Identification of Peptides in Proteomics Supported by Prediction of Peptide Retention by Means of Quantitative Structure–retention Relationships

Quantitative structure–retention relationships (QSRR) have been derived for prediction of RP-HPLC retention of peptides obtained by online digestion of myoglobin. To characterize the structure of a peptide quantitatively, and then to predict its retention time under gradient HPLC conditions, the structural descriptors used were: the logarithm of the sum of retention times of the amino acids of the peptide, log SumAA; the logarithm of the Van der Waals volume of the peptide, log VDWVol; and the logarithm of its calculated n-octanol–water partition coefficient, clog P. The predictive power of the QSRR model was checked by use of a myoglobin digest, after separation and identification of the peptides by LC–ESI-MS–MS. On-line protein digestion was performed by use of trypsin immobilized on an epoxy-modified silica monolithic support coupled on-line to LC–ESIMS–MS. The predicted gradient retention times of the peptides were related to the experimental retention times obtained after on-line digestion of myoglobin. Identification of the components of the protein digest was supported by QSRR analysis. The QSRR approach was used as an additional constraint in proteomic research to verify results from MS–MS ion search, and to confirm both correctness of peptide identifications and indications of potential false positive and false negative results. The results suggest that because of the use of QSRR for prediction of peptide retention, information derived from standard liquid chromatographic separation in proteomics research could also be useful for eventual identification of the peptides.