✍ Scribed by Christian F. W. Becker; Ron Wacker; Werner Bouschen; Ralf Seidel; Branko Kolaric; Pascal Lang; Hendrick Schroeder; Oliver Müller; Christof M. Niemeyer; Bernhard Spengler; Roger S. Goody; Martin Engelhard
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Microarray technology allows the analysis of a large number of different parameters simultaneously by using a variety of readout systems based on fluorescence, chemiluminescence, electrochemistry, radioactivity, or mass spectrometry (MS). [1] Of these readout systems mass spectrometry is unique, since it provides information on an intrinsic physical parameter of the analyte, its molecular weight. Such a readout system is especially useful to determine protein expression levels by using surface enhanced laser desorption ionization (SELDI), to determine enzyme activity through peptide-based approaches such as SAMDI (self-assembled monolayers for MALDI), and for the direct detection of cross-hybridization on DNA chips. [2][3][4][5][6][7] Particularly important is the capability of mass spectrometry to unequivocally identify specific proteinprotein interactions by providing the exact molecular weight of the binding partner. [7] To develop a microarray-based assay that combines the reversible immobilization of proteins with readout by MALDI mass spectrometry, we have utilized protein-DNA conjugates (DNA-directed immobilization, DDI). This method achieves highly specific but noncovalent and therefore reversible binding of protein-DNA conjugates to com-
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A number of different procedures have been developed for use with matrix-assisted laser desorption/ionization mass spectrometry (MALDI/MS) for the analysis of non-covalent protein-protein complexes. These include use of specific matrix and laser combinations, accumulation of "first shot" spectra, mo
Proteins play a key role in many biological processes by tein complexes, and assess the contribution of individual amino forming specific noncovalent complexes with DNA, small acid residues to a protein's function. Here, it is our goal to summarize these approaches and highlight recent, biologically