Journal
JOURNAL OF PROTEOME RESEARCH
Volume 14, Issue 5, Pages 2190-2198Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr501321h
Keywords
proteomics; cross-linking; mass spectrometry; protein structure
Categories
Funding
- National Science Foundation MRI [0923536]
- National Institutes of Health National Institute of General Medical Sciences [2P50 GM076547/Center for Systems Biology, GM087221, S10RR027584, P41 GM103533]
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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 of 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.
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