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New methods for drugs analysis, disease diagnosis, and protein analysis by using modern mass spectrometry are developed in this thesis. In drugs analysis, we develop a rapid assessment of molecular similarity between an extremely complex innovator product and a candidate biosimilar by mass spectrometry. Protease digestion combined with Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry were successfully used to peptides mapping and de novo peptides sequencing. Overall ion signals obtained by MALDI-TOF/MS were processed by two multivariate statistics including principle component analysis (PCA) and hierarchical clustering analysis. Based on the variances of the peptide profile, innovator product and normally synthesized biosimilar were grouped on the PCA score plot, while impure biosimilar or abnormally synthesized biosimilar were distinctly separated. The results of hierarchical cluster analysis also revealed high conformity between innovator product and normally synthesized biosimilar. Abnormally synthesized products, as a set of quality controller, could be discriminated from innovator product favorably. Another quality control strategy developed in this study is building classification model, batches of product is successfully evaluated. Furthermore, the similarity of molecular weight distribution between these complex drugs is determined. Another target of drug analysis is to develop a vital analytical method to directly detect the peptides synthesized on the resin. Except an organic solvent is transformed to disperse the resin-peptides samples, no other sample pretreatments are required before the MS detection. When using conventional destructive analytical methods to characterize masses of compounds on the solid supports, acid hydrolysis or acid cleavage of the peptide molecules depart from insoluble resin is required. In consequence, side-reactions such as de-blocked or de-protected cause additional fragments in the system, and determination of the intermediates or products are confusing and difficult. Unlike these acid release methods, the molecular weight information of the intact peptide molecules can be obtained in our direct analyses system, and sample consumption is also great reduced. Moreover, our strategy performed the analysis in the ambient environment is more straightforward for real-time monitor reaction and quality control than those techniques in high vacuum system. This direct non-destructive on-line monitoring method would allow following step by step peptide solid-phase synthesis be well quality controlled. In the disease diagnose part, MALDI-TOF mass spectrometry combined with statistics were used to perform semi-quantitative albuminuria diagnoses. Based on the fact that the contributions of singly, doubly, triply, and quadruply charged albumin ions from the samples were inflected according to the concentration change. The severity of albuminuria of patients can be estimated by 2D peaks distribution (peaks ranking by p-value) or supervised principal component analysis (PCA). In protein analysis study, we use liquid electrospray laser desorption ionization mass spectrometry (liquid-ELDI/MS) to directly characterized the proteins stored in different solutions containing acids, bases, buffers, organic solvents, or detergents without extra sample pretreatment. A drop of the sample solution was applied on a stainless steel plate., and then the surface of the sample drop was irradiated with a pulsed laser. The laser energy absorbed by the metal plate and surrounding solvent led to the desorption of protein molecules or the formation of fine droplets containing protein molecules. The desorbed protein species were then post-ionized within an electrospray plume to generate the ESI-like protein ions. Since no pH or composition adjustment of the sample solution is needed, this technique is useful for rapid and high throughput screening of the proteins in a solution to check their integrality after storage or prior to further biochemical treatment. In addition,, native and denatured conformation of the proteins can be distinctly examined by using acid-free and organic solvent-reduced ESI solutions in liquid-ELDI.

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The ionization of chemicals in solids or liquids under ambient conditions, known as ambient ionization mass spectrometry, is currently a fruitful research area in mass spectrometry. To classify those ambient ionization techniques from preexisting atmospheric pressure ionization methods, the former are commonly defined as those mass spectrometric ionization methods that operate under ambient conditions and require minimal or no sample pretreatment. A characteristic of this technology is that sample introduction and ionization are usually separate events, thereby allowing independent control of each set of conditions. A two-step ESI-based technique, named electrospray laser desorption ionization (ELDI), has been developed to characterize nonvolatile analyte molecules directly from the surfaces of solid samples in 2005 by J. Shiea and his co-workers. The analyte molecules are produced by laser irradiating of the sample surfaces, and then post-ionized in an ESI plume. However, the pulsed laser used in ELDI-MS system is quite expensive. Our aim in this research is to develop simple, convenient, and cheap desorption methods and coupled them to post-ionization techniques for direct analysis of liquid and solid sample analysis. They includes: (a) the use of continuous wave (CW) laser instead of pulsed laser to desorb analytes in liquid samples and ointments, and (b) the use of thermal probe to desorb analytes in solid and liquid samples. All of the desorbed neutral species like molecules or droplets are then post-ionized via ESI or APCI processes. The first topic of the research is to develop a cheaper laser system to introduce analytes in solids or liquids into reaction region for post-ionization. In this section, we use a CW laser instead of a pulsed laser for the sampling of analytes. The titanium foil and stainless steel foil sample plate is quite useful and shows a great of desorption efficiency for liquid samples while irradiating by a CW laser. The detection limit by using a CW laser for sampling and ESI for post-ionization is 0.1 £gM for Benzethonium chloride and 1 £gM for cytochrome c, respectively. The combination of CW laser desorption and ESI post-ionization mass spectrometry can be applied in drug components, food safety and biomedical sample analysis. As a result of small size, lightness and lower prices of CW laser system, it not only shows large potential to use as a high efficiency desorption device for novel ionization source of mass spectrometer but also available for a wide range of useful application in many fields. The second topic of the research is to develop a new thermal probe for the direct desorption of sample surface. The home-made thermal probe is used to touch surface of solid sample or liquid sample to generate gas phase molecules or micro analyte droplets. Those neutral analytes are then post-ionized via ESI or APCI processes. In this study, the setting temperature of thermal probe is 250¢J. When the thermal probe touches liquid sample, it makes droplets boiling away explosively and then fused with ESI plume to generate ions. The detection limit by using a thermal probe for sampling and ESI or APCI for post-ionization is 1 £gM for both melamine and cytochrome c. This technique is also applied to analyze controversial additives in drinks. It also shows large potential to use as a high efficiency desorption device for novel ionization source of mass spectrometer and useful for a wide range of useful application in many fields.