Influence of Matrix Solution Conditions on the MALDI-MS Analysis of Peptides and Proteins

TLDR

Sample–matrix preparation strongly affects MALDI mass spectra quality for peptides and proteins. The study delineates conditions enabling successful measurement of most components in complex peptide and protein mixtures. Mass discrimination with 4‑hydroxy‑α‑cyanocinnamic acid depends on solution composition, pH, and crystal growth rates, underscoring the need for careful MALDI analysis and revealing a reverse‑phase chromatographic‑like dimension that can be exploited for optimization.

Abstract

Sample−matrix preparation procedures are shown to greatly influence the quality of the matrix-assisted laser desorption/ionization (MALDI) mass spectra of peptides and proteins. In particular, dramatic mass discrimination effects are observed when the matrix 4-hydroxy-α-cyanocinnamic acid is used for analyzing complex mixtures of peptides and proteins. The discrimination effects are found to be strongly dependent on the sample−matrix solution composition, pH, and the rates at which the sample−matrix cocrystals are grown. These findings demonstrate the need to exercise great care in performing and interpreting the MALDI analysis of biological samples. The results also indicate that there is a reverse-phase chromatographic-like dimension in the sample−matrix preparation procedures that can be exploited to optimize the analysis. The present work describes the conditions under which the majority of components of a complex mixture of peptides and proteins can be successfully measured.