{"doi":"10.1074/mcp.m111.008490","title":"Published and Perished? The Influence of the Searched Protein Database on the Long-Term Storage of Proteomics Data","abstract":null,"journal":"Molecular & Cellular Proteomics","year":2011,"id":606065,"datarank":0.4943755299006494,"base_score":3.295836866004329,"endowment":3.295836866004329,"self_citation_contribution":0.4943755299006494,"citation_network_contribution":0.0,"self_endowment_contribution":0.4943755299006494,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":26,"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":120145,"name":"Richard G. Côté","orcid":null,"position":1,"is_corresponding":false},{"id":1555650,"name":"Christopher Gerner","orcid":null,"position":2,"is_corresponding":false},{"id":5922,"name":"Henning Hermjakob","orcid":"0000-0001-8479-0262","position":3,"is_corresponding":false},{"id":1555651,"name":"Juan Antonio Vizcaíno","orcid":null,"position":4,"is_corresponding":false},{"id":79929,"name":"Johannes Griss","orcid":"0000-0003-2206-9511","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Published and Perished? The Influence of the Searched Protein Database on the Long-Term Storage of Proteomics Data","abstract":"In proteomics, protein identifications are reported and stored using an unstable reference system: protein identifiers. These proprietary identifiers are created individually by every protein database and can change or may even be deleted over time. To estimate the effect of the searched protein sequence database on the long-term storage of proteomics data we analyzed the changes of reported protein identifiers from all public experiments in the Proteomics Identifications (PRIDE) database by November 2010. To map the submitted protein identifier to a currently active entry, two distinct approaches were used. The first approach used the Protein Identifier Cross Referencing (PICR) service at the EBI, which maps protein identifiers based on 100% sequence identity. The second one (called logical mapping algorithm) accessed the source databases and retrieved the current status of the reported identifier. Our analysis showed the differences between the main protein databases (International Protein Index (IPI), UniProt Knowledgebase (UniProtKB), National Center for Biotechnological Information nr database (NCBI nr), and Ensembl) in respect to identifier stability. For example, whereas 20% of submitted IPI entries were deleted after two years, virtually all UniProtKB entries remained either active or replaced. Furthermore, the two mapping algorithms produced markedly different results. For example, the PICR service reported 10% more IPI entries deleted compared with the logical mapping algorithm. We found several cases where experiments contained more than 10% deleted identifiers already at the time of publication. We also assessed the proportion of peptide identifications in these data sets that still fitted the originally identified protein sequences. Finally, we performed the same overall analysis on all records from IPI, Ensembl, and UniProtKB: two releases per year were used, from 2005. This analysis showed for the first time the true effect of changing protein identifiers on proteomics data. Based on these findings, UniProtKB seems the best database for applications that rely on the long-term storage of proteomics data.","is_dataset_classified":null,"base_score":3.295836866004329,"endowment":3.295836866004329,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"21700957","pmcid":"PMC3186200","openalex_id":"https://openalex.org/W2098932404","authors":[],"funders":[{"funder_name":"Wellcome Trust","grant_id":"WT085949MA","title":null},{"funder_name":"European Commission FP7","grant_id":"FP7_226073","title":null},{"funder_name":"European Commission FP7","grant_id":"FP7_260558","title":null},{"funder_name":"European Commission FP7","grant_id":"FP7_202272","title":null},{"funder_name":"Austrian Science Fund FWF","grant_id":"L 670-B13","title":null},{"funder_name":"Wellcome Trust","grant_id":"085949","title":"The Proteomics Identifications Database (PRIDE)."},{"funder_name":"Austrian Science Fund (FWF)","grant_id":"L 670","title":"A New Strategy for Biomarker Discovery Applied to Melanoma"},{"funder_name":"European Commission","grant_id":"202272","title":"Lipid droplets as dynamic organelles of fat deposition and release: Translational research towards human disease"},{"funder_name":"European Commission","grant_id":"226073","title":"Serving Life-science Information for the Next Generation"},{"funder_name":"European Commission","grant_id":"260558","title":"International Data Exchange and Data Representation Standards for Proteomics"},{"funder_name":"Wellcome Trust","grant_id":"","title":null},{"funder_name":"Wellcome Trust","grant_id":"","title":null}],"total_grants":12,"fwci":2.3245,"citation_percentile":0.87643966,"influential_citations":0,"citation_trend":[{"year":2012,"count":5},{"year":2013,"count":7},{"year":2014,"count":3},{"year":2015,"count":2},{"year":2016,"count":1},{"year":2023,"count":2},{"year":2024,"count":2},{"year":2025,"count":2},{"year":2026,"count":1}],"oa_status":"hybrid","license":"cc-by","oa_locations":[{"url":"http://www.mcponline.org/article/S1535947620301614/pdf","host_type":"journal"},{"url":"http://www.mcponline.org/article/S1535947620301614/pdf","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S1535947620301614?httpAccept=text/xml","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S1535947620301614?httpAccept=text/plain","host_type":"publisher"},{"url":"https://syndication.highwire.org/content/doi/10.1074/mcp.M111.008490","host_type":"publisher"},{"url":"https://doi.org/10.1074/mcp.m111.008490","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/21700957","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3186200","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC3186200","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC3186200?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1074/mcp.M111.008490","host_type":""},{"url":"https://dx.doi.org/10.1074/mcp.m111.008490","host_type":""}],"fields_of_study":["Advanced Proteomics Techniques and Applications","Genomics and Phylogenetic Studies","Metabolomics and Mass Spectrometry Studies","0301 basic medicine","0303 health sciences","03 medical and health sciences","Algorithms","Amino Acid Sequence","Animals","Databases, Protein","Humans","Information Science","Molecular Sequence Data","Proteins","Proteomics","Software"],"mesh_terms":["Algorithms","Amino Acid Sequence","Animals","Humans","Information Science","Molecular Sequence Data","Proteins","Software","Databases, Protein","Proteomics"],"keywords":["UniProt","Identifier","Ensembl","Computer science","Proteomics","Database","Unique identifier","Protein sequencing","Reference database","Information retrieval","Computational biology","Data mining","Biology","Peptide sequence","Genome","Genomics","Genetics","Molecular Sequence Data","Technological Innovation and Resources","Proteins","Animals","Humans","Amino Acid Sequence","Databases, Protein","Algorithms","Information Science","Software"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Partnerships for the goals"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"uniprot"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-30T03:49:44.014443Z","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":[]}