Improved analysis of crosslinking mass spectrometry data with Kojak 2.0, advanced by integration into the Trans-Proteomic Pipeline

ABSTRACT: Fragmentation ion spectral analysis of chemically crosslinked proteins is an established technology in the proteomics research repertoire for determining protein interactions, spatial orientation, and structure. Here we present Kojak version 2.0, a major update to the original Kojak algorithm, which was developed to identify crosslinked peptides from fragment ion spectra using a database search approach. A substantially improved algorithm with updated scoring metrics, support for cleavable crosslinkers, and identification of crosslinks between 15N-labeled homomultimers are among the newest features of Kojak 2.0 presented here. Kojak 2.0 is now integrated into the Trans-Proteomic Pipeline, enabling access to dozens of additional tools within that suite. In particular, the PeptideProphet and iProphet tools for validation of crosslinks improve the sensitivity and accuracy of correct crosslink identifications at user-defined thresholds. These new features improve the versatility of the algorithm, enabling its use in a wider range of experimental designs and analysis pipelines. Kojak 2.0 remains open-source and multi-platform.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Bos Taurus (bovine) Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Michael Hoopmann  

LAB HEAD: Robert L. Moritz

PROVIDER: PXD037492 | Pride | 2023-01-18

REPOSITORIES: Pride