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.

Contact: felix.mueller-planitz@med.uni-muenchen.de

Supplementary information: Supplementary data are available at Bioinformatics online.