MS3 for TMT, not me! TMTProC- improved MS2 accuracy and sensitivity using complementary ions.

Quantitative multiplexed proteomic techniques, such as TMT, are a powerful tool for analysing and quantifying proteins in a cell. These techniques rely on the quantification of reporter ions that are released from tagged peptides following fragmentation. Differentiation of reporter ions from co-isolated peptides requires complex acquisition strategies combined with advance mass spectrometers.

Johnson et al. demonstrate a new method, termed TMTProC (which can be applied on a wide variety of LC-MS systems), that analyses and quantifies complementary peptide fragments created during the release of reporter ions allowing for enhanced detection and quantification of peptides. Using IonOpticks Aurora Series packed emitter columns coupled to an Orbitrap Fusion Lumos Mass Spectrometer, the number of peptides quantified were significantly enhanced. For example, the number of quantified peptides using TMTProC was >18,000 peptides compared to <12,000 peptides with conventional TMT methods. This equates to over 3500 quantified proteins with TMTProC compared to only 2200 proteins in conventional methods.

These enhancements in protein and peptide quantification shows promise for developing insights in understanding differences in protein levels between healthy and diseased cells. These investigations can lead to developing better ways to treat disease.

Read the full paper
TMTPro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level.

Journal of Proteome Research, 20(6), 3043-3052. doi: https://doi.org/10.1021/acs.jproteome.0c00813
Johnson, A., Stadlmeier, M., & Wühr, M. (2021). 

Commentary by Muhammad Zenaidee, PhD

About the author
Muhammad holds a PhD in Chemistry from The University of New South Wales and has a strong background in the development of tools to enhance top-down and bottom-up proteomics. He utilises his knowledge and training to develop new proteomics tools and technologies for the proteomics community.