Extracting Monoisotopic Single-Charge Peaks From Liquid Chromatography-Electrospray Ionization-Mass

Peak extraction from raw data is the first step in analysis of mass spectrometry (MS) data. The quality of this procedure is very important because it affects the quality of all subsequent analysis, such as database searches and peak quantitation. Many methods have been proposed in the literature, yet the number of practical solutions in terms of available software is rather limited. Virtual Expert Mass Spectrometrist (VEMS) v3.0 includes an algorithm for extracting monoisotopic single-charged peaks and their corresponding retention time from liquid chromatography (LC)-MS data. The extracted peaks can subsequentially be exported to other programs or used internally by VEMS to perform peptide mass fingerprinting searches or peptide quantitation. Additionally, VEMS interfaces the commercial program ProteinLynx Global server v2.0.5 for automatic peak extraction from MS/MS spectra obtained by LC-MS/MS.