TAPAS: tools to assist the targeted protein quantification of human alternative splice variants

Abstract 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:  [email protected] or [email protected] Supplementary information:  Supplementary data are available at Bioinformatics online.