MALDI Mass Spectrometry for Quantitative Proteomics – Approaches, Scopes and Limitations

The determination of absolute protein amounts and the quantification of differentially expressed proteins belong to the most important goals in proteomics. Despite being one of the key technologies for the identification of proteins, the application of matrix assisted laser desorption/ionization (MALDI) mass spectrometry (MS) for quantitative analyses is hampered by several inherent factors. The goal of the present paper is to outline these difficulties but also to present some selected approaches which enable MALDI MS to be used for the quantification of biomolecules. In particular, methods for the improvement of the homogeneity of MALDI samples and the use of internal standards for the relative quantification are discussed. Strategies for in-vivo and in-vitro labelling of peptides and proteins with stable isotopes are presented. The need for guidelines for the presentation and evaluation of data as well as for bioinformatical approaches for the interpretation of quantitative data will be addressed.