Mass spectrometry originated from quantitative measurements of the mass and charge of electrons [1]. Since that time the application of mass spectrometry has moved from the analysis of inorganic elements to organic molecules and finally to macromolecules. Over the past decade spectacular improvements were made in instrumental development regarding performance and new mode of operations in particular with hybrid instruments. Orbitrap, Fourier transform or triple quadrupole linear ion trap mass spectrometers could be used routinely only for the past few years and their potential is certainly not fully exploited yet. The strength of mass spectrometry lies in its sensitivity (femtomoles, atomoles); and in many applications the analyte of interest can be detected in its intact form. The challenge in life sciences bioanalysis is the diversity and the number of the molecules to analyze as well as the concentration range.

Analysis of pharmaceutical compounds in biological matrices with liquid chro-matography coupled to mass spectrometry (LC-MS) has become a routine technique in many laboratories. However, certain issues such as non-standardized ionization response and matrix effects still need further investigation and improvement. The application of LC-MS for metabolomics studies [89] is gaining interest. Therefore, it is expected that accurate and high throughput quantitation of low molecular weight biomarkers will be one of the major challenges in the near future. Identification and quantification of proteins has progressed significantly; however in many cases the numbers of proteins which can be analyzed still remains limited. Electrospray ionization has been shown to be very powerful for single protein analysis but the technique is also well suited for the characterization of very large non-covalent complexes of proteins, which may lead to an increasing understanding of protein assemblies [90].

Single nucleotide polymorphism (SNP) genotyping has become a key technology in gaining a partial understanding of complex diseases or why patients react differently to drug treatment. Matrix assisted laser desorption especially with high speed laser allows real high throughput and is well suited for the analysis of oli-gonucleotides. MALDI is therefore an interesting approach for SNP discovery and genotyping, molecular haplotyping, methylation analysis, and RNA and allele-specific expression but needs further optimization before routine application [42, 91].

Significant progress has been realized in the miniaturization of separation sciences and mass spectrometric detection. Presently, the samples are transferred to highly specialized laboratories for analysis. But in the future it may become feasible to bring mass spectrometry as a portable technique to the bed for diagnostic or therapeutic monitoring.

Table 1.6 Common definitions and abbreviations.

Accurate mass

Atomic mass

Average mass Exact mass

Mass defect

Mass defect filter (MDF)

Mass range Monoisotopic mass

Symbol used to denote the dimensionless quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). m/z should be written in italic and lower case. The Thomson (Th) is sometimes used as unit but it is not recommended.

Molecular ion, the ion results from the loss of one electron from the neutral molecule

Protonated molecule formed by the addition of a proton to a neutral molecule (teh terms pseudo-molecular ion or quasi-molecular ion should not be used)

Symbol for atomic mass unit

Experimentally determined mass of an ion that is used to determine an elemental formula. The precision of the measure is indicated in parts per millions (ppm).

The average of the atomic masses of all the chemical element's isotopes (also known as atomic weight and average atomic mass)

Mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance

Calculated mass of an ion or molecule containing a single isotope of each atom, most frequently the lightest isotope of each element, calculated from the masses of these isotopes using an appropriate degree of accuracy

The difference between the exact mass of an atom molecule, ion and its integer mass in MS. In physics, the mass defect represents the difference between the mass of an atom and the sum of the masses of its unbound constituents.

A software filter which allows the removal of interference ions from drug metabolites in accurate mass liquid chromatography-mass spectrometry

Operating m/z range of a mass analyzer

Exact mass of an ion or molecule calculated using the mass of the most abundant isotope of each element

Relative molecular mass: mass of one molecule of a compound, with specified isotopic composition, relative to one-twelfth of the mass of one atom of 12C

56 | 1 Mass Spectrometry in Bioanalysis - Methods, Principles and Instrumentation Table 1.6 (continued)

Nominal mass

Metastable ion


Base peak (BP) Total ion current (TIC)

Extracted ion current (XIC) Mass resolving power

Unit mass resolution Mass resolution

Ionization Even-electron ion

Odd-electron ion

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