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

Bioinformatics. 2014 Oct 15;30(20):2989-90. doi: 10.1093/bioinformatics/btu428. Epub 2014 Jul 4.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Alternative Splicing*
  • Databases, Protein
  • Humans
  • Internet
  • Mass Spectrometry / methods*
  • Peptides / chemistry
  • Protein Isoforms / analysis
  • Protein Isoforms / chemistry
  • Protein Isoforms / genetics
  • Proteomics / methods*


  • Peptides
  • Protein Isoforms