Effect of Matrix-Assisted Laser Desorption Ionization-Time of Flight-Mass Spectrometric Analysis Conditions and Accuracy Rating on Protein Database Search in Peptides Mass Fingerprint Identify Proteins

To inspect the effect of main MS analysis conditions and data accuracy through matrix-assisted laser desorption ionization-time of flight-mass spectrometry and to obtain peptides mass fingerprint (PMF) for protein search results. BSA had been separated by SDS-PAGE, hydrolyzed by trypsin, and identified by MS, and PMF data were searched through MS-Fit search engine. The results showed that the sequence coverage and the peptide coverage gradually increase when laser strike numbers under 300 and numbers at 400, which appeared to descend tendency. Target protein score, amino acid sequence, and peptide coverage appeared to increase following increase in laser intensity, and when laser intensity was at 1413, there was a tendency to descend. Peptide coverage showed an increasing tendency following delay-time increase, and when delay time was at 260 ns, there was a tendency to descend. On the basis of optimized analysis conditions and on checking the same site for 3 times, the result showed that reproducibility was better. To inspect the accuracy of MS data, Mix 2 was used as external standard to remedy MS primitive data. It was found to score higher, order ahead, detect fewer numbers, and show better reliability as the MS data approached standard value. In contrast, we almost didn't get target protein. The results showed that MS accuracy and analysis conditions were present, which distinguished the influence on protein database search.