Crossfinder-assisted mapping of protein crosslinks formed by site-specifically incorporated crosslinkers

UNLABELLED Protein crosslinking has been used for decades to derive structural information about proteins and protein complexes. Only recently, however, it became possible to map the amino acids involved in the crosslinks with the advent of high resolution mass spectrometry (MS). Here, we present Crossfinder, which automates the search for crosslinks formed by site-specifically incorporated crosslinking amino acids in LC-MS-MS data. AVAILABILITY AND IMPLEMENTATION An executable version of Crossfinder for Windows machines (64-bit) is freely available to non-commercial users. It is bundled with a manual and example data.