ArticleJournal of proteome research2021
TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level.
Article in Journal of proteome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Dissecting Detergent-Insoluble Proteome in Alzheimer's Disease by TMTc-Corrected Quantitative Mass Spectrometry.Molecular & cellular proteomics : MCP · 2023Pooled it
- Mass spectrometry proteomics for studying mitostasis.Protein science : a publication of the Protein Society · 2026Review
- Proteomics in Antitumor Drug Target Discovery, Toxicity, Resistance, and Precision Oncology.Drug design, development and therapy · 2026Review
- Multiplexed Data-Independent Acquisition-Based Proteomics Enabled by TMTpro Complementary Ions.Analytical chemistry · 2025Article
- Expanding Targeted Instrumentation for Discovery Applications: Complement Reporter Ion Quantification with a Quadrupole-Ion Trap Instrument.Journal of proteome research · 2025Article
- Synergistic Arg-C Ultra and Lys-C Digestion for Quantitative Proteomics.bioRxiv : the preprint server for biology · 2025Article
- Boosting the Sensitivity of Quantitative Single-Cell Proteomics with Infrared-Tandem Mass Tags.Journal of proteome research · 2025Article
- OmpA controls order in the outer membrane and shares the mechanical load.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- ERK synchronizes embryonic cleavages in Drosophila.Developmental cell · 2024Article
- Enhanced Sample Multiplexing-Based Targeted Proteomics with Intelligent Data Acquisition.Journal of the American Society for Mass Spectrometry · 2024Article
- Mitochondrial ATP generation is more proteome efficient than glycolysis.Nature chemical biology · 2024Article
- A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics.ACS measurement science au · 2024Review
- Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation.Nature communications · 2024Article
- Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm.Journal of the American Society for Mass Spectrometry · 2024Article
- Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP.Journal of the American Society for Mass Spectrometry · 2024Article
- Article
- Evidence for widespread cytoplasmic structuring into mesoscale condensates.Nature cell biology · 2024Article
- A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics.Molecular & cellular proteomics : MCP · 2024Article
- Development of novel isobaric tags enables accurate and sensitive multiplexed proteomics using complementary ions.Analytical and bioanalytical chemistry · 2023Article
- Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics.Journal of the American Chemical Society · 2023Article
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Authors and funding
3 authors.
Funding
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. Interference can be reduced by using MS3-based quantification, but this reduces sensitivity and requires specialized instrumentation. An alternative approach is quantification by complementary ions, the balancer group-peptide conjugates, which allows accurate and precise multiplexed quantification at the MS2 level and is compatible with most proteomics instruments. However, complementary ions of the popular TMT-tag form inefficiently and multiplexing is limited to five channels. Here, we evaluate and optimize complementary ion quantification for the recently released TMTpro-tag, which increases complementary ion plexing capacity to eight channels (TMTproC). Furthermore, the beneficial fragmentation properties of TMTpro increase sensitivity for TMTproC, resulting in ∼65% more proteins quantified compared to TMTpro-MS3 and ∼18% more when compared to real-time-search TMTpro-MS3 (RTS-SPS-MS3). TMTproC quantification is more accurate than TMTpro-MS2 and even superior to RTS-SPS-MS3. We provide the software for quantifying TMTproC data as an executable that is compatible with the MaxQuant analysis pipeline. Thus, TMTproC advances multiplexed proteomics data quality and widens access to accurate multiplexed proteomics beyond laboratories with MS3-capable instrumentation.
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Registered trials
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