title: TAPAS: tools to assist the targeted protein quantification of human alternative splice variants.
abstract: BACKGROUND
  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.
  
  
  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.
  
  
  METHODS
  The TAPAS server is available at URL http://davinci.crg.es/tapas/.
  
  
  BACKGROUND
  luis.serrano@crg.eu or christina.kiel@crg.eu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Jae-Seong
authors.initials: JS
authors.lastname: Yang
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Eduard
authors.initials: E
authors.lastname: Sabidó
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Luis
authors.initials: L
authors.lastname: Serrano
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Christina
authors.initials: C
authors.lastname: Kiel
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry; D020033:Protein Isoforms / Q000032:analysis / Q000737:chemistry / Q000235:genetics; D040901:Proteomics / Q000379:methods*
chemical_list: D010455:Peptides; D020033:Protein Isoforms