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.