High flow LC-MS analysis of plasma digest for protein identification

Proteome analysis can play an important role in the discovery of target biomarkers in matrices such as plasma, serum or urine. One way to examine the human proteome is through liquid chromatography mass spectrometry (LC-MS). LC-MS analysis of digested human plasma allows the detection of thousands of peptides within one run. Bioinformatic analysis then allows the identification of signature peptides that may be used to identify proteins. Data from high flow rate LC-MS has been shown to be able to simultaneously identify hundreds of proteins that may then be used as targets for future studies. In this application note from Thermo Fisher Scientific, discover how protein and peptide IDs were determined from data-dependent (DDA) and data-independent (DIA) scans. Selectively reducing the database size was demonstrated to increase the resolving power of the identification method, significantly increasing the number of protein and peptide IDs for DDA and DIA scans.