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Ambient mass spectrometry (MS) is a new and growing sub-field in MS which has opened new research avenues, particularly for applications relating to the analysis of solid samples. Results on the implementation and application of ambient MS techniques including: desorption electrospray ionization (DESI) and direct analysis in real time (DART) indicated that these techniques could serve as complementary tools for the rapid qualitative screening of pharmaceuticals, allowing up to two orders of magnitude improvement in throughput compared to traditional methods such as liquid chromatography MS. The selectivity of DESI could be enhanced by performing the experiment in the reactive mode. In this mode, complexation reactions between reagents added to the spray solvent and analytes on the sample surface resulted in analyte stabilization, inhibiting fragmentation. They also resulted in a concomitant enhancement in the analyte surface activity, facilitating their evaporation from secondary droplets culminating in an improvement in sensitivity. Also for drug tablets analysis, the analyte signal dependency on DESI geometrical set-up variables could be mitigated following the careful and controlled addition of an isotopically labeled internal standard (IS) to the sample or by spraying samples with a pair of reagents with different affinities for the analyte. Either of these approaches resulted in an analyte-to-IS signal ratio (in the former) or an analyte complex ratio (in the later), which was largely independent of DESI experimental variables allowing quantitative analysis using this technique. DESI MS was also observed to be a very powerful tool for determining the 2-D distribution of various pharmaceutically important compounds on tablet and tissue surfaces. The ability to map the distribution of molecules of interest by DESI MS has very great implications in drug tablet quality control and in determining the role of chemical signals presented on tissue surfaces. DESI was observed to be limited to ionizing molecules of medium to high polarities without much limitation in terms of mass range, whereas DART was better suited for the analysis of molecules within a broader range of polarities, but within a more limited mass range (up to 800 Da approximately). These limitations were circumvented by implementing a novel multimode ambient ion source, desorption electrospray/metastable-induced ionization (DEMI), which combines various aspects of DESI and DART. Initial experiments with the DEMI ion source demonstrated its ability to enable the simultaneous analysis of molecules within a broader range of polarities and masses than DESI and DART alone.

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<p>Ambient ionization mass spectrometry enables rapid <i>in-situ</i> analysis of a plethora of analytes that are relevant to the forensic and defense communities. As the arsenal of ambient ionization techniques, aimed at solving specific targeted problems, continues to expand, the adoption of these techniques into non-academic settings has been relatively slow. At times, although the technique can provide answers in a more rapid and cheaper manner, the technique does not pass all of the required legal rules for a particular analysis when dealing with forensic evidence. This can be demonstrated with the rapid detection of drugs by paper spray ionization mass spectrometry. Paper spray ionization mass spectrometry can have drugs deposited onto the paper substrate, the paper can wipe a surface for trace analytes, and there are commercial and automated ionization sources for this process. While analysis by paper spray is rapid, the Scientific Working Group for the Analysis of Seized Drugs (SWGDRUG) states that a minimum of two instrumental techniques need to be utilized. Utilizing paper substrates that have nanoparticles embedded for surface enhanced Raman spectroscopy, that can also be utilized for paper spray ionization mass spectrometry, makes ambient ionization more appealing as it completes that first legal requirement. </p> <p>Other times, the slow adoption of these new ambient ionization techniques is due to specific communities not being aware of ambient ionization, and specific applications have not yet been demonstrated. Swab touch spray ionization mass spectrometry follows similar processes as paper spray ionization, as the swab acts both as the sampling substrate and the ionization source and can swab for analytes in a manner where the paper substrate may be damaged and unable to perform the ionization for analysis. This can be seen for the swabbing of organic gunshot residues and explosives, both of which current methods already use a swab for sampling but then need lengthy extraction techniques. The applicability of paper spray ionization and swab touch spray ionization for these forensic and defense analyses is only furthered by the fact that they both couple extremely well with portable mass spectrometers for analysis in the field.</p> <p>There are also many fields that ambient ionization is just starting to take its place in the analytical toolbox. Two such defense fields that are just beginning to expand into ambient ionization are the analysis of pyrotechnics and microelectronics. Pyrolysis gas-chromatography mass spectrometry methods have been developed and utilized for environmental tests for pyrotechnic formulation, but they are slow and there is an abundance of cleaning steps between analyses to prevent carry over and contamination. Using paper and swabs as the collection device and ionization source for environmental analysis of these pyrotechnics allow for them to be functioned at ambient conditions at the scale at which will be utilized in the field by the Warfighter. Similarly, authenticating microelectronics by desorption electrospray ionization mass spectrometry removes the subjectivity of the current methods, while rendering the integrated circuit intact enabling future use if deemed as a genuine part. By taking slower or more subjective tests, in a field that has not utilized ambient ionization heavily in the past and adding these new capabilities to their tool chest expands the acceptance and future applications of the technique.</p> <p>As acceptance and utilization of ambient ionization grows, the next generation of scientists need to have hands on training in these techniques. Through the development of new teaching laboratories that couple both the fundamentals of the technique at hand, while also examining an interesting application to better engage the students, a number of laboratory exercises have been developed. The creation of new laboratory exercise utilizing the next generation of instrumentation and analytical techniques is vital for the future and rapid application of these techniques. The work discussed herein chronicles the utilization and demonstration of ambient ionization mass spectrometry in monitoring clandestine activities, supporting the Warfighter, and redeveloping chemical laboratory education. </p>

