Experiences and perspectives of MALDI MS and MS/MS in proteomic research

The simplicity, robustness, and sensitivity of MALDI have made it a fundamental technique of proteomics. Here we report on our experience in high throughput protein identification by MALDI peptide mass fingerprinting. A streamlined system has been developed that encompasses spot excision, digestion and sample/matrix preparation, data acquisition, database searching and logging of the results. Despite achieving robust and high throughput identification we find that MALDI peptide mass fingerprinting alone is not sufficiently selective for current demands in proteomic research. However, the combination of MALDI with tandem mass spectrometry such as joining a quadrupole with a TOF analyser pairs highly parallel analysis with high selectivity. Thus MALDI will remain an important technique in the modem proteomic laboratory. (C) 2002 Elsevier Science B.V. All rights reserved.