Abstract: Objective Analyze the characteristics of ultrasound-assisted digestion for in-solution protein sample. Methods Bovine serum albumin was in-solution digested by ultrasound-assisted digestion and overnight digestion methods, and the digested peptides were analyzed by MALDI-TOF mass spectrometry. After database searching the identified peptides from two methods were analyzed. Results The digestion time of ultrasound-assisted method can be shortened to 10 minutes, but the peptide recovery was 8% lower than overnight method. For peptide identifications the MASCOT score, protein coverage and peptide number of ultrasound-assisted method was about 1 fold, 10% and 40% higher than that of overnight method, but the miscleavage peptide rate was 22% higher. Analysis of the peptides only identified from ultrasound-assisted method showed that molecular weight distribution was 2~3ku and most of them was miscleavage peptides. Conclusions Ultrasound-assisted digestion method can significantly shorten protein digestion time and obtain better peptide identifications, but the sample loss will be increased and part of the peptides were not completely digested.

Key words: Key words: proteome, ultrasound-assisted digestion, in-solution digestion