This recently published minireview in the JCM discusses the use of mass spectrometry in biomarker discovery, the current utility of these markers for bacterial identification after culture, and the potential for non-culture-based diagnosis of infectious diseases. The bases of these thoughts are the independent revolutions that have occurred in the fields of molecular biology and analytical chemistry, leading to the current interrelatedness of genomics, proteomics, and bioinformatics.
The particular focus is on protein markers and proteomics, which are today essentially synonymous with biomedical mass spectrometry. The methods and approaches, while discussed here in the context of bacterial identification, are equally applicable to viruses, fungi, and parasites. To gain a better understanding of the current state of the art, it is important to understand what mass spectrometry has achieved, what are its current capabilities, and what might be expected in the not-too-distant future.
The molecular biology revolution included the development of the PCR and use of restriction enzymes for recognition of sequence differences among organisms by employing "known" genetic markers. The process of marker discovery has been greatly aided in recent years by whole-genome sequencing. In turn, there has been a revolution in mass spectrometry, leading to sequencing of the expressed protein products of these genomes (proteomics). Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry (MS) and tandem mass spectrometry (MS-MS) have been at the core of these developments.

Reference:
Fox, A. 2006 Mass Spectrometry for Species or Strain Identification after Culture or without Culture: Past, Present, and Future J. Clin. Microbiol. 2006;44 2677-2680