Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011:696:319-26.
doi: 10.1007/978-1-60761-987-1_20.

Identification of alternatively spliced transcripts using a proteomic informatics approach

Rajasree Menon  1 , Gilbert S Omenn
Affiliations

Identification of alternatively spliced transcripts using a proteomic informatics approach

Rajasree Menon et al. Methods Mol Biol. 2011.

Abstract

We present the protocol for the identification of alternatively spliced peptide sequences from tandem mass spectrometry datasets searched using X!Tandem against our modified ECgene resource with all potential translation products and then matched with the Michigan Peptide to Protein Integration (MPPI) scheme. This approach is suitable for human and mouse datasets. Application of the method is illustrated with a study of the Kras activation-Ink4/Arf deletion mouse model of human pancreatic ductal adenocarcinoma.

PubMed Disclaimer

Figures

Figure
Figure
The Flow chart displaying the analytical work flow of the X!Tandem search results for the identification of Alternative Splice Variant proteins.
See this image and copyright information in PMC

References

    1. Bracco L, Kearsey J. The relevance of alternative RNA splicing to pharmacogenomics. Trends in Biotechnology. 2003;21:346–353. - PubMed
    1. Faustino NA, Cooper TA. Pre-mRNA splicing and human disease. Genes & Development. 2003;17:419–437. - PubMed
    1. Garcia-Blanco MA, Baraniak AP, Lasda EL. Alternative splicing in disease and therapy. Nat Biotech. 2004;22:535–546. - PubMed
    1. Venables JP. Aberrant and Alternative Splicing in Cancer. Cancer Res. 2004;64:7647–7654. - PubMed
    1. Kim N, Shin S, Lee S. ECgene: Genome-based EST clustering and gene modeling for alternative splicing. Genome Res. 2005;15:566–576. - PMC - PubMed

LinkOut - more resources