Solvent-free MALDI-MS for the analysis of beta-amyloid peptides via the mini-ball mill approach: qualitative and quantitative advances.

Manual and automated solvent-free mini-ball mill (MBM) matrix-assisted laser desorption/ionization (MALDI) analysis of mixtures of beta-amyloid peptides (1-11), (33-42), (1-42) and non-beta-amyloid component of Alzheimer's disease peptide yielded interpretable spectra for all of the peptides present regardless of their relative amounts in the samples. This was not the case for solvent-based MALDI analysis using traditional acidic aqueous/organic solvent conditions, which resulted in severe over-representation of hydrophilic peptide (1-11) and provided no spectra for insoluble amphiphilic peptide (1-42) even when present at 50% relative molar amount. Less accurate representation of components in mixtures by the traditional method appears to be a combination of poor dissolution of peptides in the solvent and preferential ionization of more hydrophilic peptides in the mixture. Consequently, only MBM provided a complete tryptic map of beta-amyloid (1-42) compared to 67% coverage by traditional MALDI. Acetonitrile (0.1% TFA) led to improved coverage only at a 50% molar ratio of peptide (1-42), but also to a side product of (1-42), Met oxidation (amino acid 35), a phenomenon not observed in MBM MALDI analysis. Traditional MALDI analysis resulted in over-representation of hydrophilic soluble beta-amyloid (1-11) in defined mixtures and autoproteolytic peptides of trypsin. In contrast, over-representation and under-representation were less pronounced in solvent-free MALDI in all of the investigated cases. Analysis of defined peptide and tryptic peptide mixtures showed that MBM MALDI yielded greater qualitative reliability, which also improved quantitative response relative to the solvent-based approach.