Mass spectrometry and tandem mass spectrometry characterization of protein patterns, protein markers and whole proteomes for pathogenic bacteria

There have been many recent reviews published on MALDI-TOF MS (matrix assisted laser desorption/ionization time-of-flight) MS (mass spectrometry) for identification of bacteria particularly with relevance to clinical microbiology. MALDI-TOF MS is now a mature technique for bacterial identification with great promise. The purpose of this review is to put into perspective MALDI-TOF MS and other widely used mass spectrometry methods for characterization of proteins. MALDI-TOF MS is used for rapid determination of a mass pattern of proteins for bacterial characterization; these proteins are generally not identified. Alternatively after gel separation, MALDI-TOF-TOF MS-MS (tandem mass spectrometry) or on-line LC-ESI MS-MS (liquid chromatography-electrospray tandem mass spectrometry) specific protein markers can be identified and peptide sequence variation among species assessed. Unlike direct MALDI-TOF MS, sample preparation for gel separation/MALDI-TOF-TOF MS and MS-MS remains quite demanding. Specific marker proteins are readily identified. Sample preparation is quite straight-forward for LC-MS-MS. Massive amounts of information (whole proteomes) are provided but bioinformatics is complex. Chromatography and electrospray mass spectrometry instrumentation is also not widely used among microbiologists. Thus, there is a need for further development in sample preparation and instrumental development for rapid and simplified analysis. As MS-MS for microbial characterization reaches maturity, it is to be anticipated that further developments in bioinformatics will also become essential. The genome codes for all proteins that might be synthesized under certain growth conditions but only direct protein identification can prove that specific proteins or networks of proteins are actually expressed which might be of relevance in improving our understanding of bacterial pathogenesis.