Principal component analysis of mass spectra of peptides generated from the tryptic digestion of protein mixtures

Principal component analysis (PCA) has been used to analyse mass spectral p eptide profiles obtained from the enzymatic digestion of standard protein m ixtures. Scores and loadings plots clearly revealed peptide fragments that differentiated one protein mixture from another. Peptide map search results identified with a high degree of certainty any additional proteins in thes e mixtures. As a proof-of-concept this methodology was applied to hepatic p rotein mixtures obtained from rats treated with two hepatotoxic compounds: methapyriline and SB-219994. Liver proteins were extracted, pre-separated b y one-dimensional polyacrylamide gel electrophoresis, subjected to tryptic digestion and analysed by mass spectrometry. Two up-regulated proteins, glu tathione S-transferase with methapyrilene and peroxisomal bifunctional enzy me with SB-219994, were identified in this manner. Copyright (C) 2001 John Wiley & Sons, Ltd.