**1. Introduction**

Since its discovery 100 years ago by Sir J.J. Thompson for the quantitative measurement of the mass and charge of cathode rays, mass spectrometer eventually evolved as a reliable analytical platform aimed at the analysis of small and large molecules [1]. While hyphenation of mass spectrometry with gas chromatography achieved its early success, however, liquid chromatography could not due to indigent mass spec interfaces. This is given the inability of interfaces to handle

higher flow rates of liquid sample. Additionally, ionization techniques such as chemical and electron impact ionization did not suit for thermolabile and high molecular weight compounds [2, 3]. Advancement in ionization techniques such as fast atom bombardment that suited for analysis of large molecules, thermospray and particle beam ionization which were efficient for small molecules enabled the fruitful hyphenation of liquid chromatography with mass spectrometry [4–7]. Thermospray in general forms ammonium adducts, while particle beam generated electron impact spectra. Within a few years thermospray was succeeded by atmospheric pressure ionization techniques such electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), atmospheric pressure photoionization (APPI) and atmospheric pressure matrix assisted laser desorption ionization (AP-MALDI). Mass spectrometer operates on the principle of ionization of analytes followed by their separation based on their mass-to-charge ratio [8]. Various mass spectrometer analyzers ranging from linear trap, ion trap, triple quadrupole, time of flight and orbitrap have specific applications for sample analysis in preclinical drug discovery and development.

Medicinal chemistry efforts in drug discovery is majorly focused on understanding the right combination of new chemical entity (NCE) properties that helps in cherry-picking the compounds with promising properties to progress from discovery to development phase. In the process of lead optimization, NCE's are subjected to a series of drug metabolism and pharmacokinetic assays to assess the druggable properties and mitigate late stage failures. Almost 40% of failures in development phase were due to poor pharmacokinetic properties of NCE's [9]. However, this percentage had gradually decreased to 10% as major pharmaceutical companies incorporated drug metabolism and pharmacokinetic screening (DMPK) in lead optimization phase of drug discovery. In this view, compounds must pass through a series of screens that scrutinize the problematic compounds until a small number have been selected for more rigorous testing in the development phase. Hence, lead optimization typically is an iterative process that uses the DMPK data to optimize the druggable properties of NCE's. Regardless of the screening panel, qualitative and quantitative analytical results to understand absorption, distribution, metabolism and excretion (ADME) properties were generated using liquid chromatography–tandem mass spectrometry (LC–MS/MS) [10–17]. In this chapter, we have briefly discussed on various atmospheric pressure ionization techniques/mass analyzers, and applications of mass spectrometer in drug discovery with special emphasis on drug metabolism and pharmacokinetic assays.
