Anal Bioanal Chem (2006) 386: 24–37 DOI 10.1007/s00216-006-0600-5 REVIEW Andreas Tholey . Elmar Heinzle Ionic (liquid) matrices for matrix-assisted laser desorption/ionization mass spectrometry—applications and perspectives Received: 4 April 2006 / Revised: 6 June 2006 / Accepted: 7 June 2006 / Published online: 8 July 2006 # Springer-Verlag 2006 Abstract A large number of matrix substances have been used for various applications in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The majority of matrices applied in ultraviolet-MALDI MS are crystalline, low molecular weight compounds. A problem encountered with many of these matrices is the formation of hot spots, which lead to inhomogeneous samples, thus leading to increased measurement times and hampering the application of MALDI MS for quantitative purposes. Recently, ionic (liquid) matrices (ILM or IM) have been introduced as a potential alternative to the classical crystalline matrices. ILM are equimolar mixtures of conventional MALDI matrix compounds such as 2, 5-dihydroxybenzoic acid (DHB), α-cyano-4-hydroxycin- namic acid (CCA) or sinapinic acid (SA) together with organic bases [e.g., pyridine (Py), tributylamine (TBA) or N,N-dimethylethylenediamine (DMED)]. The present article presents a first overview of this new class of matrices. Characteristic properties of ILM, their influence on mass spectrometric parameters such as sensitivity, resolution and adduct formation and their application in the fields of proteome analysis, the measurement of low molecular weight compounds, the use of MALDI MS for quantitative purposes and in MALDI imaging will be presented. Scopes and limitations for the application of ILM are discussed. Keywords Quantitative MALDI MS . Ionic matrices . Ionic liquid matrices . Low molecular weight compounds . MALDI imaging Introduction Since its introduction in the late 1980s [1], matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has become one of the most valuable tools for the investigation of polymeric biomolecules such as peptides, proteins and oligonucleotides. Other fields of applications include the analysis of technical polymers, small organic molecules and low molecular weight compounds of bio- logical interest including amino acids, lipids and sugars [2]. Recently, additional applications such as imaging of blotted samples, gels or tissues have been developed [3]. MALDI MS has been most frequently used for qualitative analysis, but there are an increasing number of reports applying this method to quantitative analysis. The most striking features of MALDI MS are the relatively simple sample preparation, low sample consumption and high sensitivity, moderate tolerance against impurities like salts and detergents, the speed and throughput encountered with the possibility of multiplexed analyses and the relatively straightforward analysis of the spectra also supported by the formation of singly charged analyte ions. A basic characteristic of MALDI MS is the application of a mixture of the analyte with a suitable matrix substance. This mixture is irradiated by a pulsed laser, thus inducing ablation of analyte and matrix molecules together with ionization of the analytes. The mechanism of the MALDI process itself is complex and not completely understood by far and will not be discussed in detail here. A good overview of the present knowledge about the fundamental processes can be found in several reviews [4–6]. The details of analyte–matrix interactions including analyte incorporation in matrix crystals [7] as well as the ionization state of the analytes in the sample preparations [8] will also not be addressed here. The choice of matrix and the sample preparation are two critical issues for a successful MALDI analysis. They influence the ionization behavior, the formation of adducts, the stability (or fragmentation) of the analytes and also have practical implications on the performance of the experiments. Inhomogeneous samples lead to prolonged A. Tholey (*) . E. Heinzle Technische Biochemie, Geb. 1.5, Universität des Saarlandes, 66123 Saarbrücken, Germany e-mail: a.tholey@mx.uni-saarland.de Tel.: +49-681-3024157 Fax: +49-681-3024572