An informatic framework for decoding protein complexes by top-down mass spectrometry

Owen S. Skinner; Pierre C. Havugimana; Nicole A. Haverland; Luca Fornelli; Bryan P. Early; Joseph B. Greer; Ryan T. Fellers; Kenneth R. Durbin; Luis H.F. Do Vale; Rafael D. Melani; Henrique S. Seckler; Micah T. Nelp; Mikhail E. Belov; Stevan R. Horning; Alexander A. Makarov; Richard D. LeDuc; Vahe Bandarian; Philip D. Compton; Neil L. Kelleher

doi:10.1038/nmeth.3731

An informatic framework for decoding protein complexes by top-down mass spectrometry

Owen S. Skinner, Pierre C. Havugimana, Nicole A. Haverland, Luca Fornelli, Bryan P. Early, Joseph B. Greer, Ryan T. Fellers, Kenneth R. Durbin, Luis H.F. Do Vale, Rafael D. Melani, Henrique S. Seckler, Micah T. Nelp, Mikhail E. Belov, Stevan R. Horning, Alexander A. Makarov, Richard D. LeDuc, Vahe Bandarian, Philip D. Compton, Neil L. Kelleher^*

^*Corresponding author for this work

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

52 Scopus citations

Abstract

Efforts to map the human protein interactome have resulted in information about thousands of multi-protein assemblies housed in public repositories, but the molecular characterization and stoichiometry of their protein subunits remains largely unknown. Here, we report a computational search strategy that supports hierarchical top-down analysis for precise identification and scoring of multi-proteoform complexes by native mass spectrometry.

Original language	English (US)
Pages (from-to)	237-240
Number of pages	4
Journal	Nature Methods
Volume	13
Issue number	3
DOIs	https://doi.org/10.1038/nmeth.3731
State	Published - Feb 25 2016

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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Skinner, O. S., Havugimana, P. C., Haverland, N. A., Fornelli, L., Early, B. P., Greer, J. B., Fellers, R. T., Durbin, K. R., Do Vale, L. H. F., Melani, R. D., Seckler, H. S., Nelp, M. T., Belov, M. E., Horning, S. R., Makarov, A. A., LeDuc, R. D., Bandarian, V., Compton, P. D., & Kelleher, N. L. (2016). An informatic framework for decoding protein complexes by top-down mass spectrometry. Nature Methods, 13(3), 237-240. https://doi.org/10.1038/nmeth.3731

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abstract = "Efforts to map the human protein interactome have resulted in information about thousands of multi-protein assemblies housed in public repositories, but the molecular characterization and stoichiometry of their protein subunits remains largely unknown. Here, we report a computational search strategy that supports hierarchical top-down analysis for precise identification and scoring of multi-proteoform complexes by native mass spectrometry.",

author = "Skinner, {Owen S.} and Havugimana, {Pierre C.} and Haverland, {Nicole A.} and Luca Fornelli and Early, {Bryan P.} and Greer, {Joseph B.} and Fellers, {Ryan T.} and Durbin, {Kenneth R.} and {Do Vale}, {Luis H.F.} and Melani, {Rafael D.} and Seckler, {Henrique S.} and Nelp, {Micah T.} and Belov, {Mikhail E.} and Horning, {Stevan R.} and Makarov, {Alexander A.} and LeDuc, {Richard D.} and Vahe Bandarian and Compton, {Philip D.} and Kelleher, {Neil L.}",

note = "Funding Information: The authors thank members of the Kelleher research group and V. Wysocki for helpful discussions and advice. O.S.S. is supported by a US National Science Foundation Graduate Research Fellowship (2014171659). P.C.H. is a recipient of a Northwestern University Chemistry of Life Processes Institute Postdoctoral Fellowship Award. L.H.F.D.V. is supported under CNPq research grant 202011/2012-7 from the Brazilian government. H.S.S. is supported under the Science Without Borders scholarship 88888.075416/2013-00 from the Coordination for the Improvement of Higher Education Personnel under the Brazilian government. This work was supported by grants from the W.M. Keck Foundation (DT061512) and the US National Institutes of Health (GM067193) to N.L.K. Publisher Copyright: {\textcopyright} 2016 Nature America, Inc.",

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Skinner, OS, Havugimana, PC, Haverland, NA, Fornelli, L, Early, BP, Greer, JB, Fellers, RT, Durbin, KR, Do Vale, LHF, Melani, RD, Seckler, HS, Nelp, MT, Belov, ME, Horning, SR, Makarov, AA, LeDuc, RD, Bandarian, V, Compton, PD & Kelleher, NL 2016, 'An informatic framework for decoding protein complexes by top-down mass spectrometry', Nature Methods, vol. 13, no. 3, pp. 237-240. https://doi.org/10.1038/nmeth.3731

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AU - Early, Bryan P.

AU - Greer, Joseph B.

AU - Fellers, Ryan T.

AU - Durbin, Kenneth R.

AU - Do Vale, Luis H.F.

AU - Melani, Rafael D.

AU - Seckler, Henrique S.

AU - Nelp, Micah T.

AU - Belov, Mikhail E.

AU - Horning, Stevan R.

AU - Makarov, Alexander A.

AU - LeDuc, Richard D.

AU - Bandarian, Vahe

AU - Compton, Philip D.

AU - Kelleher, Neil L.

N1 - Funding Information: The authors thank members of the Kelleher research group and V. Wysocki for helpful discussions and advice. O.S.S. is supported by a US National Science Foundation Graduate Research Fellowship (2014171659). P.C.H. is a recipient of a Northwestern University Chemistry of Life Processes Institute Postdoctoral Fellowship Award. L.H.F.D.V. is supported under CNPq research grant 202011/2012-7 from the Brazilian government. H.S.S. is supported under the Science Without Borders scholarship 88888.075416/2013-00 from the Coordination for the Improvement of Higher Education Personnel under the Brazilian government. This work was supported by grants from the W.M. Keck Foundation (DT061512) and the US National Institutes of Health (GM067193) to N.L.K. Publisher Copyright: © 2016 Nature America, Inc.

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An informatic framework for decoding protein complexes by top-down mass spectrometry

Abstract

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