Mass spectrometric analysis requires that atoms from the sample be ionized in the gas phase. Secondary ion mass spectrometry achieves this by sputtering samples with an energetic primary ion beam. Several investigations of the sputtering and ionization process have been conducted. Oxygen is commonly used in secondary ion mass spectrometry (SIMS) to increase ion yields, but also can complicate the interpretation of SIMS analyses. An 18O implant in silicon has been used to quantify the oxygen concentration at the surface of sputtered silicon in order to study the dependence on oxygen of several sputtering and depth profile phenomena. The ion yield dependence of trace elements in silicon on the surface oxygen concentration is a function of the ionization potential of the element. The ion yield is high and unaffected by oxygen for elements with low ionization potential and ranges over several orders of magnitude for elements with high ionization potential. Depth resolution in sputter profiles has been shown to be degraded by the presence of oxygen, the mechanism of this effect has been investigated using an 18O implant to quantify oxygen levels and it is shown that the process does not appear to be a consequence of surface oxide formation. Molecular ions are a source of mass interference in SIMS analysis, and multiply charged atomic ion signals might be interference-free due to the possible instability of multiply-charged molecular ions. Sputtered SiH2+, AlH2+, BeH2+, Mo22+ and Mg22+ ions have been observed and appear surprisingly stable. The formation mechanism of some of these species has been explored.

Cancer claims hundreds of thousands of lives every year in US alone. Finding ways for early detection of cancer onset is crucial for better management and treatment of cancer. Thus, biomarkers especially protein biomarkers, being the functional units which reflect dynamic physiological changes, need to be discovered. Though important, there are only a few approved protein cancer biomarkers till date. To accelerate this process, fast, comprehensive and affordable assays are required which can be applied to large population studies. For this, these assays should be able to comprehensively characterize and explore the molecular diversity of nominally "single" proteins across populations. This information is usually unavailable with commonly used immunoassays such as ELISA (enzyme linked immunosorbent assay) which either ignore protein microheterogeneity, or are confounded by it. To this end, mass spectrometric immuno assays (MSIA) for three different human plasma proteins have been developed. These proteins viz. IGF-1, hemopexin and tetranectin have been found in reported literature to show correlations with many diseases along with several carcinomas. Developed assays were used to extract entire proteins from plasma samples and subsequently analyzed on mass spectrometric platforms. Matrix assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometric techniques where used due to their availability and suitability for the analysis. This resulted in visibility of different structural forms of these proteins showing their structural micro-heterogeneity which is invisible to commonly used immunoassays. These assays are fast, comprehensive and can be applied in large sample studies to analyze proteins for biomarker discovery.

Polydimethyl siloxane is a commonly used fabrication material for microfluidic devices. However, its hydrophobic nature and protein adsorption on the surface restricts its use for microfluidic applications. Also, it is critical to control the electroosmotic flow for electrophoretic and dielectrophoretic manipulations. Therefore, surface modification of PDMS is essential to make it well suited for bioanalytical applications. In this project, the role of polyethylene oxide copolymers F108 and PLL-PEG has been investigated to modify the surface properties of PDMS using physisorption method. Measuring electroosmotic flow and adsorption studies tested the quality and the long-term stability of the modified PDMS surface. Static and dynamic coating strategies were used to modify the PDMS surface. In static coating, the PDMS surface was incubated with the coating agent prior to the measurements. For dynamic coating, the coating agent was always present in the solution throughout the experiment. F108 and PLL-PEG were equally effective to prevent the protein adsorption under both strategies. However, dynamic coating was more time saving. Furthermore, effective reduction of EOF was observed with F108 coating agent under dynamic conditions and with PLL-PEG coating agent under static conditions. Moreover, PLL-PEG dynamic coatings exhibited reversal of EOF. These important findings could be used to manipulate EOF and suggest optimal coating agent and strategies for PDMS surface treatment by the physisorption method.