<p dir="ltr">Mass spectrometry has been at the forefront of complex mixture analysis and, as a result, has greatly advanced the understanding of biological systems with its application in the biological sciences. One area in which mass spectrometry has succeeded is the area of microbiology and the identification of pathogens and has gained much attention from the biothreat detection community. Although this technology has matured in the past decade, very few systems have been developed for point-of-need analysis in cases such as the detection of biothreats. Current MS systems for the analysis of microbes utilizing MALDI-TOF-MS require large instruments to accommodate a drift tube long enough for high resolution mass analysis and high vacuum which is not amenable to the miniaturization requirements of point-of-need analysis. The previously mentioned methods also require extensive manipulation of the sample which takes time and can pose a risk to instrument operators in the biothreat detection space. Additionally, most mass spectrochemical instruments provide only one-dimension of data which can limits classification accuracy when using classification algorithms to provide an identity on a microbiological sample which could consist of any of the numerous common bacterial pathogens or biothreats.</p><p dir="ltr">A possible solution to this problem is the implementation of two-dimensional tandem mass spectrometry (2D MS/MS) which allows the analysis of the product ions of all precursor ions representing the result in the 2D MS/MS data domain. This methodology is possible with a linear quadrupolar ion trap mass analyzer and can be applied to miniature ion trap technology for portability. In this dissertation, a progression of mass spectrochemical analysis of biological systems from conventional methods to the implementation of 2D MS/MS is demonstrated: by (i) the development of a rapid biomolecule extraction method to analyze bacterial spores, using a (ii) modified linear quadrupolar ion trap mass spectrometer, (iii) then a miniature ion trap mass spectrometer, and (iv) finally adding numerical methods to discriminate between biological systems using data acquired on each 2D MS/MS instrument. This work is then taken a step further by developing a high throughput experimentation method in which DESI is coupled to 2D MS/MS to analyze a moderate number of samples rapidly, automatically, and with high reproducibility.</p>