{"doi":"10.1093/bioinformatics/btu428","title":"TAPAS: tools to assist the targeted protein quantification of human alternative splice variants","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Motivation: In proteomes of higher eukaryotes, many alternative splice variants can only be detected by their shared peptides. This makes it highly challenging to use peptide-centric mass spectrometry to distinguish and to quantify protein isoforms resulting from alternative splicing events.</jats:p>\n               <jats:p>Results: We have developed two complementary algorithms based on linear mathematical models to efficiently compute a minimal set of shared and unique peptides needed to quantify a set of isoforms and splice variants. Further, we developed a statistical method to estimate the splice variant abundances based on stable isotope labeled peptide quantities. The algorithms and databases are integrated in a web-based tool, and we have experimentally tested the limits of our quantification method using spiked proteins and cell extracts.</jats:p>\n               <jats:p>Availability and implementation: The TAPAS server is available at URL http://davinci.crg.es/tapas/ .</jats:p>\n               <jats:p>Contact:  luis.serrano@crg.eu or christina.kiel@crg.eu</jats:p>\n               <jats:p>Supplementary information:  Supplementary data are available at Bioinformatics online.</jats:p>","journal":"Bioinformatics","year":2014,"id":30645,"datarank":0.12296004903039547,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.018987971946403656,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.018987971946403656,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":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":166050,"name":"Eduard Sabidó","orcid":null,"position":1,"is_corresponding":false},{"id":118776,"name":"Luis Serrano","orcid":null,"position":2,"is_corresponding":false},{"id":166051,"name":"Christina Kiel","orcid":null,"position":3,"is_corresponding":false},{"id":150036,"name":"Jae-Seong Yang","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"24996896","pmcid":null,"openalex_id":"https://openalex.org/W2136950317","authors":[],"funders":[{"funder_name":"European Commission","grant_id":"278568","title":"PRIMES: Protein interaction machines in oncogenic EGF receptor signalling"}],"total_grants":1,"fwci":0.0,"citation_percentile":0.10760113,"influential_citations":0,"citation_trend":[{"year":2018,"count":1}],"oa_status":"bronze","license":null,"oa_locations":[{"url":"https://academic.oup.com/bioinformatics/article-pdf/30/20/2989/48929798/bioinformatics_30_20_2989.pdf","host_type":"journal"},{"url":"https://academic.oup.com/bioinformatics/article-pdf/30/20/2989/48929798/bioinformatics_30_20_2989.pdf","host_type":"BRONZE"},{"url":"https://academic.oup.com/bioinformatics/article-pdf/30/20/2989/48929798/bioinformatics_30_20_2989.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/bioinformatics/btu428","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/24996896","host_type":"repository"},{"url":"https://academic.oup.com/bioinformatics/article-pdf/30/20/2989/17148032/btu428.pdf","host_type":""},{"url":"https://dx.doi.org/10.1093/bioinformatics/btu428","host_type":""},{"url":"http://dx.doi.org//10.1093/bioinformatics/btu428","host_type":""},{"url":"https://doi.org/https://doi.org/10.1093/bioinformatics/btu428","host_type":""}],"fields_of_study":["Advanced Proteomics Techniques and Applications","RNA Research and Splicing","RNA and protein synthesis mechanisms","Computer Science","Medicine","Biology","0301 basic medicine","0303 health sciences","03 medical and health sciences","Algorithms","Alternative Splicing","Databases, Protein","Humans","Internet","Mass Spectrometry","Peptides","Protein Isoforms","Proteomics"],"mesh_terms":["Algorithms","Humans","Peptides","Mass Spectrometry","Alternative Splicing","Protein Isoforms","Internet","Databases, Protein","Proteomics"],"keywords":["splice","Alternative splicing","Proteome","Computational biology","Peptide","Gene isoform","Set (abstract data type)","Biology","RNA splicing","Computer science","Bioinformatics","Genetics","Biochemistry","Gene","Proteomics","570","Internet","610","Mass Spectrometry","Humans","Protein Isoforms","Databases, Protein","Peptides","Algorithms"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-09T04:17:49.217563Z","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":[]}