The TPP provides robust support for alternative MS data searching including Kojak (Hoopmann et al., submitted, this issue) for standard or cleavable MS2based crosslinking techniques, and Magnum 31 for open modification database searching. Crosslinking-based MS analyses are employed to elucidate proteinprotein interactions and facilitate protein structure and topology predictions. MS2based crosslinking methodologies are similar to those employed by standard shotgun MS2-based methods, but require specialized algorithms for data analysis. Kojak is designed to identify two independent peptides covalently bonded with a crosslinker and fragmented in a single MS2 scan event. Magnum, on the other hand, is specialized in identification of non-peptide masses that are bound to peptides. The tool is capable of identifying xenobiotic mass adducts, in addition to PTMs that were uncharacterized in the search parameters. Both tools support the pepXML file format, making results easily parsed, sorted, explored, and visualized within the TPP graphical user interface. 32 TPP 6.1.0 provides a guided pipeline interface supporting these tools, that include detailed instructions on how to set all parameters and batching of the data files for fast, automated analyses.