Applications of Modern Mass Spectrometry

The need for conformational information is increasing by the time in studies on macromolecules. For example, proteins may have various functions and properties depending on their folding states that make their conformational analyses very important. Mass spectrometry is one of the most effective analytical techniques that separate ions in the gas phase by their mass-to-charge ratio. It provides useful data on molecular characterization in many areas of research with high precision, accuracy, and sensitivity. Although mass spectrometry is a very powerful analytical technique, it cannot distinguish different species having identical mass-to-charge ratio. The analytical technique combining mass spectrometry with ion mobility spectrometry (IM-MS), which provides information about the three-dimensional structure of an ion, solves this problem by separating them according to their collision cross sections (CCS) in the gas phase. This analytical method also provides the advantages of higher precision and better resolution in the rapid analysis of different types of complex samples. The separation of isomers with the same molecular weight, increasing the dynamic range and distinguishing ions from chemical noise are the most important features that this technique contributes to mass spectrometry. As improvements have been made in IM-MS technology, the number and quality of publications in the areas where this technique is used increases rapidly. In this chapter, the use of IM-MS techniques in the fields such as proteomics, glycoproteomics and polymer characterization are explained by presenting their various applications in the literature. 

With the increase of industrialization and urbanization, pollution of clean water has become a critical issue in the contemporary world. Despite organic pollutants such as pharmaceuticals, pesticides, industrial chemicals, poly- and per-fluoroalkyl substances (PFASs) and hormones, contaminants originating from the industrial effluents, urban run-offs, agricultural run-offs and domestic sewage have become a greater threat to the aquatic eco-systems. The availability of some of these highly potent contaminants at low concentrations and the simultaneous analysis of multiple samples have been identified as the major concerns in current analytical methods in water pollution analysis. In this regard, modern mass spectrometric methods have emerged as suitable techniques for the analysis of smallest concentrations even at a level of nanograms or femtograms while allowing the detection of hundreds of analytes in a single analysis within a short duration of time. 

Recently, combinational mass spectrometric analysis has become the state of the art in several qualitative and quantitative analyses of organic pollutants in water. The sensitivity of the detection has been enhanced by coupling with various sample extraction methods, chromatographic techniques and different mass analyzers in mass spectrometry. Utilization of modern sample extraction methods coupled with mass analyzers has facilitated the accuracy of the detection of organic pollutants in water samples. Sample extraction methods involve sophisticated solid-phase extraction, solid-phase microextraction, and liquid-liquid extraction methods, whereas mass analyzers include time-of-flight, orbitrap, ion-trap and triple quadrupole, etc. The hallmark of these hyphenated techniques is the ability of allowing the screening of targeted analytes, non-targeted analytes and suspect analytes without the need of authentic standards. This chapter will focus on the recent advancement of mass spectrometry in qualitative and quantitative analysis of several organic contaminants in wastewater samples.

Alkaloids are natural metabolites containing nitrogen atoms, produced for different biological functions by plants, animals, and microorganisms. In most cases, its production is related to the defense mechanism of an organism through allelopathic effects. Because of this allelopathic property, some of these alkaloids are used as pesticides and can somehow be found in food and beverages as exogenous contaminants. Other contaminations by alkaloids come from industrial processing; so, ingestion of contaminated food or drinks can cause poisoning or death. Many of these plants, although composed of toxic substances, are also used as traditional medicines. Therefore, the compilation of these plants, their chemical constituents, and their pharmacological effects remain important. This paper aims to report traditional preparations and the use of edible plants containing toxic components, their toxicological records of a part of these poisonous metabolites, some regulations on their tolerable dose, and appropriate hyphenated techniques related to mass spectrometric for their separation, detection, quantification, and characterization. In addition, a particular emphasis will be placed on the properties of the stationary and mobile phases used for these studies. The fragmentation mechanism pathways based on mass spectrometry data for these substances will be widely described, and the diagnostic peak will be highlighted. 

In recent years, various methods and technological advances demonstrated that neurochemical measurements have contributed to significant improvements in our understanding of the relationship between chemistry in the central nervous system (CNS) and the organism. Techniques based on Liquid Chromatography-Mass Spectrometry (LC-MS) are potent approaches for separating and quantifying endogenous neuropeptides in CNS. The separation ability and reliability of LC with sensitivity and selectivity of MS have become a valuable combination for peptide analysis either qualitatively or quantitively. Thus, new peptides have been identified using this technique. When applied to disease models, pathophysiological mechanisms can be identified and used as drug targets or biomarkers. Due to the low concentrations of neuropeptides in the biological samples, they restrict developing analysis methods and the understanding of their biological function. This book chapter focuses on novel developments of LC-MS/MS for endogenous neuropeptides. It has also emphasized the applications that cite preparation techniques used for brain tissue analysis, published in recent years.

Structural proteomic techniques have recently evolved because of advances in mass spectrometry (MS). Several MS techniques, such as, Hydrogen-deuterium exchange, oxidative footprinting or radical probe mass spectrometry, chemical crosslinking, affinity purification, and ion mobility separation, can now be used to analyse protein interaction networks, conformational changes, protein structures, and other downstream applications. This article examines proteomic MS techniques' progression from convectional to advanced techniques, tandem MS techniques, MS of multiprotein complexes, and emerging MS techniques for structural proteomics. Also, the applications that were gleaned from these techniques were reviewed. Lastly, the future of this rapidly emerging field was highlighted.

Mass spectrometry has evolved significantly in recent years and has become a powerful analytical tool in the field of drug discovery and development. It allows for the identification and characterization of small molecules, peptides, and proteins in complex biological samples with high sensitivity and accuracy. This chapter provides an overview of the recent trends in modern mass spectrometry and its application towards the drug discovery and development process. It discusses the advancements in mass spectrometry technology, such as high-resolution mass spectrometry (HRMS), ambient ionization mass spectrometry (AIMS), data-independent acquisition (DIA) mass spectrometry, tandem mass spectrometry (LC-MS/MS), and how they have enabled the analysis of complex biological samples. The chapter also highlights the use of mass spectrometry in various stages of the drug discovery and development process, including target identification, hit identification, lead optimization, and drug metabolism and pharmacokinetic studies. Additionally, it discusses the challenges and future prospects of mass spectrometry in drug discovery and development. Overall, mass spectrometry has revolutionized the drug discovery and development process and will continue to play a crucial role in the future.