Dealing with substances that will be detected at very low levels, or with will be very little information about their toxicity, would result in controversies over whether the concentrations found pose a significant risk to the public health or the environment, he added Drug testing, as an example, can be carried out for multiple reasons: pathology, healthcare, and the anti-doping of both humans and animals [
29]. Their concentration in biological fluids is usually very low, so their detection requires the GC-MS, additionally, the molecules in merit are often very small (<650 Daltons) [
8,
30,
31].
3.1.1. MS-Based Quantitative Strategies and Analysis of Proteome, Genome, and Transcriptome
Cells are continuously operational biochemical laboratories, and in their versatility, biological systems are incredibly complex. The result is an almost inexhaustible object of research [
2]. The term “genome” was something that changed throughout history, so instead of the totality of genes in all chromosomes (what was its original meaning), it now designates the complete set of DNA in organisms, including all of its genes [
2]. The elementary monomeric units of DNA and RNA macromolecules are nucleotides, consisting of nitrogenous bases, monosaccharides, and phosphoric acid residues. Molecules of purine (adenine, guanine) and pyrimidine (thymine, cytosine) structures act as nitrogenous bases for DNA. The same bases are included in the nucleotides of RNA molecules, except that thymine in them is replaced by uracil. In DNA and RNA, these nitrogenous bases bind to monosaccharides deoxyribose and ribose, respectively, forming nucleosides. In nucleotides, the latter is phosphorylated at the primary OH group of a monosaccharide, and this phosphate [
33].
Even though qRT-PCR is considered the gold standard in transcriptome techniques due to its accuracy and sensitivity, RNA-seq turns out to be equivalent[
16,
17]. Transcriptomics can either refer to exploratory analysis of the entire transcriptome, primarily using RNA sequencing (RNA-seq) [
34], or to targeted analysis of known RNAs using techniques such as gene expression panels (GEPs).
Of all MS-based quantitative strategies, in the analysis of nucleic acids most often used is matrix-assisted laser desorption/ionization–mass spectrometry (MALDI-MS), recently improved with the time-of-flight (ToF) feature [
35]. This appliance should nevertheless recoil due to high initial costs, especially since it does not require trained laboratory personnel [
36]. Interestingly, RNAs are more stable than DNA, so the latter are preliminarily converted into RNA by in vitro transcription.
The scope of delivery of RNAs formed in one or a series of cells of an organism is called a "transcriptome" [
37,
38]. It consists of ribosomal (rRNA), transport (tRNA), and messenger (mRNA) RNA [
39,
40]. Out of those three forms of RNA, mRNA serves as a transmitter of genetic information [
41,
42], After translation, these RNAs are rapidly degraded. Though, the complete transcriptome is a subject of interest in transcriptomics [
43]. During translation, tRNAs take part as an intermediate between nucleic acids and proteins: they attach activated amino acid residues and transfer them to the site of synthesis of protein polypeptide chains rRNAs do not participate in the process of information transfer and constitute the bulk of the ribosomes. The sequence of nucleotides in mRNA molecules contains all the information about the amino acid sequence in a protein chain.
All types of RNA are synthesized on a DNA template, and the sequence of ribonucleotides in them is complementary to the sequence of deoxyribonucleotides in DNA. Molecules of purine (adenine, guanine) and pyrimidine (thymine, cytosine) structures act as nitrogenous bases for DNA. The elementary monomeric units of DNA and RNA macromolecules are nucleotides, consisting of nitrogenous bases, monosaccharides, and phosphoric acid residues. Though, the same bases are included in the nucleotides of RNA. Except that thymine is replaced by uracil. In DNA and RNA, these nitrogenous bases bind to monosaccharides deoxyribose and ribose, respectively, forming nucleosides Monosaccharides deoxyribose or ribose are phosphorylated in nucleotides, and this phosphate group phosphorylates the OH group of a monosaccharide of another nucleotide, because of which macromolecules of nucleic acids are formed.
Quantitative strategies relying on MS and MS within genomics/transcriptomics are only logical MS led to the concept of “OMICS”. And nowadays sequencing and MS are basic experimental tools in investigating the omics of a given biological system. Since a substantial amount of information is obtainable from sequencing-based methods, MS-based techniques can be used to investigate proteome, metabolome, and interactomes that do not involve DNA/RNA [
44].
An enormous number of processes simultaneously occur in all of our cells. Accordingly, the proteome is more of a challenge than the human genome [
45]. Not only its scale is estimated at over 1 million proteins but the increase in proteomic diversity is further increased by protein post-translational modifications (PTMs) [
46]. Precisely the analysis of PTMs could provide a comprehensive vision of molecular mechanisms for various diseases [
47]. Though, these modifications of proteins following protein biosynthesis are generally enzymatic. It refers to changes in the polypeptide chain as a result of adding distinct chemical parts to amino acid residues
To be blunt, PTMs are the foundation of complicated cellular processes, such as cell division, growth, differentiation, signaling, and regulation, the same as various processes included in the maintenance of protein structure and integrity [
48].
PTMs also regulate the metabolism and defense processes, cellular recognition, and morphology alternation [
49]. Consequently, analysis of PTMs is important for the study of cell biology and disease diagnostics and prevention. The worldwide studies of different PTMs and the proportion change of different proteins could provide new insights into the clinical approach [
25].To highlight the relevance of MS in the analysis of PTM, statistics of each PTM experimentally and putatively detected have been compiled using proteome-wide information from the Swiss-Prot database [
50].
Many physiological functions can be overviewed using MS-based quantitative strategies developed to quantify glycoprotein expression levels on a large scale [
51]. Proteomics based on MS is made feasible by the availability of gene and genome sequence databases and technical and conceptual advancements in many areas [
52,
53,
54,
55]. Typically, mass spectrometry can cover a range of functions [
56]. Time-of-flight (TOF), quadrupole (Q), Fourier transforms ion cyclotron resonance (FT-ICR), and ion trap (IT) that are used generally in labs, are usually combined in proteomics in one MS (triple quadrupole (QqQ), Q-IT, Q-TOF, TOF-TOF, IT-FTMS, etc.) [
57].
3.1.2. MS-Based Quantitative Strategies, Food, and Environment
Food science and nutrition interact with disciplines such as pharmacology, medicine, and biotechnology. Conversely, the discipline that we call environmental health, specifically environmental toxicology provides critical information and knowledge for regulatory agencies, decision-makers, and others. To help them, scientists may take advantage of MS, and students of all health-related sciences should be familiar with it.
Today’s appliances aim to identify and quantify complex protein (peptides) mixtures in a single experiment [
58,
59] in which modern analytical chemistry must provide accurate, precise, and robust methods. These methods have to be able to determine any toxic compounds or organisms that might be present in food at very low concentrations. Foodomics is a portmanteau coined in 2009 as "a discipline that studies the Food and Nutrition domains through the application and integration of advanced -OMICS technologies to improve consumer's well-being. Detection of exogenous contaminants in food, food safety, quality, and traceability with MS-based “OMICS” is always a complex area, health, and knowledge". Foodomics requires a combination of food chemistry, biological sciences, and data analysis [
60]. A framework of knowledgeability required for the average medical student in the field falls greatly beyond the topic of food cOMICS, so this review shall focus specifically on MS and its application.
In the framework of environmental health, MS is mainly the environmental toxicology tool used to put programs and policies in place to limit our exposure to these substances, thereby preventing or reducing the likelihood that a disease or other negative health outcome would occur [
61]. MS has its inevitable position in wastewater-based epidemiology for the determination of small and large molecules as biomarkers of exposure [
62,
63].