{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T13:21:37Z","timestamp":1762521697648},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,10,15]]},"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: \u00a0luis.serrano@crg.eu or christina.kiel@crg.eu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu428","type":"journal-article","created":{"date-parts":[[2014,7,5]],"date-time":"2014-07-05T02:02:58Z","timestamp":1404525778000},"page":"2989-2990","source":"Crossref","is-referenced-by-count":1,"title":["TAPAS: tools to assist the targeted protein quantification of human alternative splice variants"],"prefix":"10.1093","volume":"30","author":[{"given":"Jae-Seong","family":"Yang","sequence":"first","affiliation":[{"name":"1 EMBL\/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), 2 Universitat Pompeu Fabra (UPF), 3 Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and 4 Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), 08010 Barcelona, Spain"},{"name":"1 EMBL\/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), 2 Universitat Pompeu Fabra (UPF), 3 Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and 4 Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), 08010 Barcelona, Spain"}]},{"given":"Eduard","family":"Sabid\u00f3","sequence":"additional","affiliation":[{"name":"1 EMBL\/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), 2 Universitat Pompeu Fabra (UPF), 3 Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and 4 Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), 08010 Barcelona, Spain"},{"name":"1 EMBL\/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), 2 Universitat Pompeu Fabra (UPF), 3 Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and 4 Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), 08010 Barcelona, Spain"}]},{"given":"Luis","family":"Serrano","sequence":"additional","affiliation":[{"name":"1 EMBL\/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), 2 Universitat Pompeu Fabra (UPF), 3 Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and 4 Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), 08010 Barcelona, Spain"},{"name":"1 EMBL\/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), 2 Universitat Pompeu Fabra (UPF), 3 Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and 4 Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), 08010 Barcelona, Spain"},{"name":"1 EMBL\/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), 2 Universitat Pompeu Fabra (UPF), 3 Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and 4 Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), 08010 Barcelona, Spain"}]},{"given":"Christina","family":"Kiel","sequence":"additional","affiliation":[{"name":"1 EMBL\/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), 2 Universitat Pompeu Fabra (UPF), 3 Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and 4 Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), 08010 Barcelona, Spain"},{"name":"1 EMBL\/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), 2 Universitat Pompeu Fabra (UPF), 3 Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and 4 Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), 08010 Barcelona, Spain"}]}],"member":"286","published-online":{"date-parts":[[2014,7,4]]},"reference":[{"key":"2023012711555586800_btu428-B1","doi-asserted-by":"crossref","first-page":"2797","DOI":"10.1002\/pmic.201100660","article-title":"Including shared peptides for estimating protein abundances: a significant improvement for quantitative proteomics","volume":"12","author":"Blein-Nicolas","year":"2012","journal-title":"Proteomics"},{"key":"2023012711555586800_btu428-B2","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1089\/cmb.2009.0267","article-title":"Accurate mass spectrometry based protein quantification via shared peptides","volume":"19","author":"Dost","year":"2012","journal-title":"J. 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