ABSTRACT
Objective:To optimize the major parameters of bioinformatics analysis conditions in process of PMF(Peptide Mass Fingerprinting) identify target proteins. Methods:In this process of experiment design and analysis,we made the Bovine Carbonic anhydrase-2 and BSA from 2-DE gel,after proteolysis with porcine trypsin and gathered the peptides,subsequently identified with MALDI-TOF MS and got the peptides mass data. Then,we selected database of Swissprot and MS-Fit search engine,the standard Carbonic anhydrase-2 protein used as model to set up protein search standard conditions. Results:Our study showed that the cysteine was modified by carbamidomethylation more convenient in protein search,at the same time,the better mode of mass tolerance was percentage and 0.1% was suitable tolerance in our search. Then we used BSA mass data to check the accuracy of MS search standard conditions. Conclusions:Results show that the optimized parameters are reliable.