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2D-PC-MS_Search_Engine.pdf (1.91 MB)

Proteomic Database Search Engine for Two-Dimensional Partial Covariance Mass Spectrometry

preprint
submitted on 21.01.2021, 19:09 and posted on 22.01.2021, 13:15 by Taran Driver, Ruediger Pipkorn, Leszek Frasinski, Jon P. Marangos, Marina Edelson-Averbukh, Vitali Averbukh
We present a protein database search engine for the automatic identi?cation of peptide and protein sequences using the recently introduced method of two-dimensional partial covariance mass spectrometry (2D-PC-MS). Since 2D-PC-MS measurement reveals correlations between fragments stemming from the same or consecutive decomposition processes, the ?first-of-its-kind 2D-PC-MS search engine is based entirely on the direct matching of the pairs of theoretical and the experimentally detected correlating fragments, rather than of individual fragment signals or their series. We demonstrate that the high structural speci?city a?orded by 2D-PC-MS fragment correlations enables our search engine to reliably identify the correct peptide sequence, even from a spectrum with a large proportion of contaminant signals. While for peptides the 2D-PC-MS correlation matching procedure is based on complementary and internal ion correlations, the identi?cation of intact proteins is entirely based on the ability of 2D-PC-MS to spatially separate and resolve the experimental correlations between complementary fragment ions.

Funding

Wellcome Trust research fellowship Grant No. WT100093MA

EPSRC program Grants No. EP/I032517/1

EPSRC/DSTL MURI No. EP/N018680/1

EPSRC Pathways to Impact Grant No. EP/K503733/1

ERC ASTEX Project No. 290467.

History

Email Address of Submitting Author

m.edelson-averbukh@imperial.ac.uk

Institution

Imperial College London

Country

United Kingdom

ORCID For Submitting Author

0000-0002-7288-375X

Declaration of Conflict of Interest

No conflict of interest.

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