{"doi":"10.1021/pr9011816","title":"xComb: A Cross-Linked Peptide Database Approach to Protein−Protein Interaction Analysis","abstract":null,"journal":"Journal of Proteome Research","year":2010,"id":614392,"datarank":0.6515708132780527,"base_score":4.343805421853684,"endowment":4.343805421853684,"self_citation_contribution":0.6515708132780527,"citation_network_contribution":0.0,"self_endowment_contribution":0.6515708132780527,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":76,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1131807,"name":"Pragya Singh","orcid":"0000-0002-0631-3871","position":1,"is_corresponding":false},{"id":109685,"name":"Scott A. Shaffer","orcid":"0000-0002-5264-3257","position":2,"is_corresponding":false},{"id":267538,"name":"David R. Goodlett","orcid":"0000-0002-8045-8200","position":3,"is_corresponding":false},{"id":1583197,"name":"Alexandre Panchaud","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"xComb: A Cross-Linked Peptide Database Approach to Protein−Protein Interaction Analysis","abstract":"We developed an informatic method to identify tandem mass spectra composed of chemically cross-linked peptides from those of linear peptides and to assign sequence to each of the two unique peptide sequences. For a given set of proteins the key software tool, xComb, combs through all theoretically feasible cross-linked peptides to create a database consisting of a subset of all combinations represented as peptide FASTA files. The xComb library of select theoretical cross-linked peptides may then be used as a database that is examined by a standard proteomic search engine to match tandem mass spectral data sets to identify cross-linked peptides. The database search may be conducted against as many as 50 proteins with a number of common proteomic search engines, e.g. Phenyx, Sequest, OMSSA, Mascot and X!Tandem. By searching against a peptide library of linearized, cross-linked peptides, rather than a linearized protein library, search times are decreased and the process is decoupled from any specific search engine. A further benefit of decoupling from the search engine is that protein cross-linking studies may be conducted with readily available informatics tools for which scoring routines already exist within the proteomic community.","is_dataset_classified":null,"base_score":4.343805421853684,"endowment":4.343805421853684,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"20302351","pmcid":"PMC2884221","openalex_id":"https://openalex.org/W2079578946","authors":[],"funders":[{"funder_name":"NIAID NIH HHS","grant_id":"1U54 AI57141-01","title":null},{"funder_name":"NCRR NIH HHS","grant_id":"S10 RR023044","title":null},{"funder_name":"NCI NIH HHS","grant_id":"R33 CA099139","title":null},{"funder_name":"Swiss National Science Foundation","grant_id":"126252","title":null},{"funder_name":"NIAID NIH HHS","grant_id":"U54 AI057141","title":null},{"funder_name":"NCRR NIH HHS","grant_id":"1S10RR023044-01","title":null},{"funder_name":"NCI NIH HHS","grant_id":"R33CA099139-01","title":null}],"total_grants":7,"fwci":3.1358,"citation_percentile":0.9161439,"influential_citations":0,"citation_trend":[{"year":2012,"count":7},{"year":2013,"count":7},{"year":2014,"count":12},{"year":2015,"count":12},{"year":2016,"count":5},{"year":2017,"count":6},{"year":2018,"count":9},{"year":2019,"count":2},{"year":2020,"count":2},{"year":2021,"count":3},{"year":2022,"count":1},{"year":2023,"count":2},{"year":2024,"count":1}],"oa_status":"closed","license":null,"oa_locations":[{"url":"https://pubs.acs.org/doi/pdf/10.1021/pr9011816","host_type":"publisher"},{"url":"https://doi.org/10.1021/pr9011816","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/20302351","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2884221","host_type":"repository"}],"fields_of_study":["Advanced Proteomics Techniques and Applications","Mass Spectrometry Techniques and Applications","Machine Learning in Bioinformatics","Amino Acid Sequence","Computational Biology","Data Mining","Databases, Protein","Humans","Molecular Sequence Data","Protein Interaction Mapping","Proteins","Sequence Alignment","Sequence Analysis, Protein","Software","Tandem Mass Spectrometry"],"mesh_terms":["Amino Acid Sequence","Humans","Molecular Sequence Data","Proteins","Software","Sequence Alignment","Computational Biology","Sequence Analysis, Protein","Protein Interaction Mapping","Databases, Protein","Tandem Mass Spectrometry","Data Mining"],"keywords":["Mascot","Database search engine","Computer science","Search engine","Peptide","Sequence database","Computational biology","Tandem mass spectrometry","Database","Set (abstract data type)","Data mining","Bioinformatics","Information retrieval","Chemistry","Biology","Mass spectrometry","Biochemistry","Programming language","Gene"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-02T13:01:55.094380Z","pmid":null,"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":[]}