The Chromeleon CDS software uses the data from the peptide workbook (created by the BioPharma Finder software) to identify the peptides present in your samples. The target peptide workbook lists the targeted peptides, their amino acid sequences, and their chemical formula, retention time, theoretical mass, charge and isotope information.
Chromeleon CDS software uses retention times and masses to assign chromatographic peaks to peptides. It can also determine whether an MS spectrum displays the correct pattern of intensities; this is called composite scoring.
When the identity of a peak is confirmed, Chromeleon CDS software can take the mass that is defined as suitable for quantitation of the peptide and create an extracted ion chromatogram (XIC). By comparing areas (or heights) of specific peaks in specific XICs, Chromeleon CDS software can calculate the relative abundance of peptide modifications in your samples.