of ETD, the TMT-127 and -129 reagents were recently modified such that a (13)C was exchanged for a (15)N. As a result of this substitution, the new TMT reporter ions are 6.32 mDa lighter. Even though the mass difference between these reporter ion isotopologues is incredibly small, modern high-resolution and mass accuracy analyzers can resolve these ions. On the basis of our ability to resolve and accurately measure the relative intensity of these isobaric reporter ions, we demonstrate that we are able to quantify across eight samples simultaneously by combining the (13)C- and (15)N-containing reporter ions. Considering the structure of the TMT reporter ion, we believe this work serves as a blueprint for expanding the multiplexing capacity of the TMT reagents to at least 10-plex and possibly up to 18-plex.
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PSMs with poor quality or MS3 spectra with TMT reporter ion summed signal-to-noise ratios less than 110 were excluded from quantitation.
“PSMs with poor quality, MS3 spectra with TMT reporter ion summed signal-to-noise ratios less than 110 were excluded from quantitation53.”
From Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease (2020) · cites this paper as [53]
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Self-citation
- Authors
- McAlister, G. C., Huttlin, E. L., Haas, W., Ting, L., Jedrychowski, M. P., Rogers, J. C., Kuhn, K., Pike, I., Grothe, R. A., Blethrow, J. D., & Gygi, S. P.
- Affiliations
- Harvard University (US)
- Thermo Fisher Scientific, Rockford, Illinois 61101, United States
- Proteome Sciences (United Kingdom) (GB)
- Thermo Fisher Scientific (United States) (US)
- Corresponding author
- Gygi, Steven P.
- ORCID
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-08-20
- Volume
- 84
- Issue
- 17
- Pages
- 7469-7478
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- PMC
- PMC3715028
- OpenAlex
- W1988146323
- Cited by
- 605
- References
- 46
- Citations by year
- 2026: 21 · 2025: 37 · 2024: 45 · 2023: 49 · 2022: 42 · 2021: 63 · 2020: 61 · 2019: 58 · 2018: 50 · 2017: 52 · 2016: 36 · 2015: 48 · 2014: 33 · 2013: 10
- FWCI
- 12.87
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Analytical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (HG3456, R01HG003456)
- National Institute of General Medical Sciences (GM 67945, R01GM067945, R01GM103785)
- 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
- tandem mass tags, Trail Making Test, 13C substitution, sample throughput, tandem mass spectrometry, high-resolution mass spectrometry
- MeSH terms
- Animals, Brain, Carbon Isotopes, Chromatography, High Pressure Liquid, HeLa Cells, Humans, Nitrogen Isotopes, Spleen, Thiazoles, Proteome, Mice, Tandem Mass Spectrometry
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