Chapter 47 - Proteome Specific Sample Preparation Methods for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Abstract

This chapter presents proteome specific sample preparation methods for matrix-assisted laser desorption or ionization mass spectrometry. In the traditional sample preparation method for matrix-assisted laser desorption/ionization (MALDI) MS, the analyte and matrix solutions are mixed directly on the MALDI target, referred to as the dried droplet method. The analyte molecules were eluted directly into a nano-ESI capillary needle by centrifugation prior to mass analysis. Later, this sample preparation was simplified by using Eppendorf GELoader tips packed with chromatographic material or pre-packed micro columns. The use of micro columns allows upconcentration and desalting of highly diluted samples prior to MS analysis, resulting in an increase in the sensitivity and of the overall quality of the mass spectra. An increased tolerance toward salts is observed, presumably because the peptides co-crystallize with matrix in the center, whereas the salt molecules are up-concentrated in the hydrophilic DHB edge. The fast evaporation method is used less frequently in proteome analysis nowadays. However, several laboratories prepare a layer of matrix prior to spotting sample and matrix on top.