Kojak: efficient analysis of chemically cross-linked protein complexes.

ABSTRACT: Protein chemical cross-linking and mass spectrometry enable the analysis of protein-protein interactions and protein topologies; however, complicated cross-linked peptide spectra require specialized algorithms to identify interacting sites. The Kojak cross-linking software application is a new, efficient approach to identify cross-linked peptides, enabling large-scale analysis of protein-protein interactions by chemical cross-linking techniques. The algorithm integrates spectral processing and scoring schemes adopted from traditional database search algorithms and can identify cross-linked peptides using many different chemical cross-linkers with or without heavy isotope labels. Kojak was used to analyze both novel and existing data sets and was compared to existing cross-linking algorithm

SUBMITTER: Hoopmann MR 

PROVIDER: S-EPMC4428575 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature