Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus

Protein chemical cross-linking combined with mass spectrometry has become an important technique for the analysis of protein structure and protein-protein interactions. A variety of cross-linkers are well developed, but reliable, rapid, and user-friendly tools for large-scale analysis of cross-linked proteins are still in need. Here we report MetaMorpheusXL, a new search module within the MetaMorpheus software suite that identifies both MS-cleavable and noncleavable cross-linked peptides in MS data. MetaMorpheusXL identifies MS-cleavable cross-linked peptides with an ion-indexing algorithm, which enables an efficient large database search. The identification does not require the presence of signature fragment ions, an advantage compared with similar programs such as XlinkX. One complication associated with the need for signature ions from cleavable cross-linkers such as DSSO (disuccinimidyl sulfoxide) is the requirement for multiple fragmentation types and energy combinations, which is not necessary for MetaMorpheusXL. The ability to perform proteome-wide analysis is another advantage of MetaMorpheusXL compared with programs such as MeroX and DXMSMS. MetaMorpheusXL is also faster than other currently available MS-cleavable cross-link search software programs. It is imbedded in MetaMorpheus, an open-source and freely available software suite that provides a reliable, fast, user-friendly graphical user interface that is readily accessible to researchers.