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Updated: Apr 27, 2026
Detection of Alternative Splicing During Epithelial-Mesenchymal Transition
Published on: October 9, 2014
TAPAS: tools to assist the targeted protein quantification of human alternative splice variants
Jae-Seong Yang1, Eduard Sabidó1, Luis Serrano2
1EMBL/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.
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.
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.
Availability And Implementation:
The TAPAS server is available at URL http://davinci.crg.es/tapas/.
Contact:
luis.serrano@crg.eu or christina.kiel@crg.eu
Supplementary Information:
Supplementary data are available at Bioinformatics online.
