TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level
Abstract
Multiplexed proteomics is a powerful tool to assay cell states in health and disease, but accurate quantification of relative protein changes is impaired by interference from co-isolated peptides. Most widely, this issue is alleviated by MS3-based quantification, reducing sensitivity and requiring specialized instrumentation. An alternative approach is quantification by complementary ions, which allows accurate and precise multiplexed quantification at the MS2 level and is compatible with the most widely distributed instruments. However, complementary ions of the popular TMT tag form inefficiently and plexing is limited to five channels. In this work, we evaluate and optimize complementary ion quantification for the recently released TMTPro tag, which increases plexing capacity to 8 channels (TMTProC). We find that the beneficial fragmentation properties increase quantification signal five-fold compared to TMT. This increased sensitivity results in ~50% more proteins quantified compared to TMTPro-MS3 and even slightly outperforms TMTPro-MS2. Furthermore, TMTProC quantification is more accurate than TMTPro-MS2 and even superior to TMTPro-MS3. To demonstrate the power of TMTProC, we analyzed a human and yeast interference sample and were able to quantify 13,290 proteins in 24 fractions. Thus, TMTProC advances multiplexed proteomics data quality and widens access to accurate multiplexed proteomics beyond laboratories with MS3-capable instrumentation.
- Publication Date:
- Research Org.:
- Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
- OSTI Identifier:
- 1807585
- Grant/Contract Number:
- SC0018420; R35GM128813
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Proteome Research
- Additional Journal Information:
- Journal Volume: 20; Journal Issue: 6; Journal ID: ISSN 1535-3893
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; multiplexing; complementary ions; shotgun proteomics; TMTpro; CID; isobaric labeling; accurate quantification; interference-free; FAIMS
Citation Formats
Johnson, Alex, Stadlmeier, Michael, and Wühr, Martin. TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level. United States: N. p., 2021.
Web. doi:10.1021/acs.jproteome.0c00813.
Johnson, Alex, Stadlmeier, Michael, & Wühr, Martin. TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level. United States. https://doi.org/10.1021/acs.jproteome.0c00813
Johnson, Alex, Stadlmeier, Michael, and Wühr, Martin. Fri .
"TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level". United States. https://doi.org/10.1021/acs.jproteome.0c00813. https://www.osti.gov/servlets/purl/1807585.
@article{osti_1807585,
title = {TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level},
author = {Johnson, Alex and Stadlmeier, Michael and Wühr, Martin},
abstractNote = {Multiplexed proteomics is a powerful tool to assay cell states in health and disease, but accurate quantification of relative protein changes is impaired by interference from co-isolated peptides. Most widely, this issue is alleviated by MS3-based quantification, reducing sensitivity and requiring specialized instrumentation. An alternative approach is quantification by complementary ions, which allows accurate and precise multiplexed quantification at the MS2 level and is compatible with the most widely distributed instruments. However, complementary ions of the popular TMT tag form inefficiently and plexing is limited to five channels. In this work, we evaluate and optimize complementary ion quantification for the recently released TMTPro tag, which increases plexing capacity to 8 channels (TMTProC). We find that the beneficial fragmentation properties increase quantification signal five-fold compared to TMT. This increased sensitivity results in ~50% more proteins quantified compared to TMTPro-MS3 and even slightly outperforms TMTPro-MS2. Furthermore, TMTProC quantification is more accurate than TMTPro-MS2 and even superior to TMTPro-MS3. To demonstrate the power of TMTProC, we analyzed a human and yeast interference sample and were able to quantify 13,290 proteins in 24 fractions. Thus, TMTProC advances multiplexed proteomics data quality and widens access to accurate multiplexed proteomics beyond laboratories with MS3-capable instrumentation.},
doi = {10.1021/acs.jproteome.0c00813},
journal = {Journal of Proteome Research},
number = 6,
volume = 20,
place = {United States},
year = {Fri Apr 30 00:00:00 EDT 2021},
month = {Fri Apr 30 00:00:00 EDT 2021}
}
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