pepmap-AnalysesFor historical reasons the analyses are termed pepmap-analyses, since this type of analysis is the type of choice for peptide maps. However, the fundamental tasks outlined below are in no way restricted to the analysis of peptide maps. They are relevant for complex mixtures of all kinds of molecules:Testing for the presence of expected moleculesin a sample: this type of analysis is needed if for example the primary structure or the disulfide linkages need to be verified.Testing for the presence of unexpected moleculesin a sample: this task may well be called the ’Needle in a Haystack’-problem and is much more demanding than the previous task. The solution presented by MassMap®is based on the subtraction of all those signals from the data set that are specific to the molecules expected and identified. The subtraction leaves only molecules not expected in the so-called difference data set, thus pointing directly to the unexpected molecules.