Peptide Composer is a multi-functional tool for calculating exact peptide mass values. This includes neutrals, ions of positive or negative polarity and of any charge number.

Peptide Composer calculates lists of possible amino acid combinations that have a predefined mass. The same is done for fragment ions of a precursor ion. The composition of a peptide can be determined based on a small number of accurate fragment ion masses and the accurate parent ion mass.

Based on a defined peptide copmposition, the program determines the most probable sequence from fragment ion signals by scoring against theoretical fragment ion mass values.

The complete process is known as composition-based sequencing (CBS).