Top-down mass spectrometry of native proteoforms and their complexes: a community study

Tanja Habeck; Kyle A. Brown; Benjamin Des Soye; Carter Lantz; Mowei Zhou; Novera Alam; Md Amin Hossain; Wonhyeuk Jung; James E. Keener; Michael Volny; Jesse W. Wilson; Yujia Ying; Jeffrey N. Agar; Paul O. Danis; Ying Ge; Neil L. Kelleher; Huilin Li; Joseph A. Loo; Michael T. Marty; Ljiljana Paša-Tolić; Wendy Sandoval; Frederik Lermyte

doi:10.1038/s41592-024-02279-6

Top-down mass spectrometry of native proteoforms and their complexes: a community study

Tanja Habeck, Kyle A. Brown, Benjamin Des Soye, Carter Lantz, Mowei Zhou, Novera Alam, Md Amin Hossain, Wonhyeuk Jung, James E. Keener, Michael Volny, Jesse W. Wilson, Yujia Ying, Jeffrey N. Agar, Paul O. Danis, Ying Ge, Neil L. Kelleher, Huilin Li, Joseph A. Loo, Michael T. Marty, Ljiljana Paša-TolićWendy Sandoval, Frederik Lermyte^*

^*Corresponding author for this work

Molecular Biosciences

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

The combination of native electrospray ionization with top-down fragmentation in mass spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and cofactors. Although this approach is powerful, both native MS and top-down MS are not yet well standardized, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics initiated a study to develop and test protocols for native MS combined with top-down fragmentation of proteins and protein complexes across 11 instruments in nine laboratories. Here we report the summary of the outcomes to provide robust benchmarks and a valuable entry point for the scientific community.

Original language	English (US)
Journal	Nature Methods
DOIs	https://doi.org/10.1038/s41592-024-02279-6
State	Accepted/In press - 2024

Funding

We are grateful to all members of the Board of Directors of the CTDP for valuable discussions. We also thank B. Krichel and S. McIlwain (University of Wisconsin-Madison) and C. Hake (TU Darmstadt) for assistance with database searching. The CTDP, a 501c3 nonprofit corporation, is grateful for the generous support from Seer, ThermoFisher Scientific, Bruker, SCIEX, Lilly, Pfizer, Newomics and Agilent. M.T.M. thanks A. Makarov and K. Fort at ThermoFisher Scientific for support on the UHMR Q Exactive HF instrument. This work was supported by National Institutes of Health (NIH)/National Institute of General Medical Sciences (NIGMS) grant R35 GM128624 to M.T.M, NIH grant R01 GM125085 and S10 OD018475 to Y.G. and NIH/NIGMS grant P41 GM108569 to N.L.K., as well as NIH grant R01GM103479, R35GM145286, S10RR028893 and US Department of Energy grant DEFC02-02ER63421 to J.A.L. We acknowledge project award (10.46936/intm.proj.2019.51141/60006696) from the Environmental Molecular Sciences Laboratory, a Department of Energy Office of Science User Facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830 to M.Z. and J.W.W. and the Ruth L. Kirschstein National Research Service Award Program at NIH (GM007185) to C.L. We are grateful for funding by the Hessian Ministry for Science and Arts via the LOEWE project \u2018TRABITA\u2019 and by the Deutsche Forschungsgemeinschaft (grant nos. 461372424 and 524226614) to F.L. The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript.

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/s41592-024-02279-6

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Habeck, T., Brown, K. A., Des Soye, B., Lantz, C., Zhou, M., Alam, N., Hossain, M. A., Jung, W., Keener, J. E., Volny, M., Wilson, J. W., Ying, Y., Agar, J. N., Danis, P. O., Ge, Y., Kelleher, N. L., Li, H., Loo, J. A., Marty, M. T., ... Lermyte, F. (Accepted/In press). Top-down mass spectrometry of native proteoforms and their complexes: a community study. Nature Methods. https://doi.org/10.1038/s41592-024-02279-6

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title = "Top-down mass spectrometry of native proteoforms and their complexes: a community study",

abstract = "The combination of native electrospray ionization with top-down fragmentation in mass spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and cofactors. Although this approach is powerful, both native MS and top-down MS are not yet well standardized, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics initiated a study to develop and test protocols for native MS combined with top-down fragmentation of proteins and protein complexes across 11 instruments in nine laboratories. Here we report the summary of the outcomes to provide robust benchmarks and a valuable entry point for the scientific community.",

author = "Tanja Habeck and Brown, {Kyle A.} and {Des Soye}, Benjamin and Carter Lantz and Mowei Zhou and Novera Alam and Hossain, {Md Amin} and Wonhyeuk Jung and Keener, {James E.} and Michael Volny and Wilson, {Jesse W.} and Yujia Ying and Agar, {Jeffrey N.} and Danis, {Paul O.} and Ying Ge and Kelleher, {Neil L.} and Huilin Li and Loo, {Joseph A.} and Marty, {Michael T.} and Ljiljana Pa{\v s}a-Toli{\'c} and Wendy Sandoval and Frederik Lermyte",

note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive licence to Springer Nature America, Inc. 2024.",

year = "2024",

doi = "10.1038/s41592-024-02279-6",

language = "English (US)",

journal = "Nature Methods",

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Habeck, T, Brown, KA, Des Soye, B, Lantz, C, Zhou, M, Alam, N, Hossain, MA, Jung, W, Keener, JE, Volny, M, Wilson, JW, Ying, Y, Agar, JN, Danis, PO, Ge, Y, Kelleher, NL, Li, H, Loo, JA, Marty, MT, Paša-Tolić, L, Sandoval, W & Lermyte, F 2024, 'Top-down mass spectrometry of native proteoforms and their complexes: a community study', Nature Methods. https://doi.org/10.1038/s41592-024-02279-6

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T2 - a community study

AU - Habeck, Tanja

AU - Brown, Kyle A.

AU - Des Soye, Benjamin

AU - Lantz, Carter

AU - Zhou, Mowei

AU - Alam, Novera

AU - Hossain, Md Amin

AU - Jung, Wonhyeuk

AU - Keener, James E.

AU - Volny, Michael

AU - Wilson, Jesse W.

AU - Ying, Yujia

AU - Agar, Jeffrey N.

AU - Danis, Paul O.

AU - Ge, Ying

AU - Kelleher, Neil L.

AU - Li, Huilin

AU - Loo, Joseph A.

AU - Marty, Michael T.

AU - Paša-Tolić, Ljiljana

AU - Sandoval, Wendy

AU - Lermyte, Frederik

PY - 2024

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AB - The combination of native electrospray ionization with top-down fragmentation in mass spectrometry (MS) allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and cofactors. Although this approach is powerful, both native MS and top-down MS are not yet well standardized, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics initiated a study to develop and test protocols for native MS combined with top-down fragmentation of proteins and protein complexes across 11 instruments in nine laboratories. Here we report the summary of the outcomes to provide robust benchmarks and a valuable entry point for the scientific community.

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Top-down mass spectrometry of native proteoforms and their complexes: a community study

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