Label-free quantification using MALDI mass spectrometry: considerations and perspectives

Profound knowledge of protein abundances in healthy tissues and their changes in disease is crucial for understanding biological processes in basic science and for the development of novel diagnostics and therapeutics. Mass spectrometrybased label-free protein quantification is used increasingly often to gain insights into physiological changes observed in perturbed systems. Although the soft ionization techniques electrospray ionization and matrix-assisted laser desorption/ionization have both been used for protein quantification, this article focuses on instrumental setups with a MALDI ion source. Beside reviewing current bioinformatic data-processing tools for label-free quantification and elaborating on the technical benefits of combining UHPLC and MALDI–MS, we outline the potential of state-of-the-art instruments by reporting unpublished results obtained from twenty-four complex biological samples. This review points out that the capabilities of LC–MALDI MS systems have not yet been fully utilized because of a lack of suitable software tools. Online Abstract Figure Graphical representation of the LC–MALDI–MS procedure for label-free protein quantification. Tryptic peptides are separated by reversed-phase ultra-high performance liquid chromatography and eluting fractions are mixed with matrix before robotic deposition on a MALDI target plate. Subsequent to analysis of each spot by MS 1 and MS 2 , bioinformatic tools are used for the label-free protein quantification