JOURNAL OF COMPUTATIONAL BIOLOGY Volume 8, Number 6, 2001 Mary Ann Liebert, Inc. Pp. 571–583 Algorithms for Identifying Protein Cross-Links via Tandem Mass Spectrometry TING CHEN, 1 JACOB D. JAFFE, 2 and GEORGE M. CHURCH 3 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 rst step nds two protein subsequences whose mass sum equals a given mass measured from the mass spectrometry; and the second step nds 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-efcient algorithms for these two steps and implemented and tested them on experimental data of cross-linked hemoglobin proteins. An interchain cross- link between two ¯ subunits was found in two tandem mass spectra. The length of the cross-linker (7.7 Å ) is very close to the actual distance (8.18 Å ) obtained from the molecular structure in PDB. Key words: proteomics, mass spectrometry, algorithms, protein cross-linking, protein-protein interactions, protein folding. 1. INTRODUCTION I n recent years, more and more genomes of model organisms have been sequenced. Using these genomic sequences, researchers have focused on the identi  cation of genes on the genome, the study of gene regulation and gene regulatory networks, the discovery of signal transduction pathways, the de- termination of protein structures, the detection of protein–protein, protein–DNA, and protein–metabolite interactions, and the elucidation of functions of genes and their protein products. A method which combines chemical cross-linking of proteins with mass spectrometry or tandem mass spectrometry may be useful in discovering protein complexes, determining their structure (Young et al., 2000) and/or quantitating in vivo concentrations. This paper focuses on new algorithms for interpretation of complex experimental data generated by protein cross-linking and tandem mass spectrometry. Traditionally, three-dimensional structures of proteins are solved by x-ray crystallography and NMR. However, generating an accurate structure that satises constraints of experimental data can be extremely 1 Department of Molecular Biology, University of Southern California, Los Angeles, CA 90089. 2 Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138. 3 Department of Genetics, Harvard Medical School, Boston, MA 02115. 571