{"doi":"10.1021/acs.jproteome.2c00670","title":"Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline","abstract":"Fragmentation ion spectral analysis of chemically cross-linked 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 cross-linked peptides from fragment ion spectra using a database search approach. A substantially improved algorithm with updated scoring metrics, support for cleavable cross-linkers, and identification of cross-links between 15 N-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 cross-links improve the sensitivity and accuracy of correct cross-link 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 multiplatform.","journal":"Journal of Proteome Research","year":2023,"id":336793,"datarank":0.44166584687496613,"base_score":2.9444389791664403,"endowment":2.9444389791664403,"self_citation_contribution":0.44166584687496613,"citation_network_contribution":0.0,"self_endowment_contribution":0.44166584687496613,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":18,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9442,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":432655,"name":"David Shteynberg","orcid":"0000-0001-7982-0498","position":1,"is_corresponding":false},{"id":565814,"name":"Alex Zelter","orcid":"0000-0002-5331-0577","position":2,"is_corresponding":false},{"id":912599,"name":"Michael Riffle","orcid":"0000-0003-1633-8607","position":3,"is_corresponding":false},{"id":565813,"name":"Andrew S. Lyon","orcid":"0000-0001-7681-4981","position":4,"is_corresponding":false},{"id":98189,"name":"David A. Agard","orcid":"0000-0003-3512-695X","position":5,"is_corresponding":false},{"id":949326,"name":"Qing Luan","orcid":"0009-0002-2437-4499","position":6,"is_corresponding":false},{"id":314360,"name":"Brad J. Nolen","orcid":"0000-0002-0224-9980","position":7,"is_corresponding":false},{"id":79569,"name":"Michael J. MacCoss","orcid":"0000-0003-1853-0256","position":8,"is_corresponding":false},{"id":430646,"name":"Trisha N. Davis","orcid":"0000-0003-4797-3152","position":9,"is_corresponding":false},{"id":78845,"name":"Robert L. Moritz","orcid":"0000-0002-3216-9447","position":10,"is_corresponding":false},{"id":432653,"name":"Michael R. Hoopmann","orcid":"0000-0001-7029-7792","position":0,"is_corresponding":true}],"reference_count":44,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:10:21.947540Z","pmid":"36629399","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}