Kojak: Efficient Analysis of Chemically Cross-Linked Protein Complexes

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 algorithms. The algorithm provided
increased cross-link identifications over existing algorithms and,
equally importantly, the results in a fraction of computational time.
The Kojak algorithm is open-source, cross-platform, and freely available.
This software provides both existing and new cross-linking researchers
alike an effective way to derive additional cross-link identifications
from new or existing data sets. For new users, it provides a simple
analytical resource resulting in more cross-link identifications than
other methods.