{"doi":"10.1021/pr900172v","title":"Mascot-Derived False Positive Peptide Identifications Revealed by Manual Analysis of Tandem Mass Spectra","abstract":null,"journal":"Journal of Proteome Research","year":2009,"id":652160,"datarank":0.6090664515819629,"base_score":4.060443010546419,"endowment":4.060443010546419,"self_citation_contribution":0.6090664515819629,"citation_network_contribution":0.0,"self_endowment_contribution":0.6090664515819629,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":57,"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":689705,"name":"Junmei Zhang","orcid":"0000-0002-5653-2554","position":1,"is_corresponding":false},{"id":250855,"name":"Gang Xing","orcid":"0000-0001-8857-9421","position":2,"is_corresponding":false},{"id":114545,"name":"Yingming Zhao","orcid":null,"position":3,"is_corresponding":false},{"id":374277,"name":"Yue Chen","orcid":"0000-0003-4088-7649","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Mascot-Derived False Positive Peptide Identifications Revealed by Manual Analysis of Tandem Mass Spectra","abstract":"False positives that arise when MS/MS data are used to search protein sequence databases remain a concern in proteomics research. Here, we present five types of false positives identified when aligning sequences to MS/MS spectra by Mascot database searching software. False positives arise because of (1) enzymatic digestion at abnormal sites; (2) misinterpretation of charge states; (3) misinterpretation of protein modifications; (4) incorrect assignment of the protein modification site; and (5) incorrect use of isotopic peaks. We present examples, clearly identified as false positives by manual inspection, that nevertheless were assigned high scores by Mascot sequence alignment algorithm. In some examples, the sequence assigned to the MS/MS spectrum explains more than 80% of the fragment ions present. Because of high sequence similarity between the false positives and their corresponding true hits, the false positive rate cannot be evaluated by the common method of using a reversed or scrambled sequence database. A common feature of the false positives is the presence of unmatched peaks in the MS/MS spectra. Our studies highlight the importance of using unmatched peaks to remove false positives and offer direction to aid development of better sequence alignment algorithms for peptide and PTM identification.","is_dataset_classified":null,"base_score":4.060443010546419,"endowment":4.060443010546419,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19368407","pmcid":"PMC2720604","openalex_id":"https://openalex.org/W1979452711","authors":[],"funders":[{"funder_name":"NIDDK NIH HHS","grant_id":"R01 DK082664","title":null},{"funder_name":"NCI NIH HHS","grant_id":"CA 126832","title":null},{"funder_name":"NCI NIH HHS","grant_id":"R01 CA126832","title":null}],"total_grants":3,"fwci":3.7617,"citation_percentile":0.93602039,"influential_citations":0,"citation_trend":[{"year":2012,"count":6},{"year":2013,"count":3},{"year":2014,"count":2},{"year":2015,"count":2},{"year":2016,"count":4},{"year":2017,"count":5},{"year":2018,"count":1},{"year":2019,"count":4},{"year":2020,"count":1},{"year":2021,"count":3},{"year":2022,"count":4},{"year":2024,"count":1},{"year":2025,"count":1}],"oa_status":"green","license":null,"oa_locations":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2720604","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2720604","host_type":"repository"},{"url":"https://pubs.acs.org/doi/pdf/10.1021/pr900172v","host_type":"publisher"},{"url":"https://doi.org/10.1021/pr900172v","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/19368407","host_type":"repository"}],"fields_of_study":["Advanced Proteomics Techniques and Applications","Mass Spectrometry Techniques and Applications","Metabolomics and Mass Spectrometry Studies"],"mesh_terms":["Chromatography, High Pressure Liquid","Peptide Fragments","Protein Processing, Post-Translational","Trypsin","Sequence Alignment","Databases, Protein","Proteomics","Tandem Mass Spectrometry"],"keywords":["False positive paradox","Mascot","Similarity (geometry)","True positive rate","Database search engine","Sequence (biology)","Tandem mass spectrometry","False discovery rate","False positive rate","Pattern recognition (psychology)","Computer science","Computational biology","Artificial intelligence","Chemistry","Mass spectrometry","Biology","Search engine","Chromatography","Genetics","Information retrieval"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Partnerships for the goals"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-10T12:08:27.041495Z","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":[]}