PChopper: high throughput peptide prediction for MRM/SRM transition design.

ABSTRACT:

Background

The use of selective reaction monitoring (SRM) based LC-MS/MS analysis for the quantification of phosphorylation stoichiometry has been rapidly increasing. At the same time, the number of sites that can be monitored in a single LC-MS/MS experiment is also increasing. The manual processes associated with running these experiments have highlighted the need for computational assistance to quickly design MRM/SRM candidates.

Results

PChopper has been developed to predict peptides that can be produced via enzymatic protein digest; this includes single enzyme digests, and combinations of enzymes. It also allows digests to be simulated in 'batch' mode and can combine information from these simulated digests to suggest the most appropriate enzyme(s) to use. PChopper also a

SUBMITTER: Afzal V 

PROVIDER: S-EPMC3230909 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature