Peptide mapping is an important analytical technique for quality contr
ol of rDNA-derived proteins. The evaluation in peptide mapping is comp
licated by variations in the digestion and the chromatographic separat
ion. The variation sources in peptide mapping are briefly reviewed. A
multivariate evaluation method that can account for the digestion vari
ations is presented. The method utilizes the entire chromatographic pr
ofile as input data, eliminating the need for peak size and retention
time determinations. The influence of chromatographic variations shoul
d be reduced by proper pretreatment of the chromatograms, in order to
allow classification of protein samples. The method is intended to fac
ilitate the evaluation in peptide mapping and is capable of handling n
umerous chromatograms in a data set.