Rationally designed synthetic peptide as versatile calibrant to improve the accuracy of protein sequence analysis using MALDI mass spectrometry

Abstract

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) plays an indispensable role in analyzing protein covalent structures. The reliable identification of amino acid residues and modifications relies on the mass accuracy, which is highly dependent on calibration. However, the accuracy provided by the currently available calibrants still needs further improvement in terms of compatibility with multiple tandem MS modes or ion polarity modes, calibratable range, and minimizing suppression of and interference with analyte signals. Here aiming at developing a versatile calibrant to solve these problem, we designed a synthetic peptide format of calibrant Rx(GDPn)m (referred to as “Gly-Asp-Pro, GDP”) according to the chemical natures of amino acids and polypeptide fragmentation rules in tandem MS. With four types of amino acid residues selected and arranged through rational designs, a GDP peptide produces highly regulated fragments that give rise to evenly spaced signals in each tandem MS mode and is compatible with both positive and negative ion modes. In internal calibration, its regulated fragmentation pattern minimizes interference with analyte signals, and using a single peptide as the input minimizes suppression of the analyte signals. As demonstrated by analyses of proteins including monoclonal antibody and Aβ-42, these features allowed significant increase of the mass accuracy and precision, which improved sequence coverage and sequence resolution in sequence analyses (including de novo sequencing). This rational design strategy may also inspire further development of synthetic calibrants that benefit structural analysis of biomolecules.