In the context of clinical or population studies using targeted proteomics (MRM/SRM), a peptide with a high natural variation is problematic. Subjects with the minor allele have a different amino acid sequence. Therefore, the targeted approach of MRM/SRM which isolates a specific m/z would register a null or noise value for the peptide target, confounding downstream analysis.
The Population Variation plug-in for Skyline presents the variant data from dbSNP and the 1000 Genome project for mutations with a calculated minor allele frequency. Three kinds of mutations that alter protein coding sequences are reported: non-synonymous variants that change a single amino acid, and frame-shift and stop-gain mutations that alter all downstream amino acids. The plug-in is regularly updated to keep current with dbSNP releases.
UPDATES
Nov 11, 2013. Version 1.3
- New dbSNP release (build 137). More use guidance. Bug fixes
