New drug discovery and development is a very expensive and time-consuming process. It can take 10 -12 years of development before a new drug is safe and effective for marketing and distribution. Many thousands of compounds need to be screened to find a few lead candidates. Speeding up the drug discovery process has become a major goal for all pharmaceutical companies. This leads to faster decision-making and saves time and money. The screening of proteins as drug interaction targets is a rapidly developing field.

Drug discovery particularly for a biological drug target faces four great challenges today:

1. Complexity in sample matrix and drug metabolites;
2. Limited amount of biological samples ;
3. Trace amount of compound of interest that requires careful sample pretreatment and concentrating prior to identifications by analytical techniques and
4. Wide dynamic range of the target sample concentration.

Because of the complexity of biological fluid, a sample cleanup and concentrating step is often required. Recent development in drug discovery techniques including combinatorial chemistry, proteomics, ADME, and toxicology profiling, demands the development of high throughput separation, high sensitivity detection, and accurate data handling techniques to speed up the discovery process.

MALDI-TOF-MS offers great advantages in the speed of identification and in the need for small sample size. MALDI-TOF-MS is effectively applied in the direct analysis of complex metabolites and drug mixtures due to its high tolerance to sample matrix. Tandem MS is the cornerstone of drug metabolite identification. It covers a variety of scanning techniques including product ion, pre-courser ion, and neutral-loss scanning. Online LC-MS is a good solution for separation, identification and quantification in drug analysis because it permits the confirmation of polar or non-volatile compounds without the need for derivatization.

Recent developments in Nano-HPLC and Nano-spray mass spectrometry have significantly increased the resolution power for complex sample analysis. It has also improved sensitivity for the trace detection of biological samples to the atta-mole range. In theory nano-HPLC is the best choice for high throughput chromatographic applications. It is the goal of this chapter to analyze the theoretical basis and to demonstrate the advantages of capillary HPLC in high throughput drug discovery and development. In addition, method development in Nano-LC-MS consumes as little as 12μl LC solvent for a 1- hour run (0.2μl/min flow rate). A 100ml solvent reservoir for 7/24 applications can last nearly one year.

Fundamentally, the promise of chromatographic speed of analysis depends heavily on the separation techniques such as the utilization of nano-particles in short column length. In addition, the implementation of online sample preparation and fully automated multi-dimensional technique and instrumentation highly enhance the sample throughput, the reproducibility and the quality of data. An ultra-high-pressure capillary-HPLC system is highly advantageous since it would allow the use of capillary-HPLC columns packed with 1.5 to 2 µm particles at high flow rates for ultra-fast analysis. As shown below that an ultra-high pressure splitless HPLC system that allows operating pressures up to 20,000 psi is required for use with ultra-high pressure capillary columns packed with 1.5µm particles. A Biomarker plateform will be presented for the applications in cancer early detection.