MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes
Open accessAbstract
Multiplexed quantitation via isobaric chemical tags (e.g., tandem mass tags (TMT) and isobaric tags for relative and absolute quantitation (iTRAQ)) has the potential to revolutionize quantitative proteomics. However, until recently the utility of these tags was questionable due to reporter ion ratio distortion resulting from fragmentation of coisolated interfering species. These interfering signals can be negated through additional gas-phase manipulations (e.g., MS/MS/MS (MS3) and proton-transfer reactions (PTR)). These methods, however, have a significant sensitivity penalty. Using isolation waveforms with multiple frequency notches (i.e., synchronous precursor selection, SPS), we coisolated and cofragmented multiple MS2 fragment ions, thereby increasing the number of reporter ions in the MS3 spectrum 10-fold over the standard MS3 method (i.e., MultiNotch MS3). By increasing the reporter ion signals, this method improves the dynamic range of reporter ion quantitation, reduces reporter ion signal variance, and ultimately produces more high-quality quantitative measurements. To demonstrate utility, we analyzed biological triplicates of eight colon cancer cell lines using the MultiNotch MS3 method. Across all the replicates we quantified 8 378 proteins in union and 6 168 proteins in common. Taking into account that each of these quantified proteins contains eight distinct cell-line measurements, this data set encompasses 174 704 quantitative ratios each measured in triplicate across the biological replicates. Herein, we demonstrate that the MultiNotch MS3 method uniquely combines multiplexing capacity with quantitative sensitivity and accuracy, drastically increasing the informational value obtainable from proteomic experiments.
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A number of studies have shown that while levels of many proteins are strongly correlated with their transcript levels, with coincident eQTL and pQTL, the correlations for most protein-transcript pairs are modest.
“A number of studies have now shown that while levels of many proteins are strongly correlated with their transcript levels, with coincident eQTL and protein QTL (pQTL), the correlations for most protein–transcript pairs are modest [51–58].”
From Multi-omics approaches to disease (2017) · cites this paper as [55]
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Self-citationShared proteomic effects of cerebral atherosclerosis and Alzheimer’s disease on the human brain
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“Each analysis used an MS3-based TMT method (McAlister et al., 2014; Ting et al., 2011), which has been shown to reduce ion interference compared to MS2”
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“MS3 isolation for quanti-fi cation used Simultaneous Precursor Selection (SPS) as described previously 85 – 87 .”
Self-citation
- Authors
- McAlister, G. C., Nusinow, D. P., Jedrychowski, M. P., Wühr, M., Huttlin, E. L., Erickson, B. K., Rad, R., Haas, W., & Gygi, S. P.
- Affiliations
- Harvard University (US)
- Department of Cell Biology , , , ,
- Corresponding author
- Gygi, Steven P.
- ORCID
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2014-06-13
- Volume
- 86
- Issue
- 14
- Pages
- 7150-7158
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- PMC
- PMC4215866
- OpenAlex
- W2041399392
- Cited by
- 1,263
- References
- 43
- Citations by year
- 2026: 71 · 2025: 86 · 2024: 136 · 2023: 154 · 2022: 121 · 2021: 146 · 2020: 153 · 2019: 115 · 2018: 107 · 2017: 76 · 2016: 51 · 2015: 36 · 2014: 10
- FWCI
- 24.72
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Analytical Chemistry (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (U41HG006673, HG6673)
- National Institute of General Medical Sciences (GM 67945, R01GM067945, R01GM103785)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD073104)
- 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, iTRAQ, differentially expressed proteins, colon cancer cell lines, dynamic range
- MeSH terms
- Algorithms, Chromatography, High Pressure Liquid, Colonic Neoplasms, HeLa Cells, Humans, Ions, Isocitrate Dehydrogenase, Sensitivity and Specificity, Reproducibility of Results, Principal Component Analysis, Proteomics, Cell Line, Tumor, Smad4 Protein, Tandem Mass Spectrometry
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