Accurate mass triggered MS/MS enhances sensitvity and specificity for verification of novel computationally predicted proteins

摘要

Current strategies for verification and quantitation of proteins in complex mixtures require prior knowledge of peptide behavior and generation of labeled synthetic peptides for analysis on triple- quadrupole MS instruments. However, literature mining or non-MS based experimental approaches may also be used to identify targets of interest in the absence of MS experimental data. In these cases, the protein sequence is digested in silico, likely fragment ions are predicted, and theoretical MRM's generated for all the peptides in an acceptable size window. These MRM's are then used as a survey scan in a data dependent experiment to detect specific peptide peaks, and each resulting MRM peak is examined by full scan MS/MS to obtain sequence verification of the hypothesized peptide. MRM-initiated detection and sequencing has been described previously for discovering posttranslational modifications (1,2) in proteins and for drug screening in blood and urine (3).