The current study introduces an approach for pattern recognition of drug ma
nufacturers according to their HPLC trace impurity data. This method consid
ers signals in phase space and accounts for two different types of noise: a
dditive and perturbative. The pharmaceutical fingerprints are estimated as
mean trajectories of HPLC trace impurity data and are used as reference mod
els for recognition of new data by the minimal length classifier. The chrom
atographic trace organic impurity patterns collected from six different man
ufacturers of L-tryptophan are analyzed as an example. The prediction abili
ty of the new method tested using three different cross-validation procedur
es remains about 95% even if the number of available data in the training s
ets decreases by 5 times. The accuracy of prediction in phase space is supe
rior compared to results calculated using a Window Preprocessing method and
artificial neural networks. The difference in performance between new and
previous methods becomes more significant under particular conditions that
are more adequate for practical application of the method. In addition, the
current approach enables simple and comprehensive interpretation of the ca
lculated results.