<p>The rapid analysis of complex samples using mass spectrometry (MS) provides valuable information in both point-of-care (e.g. drug testing) and laboratory-based applications, including the generation of spectral libraries for classification of biosamples, the identification of biomarkers through large-scale studies, as well as the synthesis and bioactivity assessments of large compound sets necessary for drug discovery. In all these cases, the inherent speed of MS is attractive, but rarely fully utilized due to the widespread use of sample purification techniques prior to analysis. Ambient ionization methodologies can help circumvent this drawback by facilitating high-throughput qualitative and quantitative analysis directly from the complex samples without any need for work-up. For instance, the use of swabs or paper substrates allows for rapid identification, quantification, and confirmation, of drugs of abuse from biofluids or surfaces of forensic interest in a matter of minutes, as described in the first two chapters of this dissertation. Faster analysis can be achieved using an automated desorption electrospray ionization (DESI) platform which allows for the rapid and direct screening of complex-sample microarrays with throughputs better than 1 sample per second, giving access to rich spectral information from tens of thousands of samples per day. The development of the bioanalytical capabilities of this platform, particularly within the context of drug discovery (e.g. bioactivity assays, biosample analysis), is described across most other chapters of this dissertation. The use of DESI, a contactless ambient ionization method developed in our laboratory and whose 20 years of history are overviewed in the introduction of this document, provides an additional advantage as the secondary microdroplets generated through the DESI process act as reaction vessels that can accelerate organic reactions by up to six orders of magnitude, facilitating on-the-fly synthesis of new compounds from arrays of starting materials. Unique implications of this microdroplet chemistry in the prebiotic synthesis of peptides and spontaneous redox chemistry at air-solution interfaces, together with its practical applications to the synthesis of new drug molecules, are also overviewed. The success obtained with the first automated DESI-MS system, developed within the DARPA Make It program, led to increased interest in a new-generation platform which was designed over the past year, as overviewed in the last section of this dissertation, and which is currently being installed for validation prior to the transfer of the technology to NCATS, where we anticipate it will make a significant impact through the consolidation and acceleration of the early drug discovery workflow.</p>

<p> Mass spectrometry imaging (MSI) is an advanced analytical technique that renders spatially defined images of complex label-free samples. Nanospray desorption electrospray ionization (nano-DESI) MSI is an ambient ionization direct liquid extraction technique in which analytes are extracted by means of a continuous liquid flow between two fused-silica capillaries. The droplet generated between the two capillaries is controlled by a delicate balance of solvent flow, solvent aspiration, capillary angles, and distance from the surface. This technique produces reproducible ion images with up to 10 µm resolution and can be used to identify and quantify multiple analytes on a given surface.  This thesis discusses some of the applications of this technique to biological systems, as well as the work done to develop methodology to further improve this technique’s specificity and sensitivity. Herein, applications that push the limits of the current capabilities of nano-DESI are presented, such as the high-resolution imaging of lipid species in skeletal muscle at the single-fiber level, and the quantification of low-abundance drug metabolites.  The second theme of this thesis, developing new capabilities, introduces ion mobility mass spectrometry imaging. This integrated technique increases the selectivity previously possible with MSI. To support these efforts, the work in this thesis has generated data analysis workflows that not only make these experiments possible but also further endeavor to increase sensitivity and combat instrument limitations on mobility resolution. Finally, this thesis present streamlined workflows for tandem MS experiments and modifications to a recently introduced microfluidic variant of the nano-DESI technique. In all, this thesis showcases the current capabilities of the nano-DESI technique and lays the groundwork for future improvements and capabilities.      </p>

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