Stabilization of N-terminal cysteines in HPLC-HRMS quality control of peptide pools

Abstract

Abstract Synthetic peptide pools are used in experimental and clinical immunology, for example, cancer immunotherapy. The analytical characterization is challenging due to the similarity of the peptides, usually only a pre-characterization of the single peptides is performed. However, regular quality control of the peptide mix would be highly desirable. Therefore, a high performance liquid chromatography-high resolution mass spectrometry (HPLC-HRMS) method for quality control of a peptide pool was developed. Peptides were synthesized and purified to > 90% each. The lyophilized single peptides were combined to a peptide pool containing 32 peptides and analyzed by HPLC-HRMS. Quantification is carried out UV detection, and identification is obtained by high resolution mass spectrometry. Before separation on a capillary reversed-phase column, alkylation of thiols was performed. Best results were obtained with a linear gradient from 96% of solvent A (water with 0.05% TFA), 4% of solvent B (acetonitrile with 0.04% TFA) to 56% of solvent A, 44% of solvent B in 100 minutes. Without sample preparation, peptides with N-terminal cysteine will yield almost no UV signal. This surprising effect could be eliminated using iodoacetic acid (IAC) as an alkylation reagent. The amount of IAC and reductant (Tris(2-carboxyethyl)phosphine (TCEP)) was carefully optimized to avoid overalkylation. By a combination of capillary HPLC and HRMS, a method could be developed for the quality control of complex synthetic peptide pools. In contrast to the analysis of single peptides, analyzing complex peptide pools requires the stabilization of cysteine-containing peptides. Good results were obtained using iodoacetic acid as an alkylation reagent.