Algorithms for identifying protein cross-links via tandem mass spectrometry

Authors:
Ting Chen;Jacob D. Jaffe;George M. Church
Affiliations:
Department of Mathematics, University of Sothern California, Los Angeles, CA;Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA;Department of Genetics, Harvard Medical School, Bostom, MA
Venue:
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Year:
2001

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Abstract

Cross-linking technology combined with tandem mass spectrometry (MS-MS) is a powerful method that provides a rapid solution to the discovery of protein-protein interactions and protein structures. We studied the problem of detecting cross-linked peptides and cross-linked amino acids from tandem mass spectral data. Our method consists of two steps: the first step finds two protein subsequences whose mass sum equals a given mass measured from the mass spectrometry; and the second step finds the best cross-linked amino acids in these two peptide sequences that are optimally correlated to a given tandem mass spectrum. We designed fast and space-efficient algorithms for these two steps, and implemented and tested them on experimental data of cross-linked Hemoglobin proteins.