Sample preparation for peptide mapping--A pharmaceutical quality-control perspective

In quality control of therapeutic proteins peptide mapping is used for confirmation of primary structure and detection of posttranslational modifications. The demands put on the experimental procedure are therefore different than in the case of determination of an unknown protein structure. It is here recognized that a peptide-mapping method for quality control of proteins should be inert (not induce or revert modifications), general, robust, and allow a high sample throughput. The steps prior to the separation of the generated peptides are identified as crucial for meeting these demands. This includes denaturation, reduction, alkylation, buffer exchange, solubilization, and digestion. A critical review of the literature regarding these steps is presented. Relevant options in all steps are experimentally evaluated. Novel approaches are developed for many of the steps. The result is a sample preparation procedure that essentially meets the stated demands.

Implementation and use of gradient predictions for optimization of reversed-phase liquid chromatography of peptides. Practical considerations

The options in the implementation of gradient theory for optimization work are critically reviewed and evaluated for the case of the reversed-phase liquid chromatography of peptides. Various models are covered together with methods for the determination of model parameters. Approaches for calculating retention times and band widths from experimental data are discussed. Different kinds of extrapolation are compared with interpolation. This study was aimed at finding the best compromise between number of experiments, accuracy of predictions and simplicity of calculations. Implementation and the use of gradient predictions can be simple, and practical recommendations are given.

Characterization of the influence of displacing salts on retention in gradient elution ion-exchange chromatography of proteins and peptides

It has been shown earlier that the choice of displacing salt has a large effect on the retention in ion-exchange chromatography of proteins and peptides. The influence of different displacing salts cannot be predicted or quantitatively explained, owing to the current lack of an adequate theoretical framework. In this work a general characterization is made by using a considerable number of proteins and peptides and all displacing salts found feasible. Principal component analysis is used to interpret the large amount of data that is generated. The results of the analysis indicate that most of the retention variations are due to non-specific effects and can be explained by changes in the apparent gradient slope, i.e., the increase in elution strength per unit volume, and the elution strength of the starting buffer. This differs from the interpretation given earlier, where the selectivity changes were attributed to specific effects of the salts. However, as it is impossible to test all existing proteins and peptides, specific effects are still possible, but they might be less common than previously considered.