Format

Send to

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

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

Author information

1
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.
2
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.

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:

luis.serrano@crg.eu or christina.kiel@crg.eu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
24996896
DOI:
10.1093/bioinformatics/btu428
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Silverchair Information Systems
Loading ...
Support Center