Libraries of Mass Spectra

Most mass spectrometers for analytical work have access to a large library of mass spectra of known compounds. These libraries are in a form that can be read immediately by a computer viz., the data corresponding to each spectrum have been compressed into digital form and stored permanently in memory. Each spectrum is stored as a list of m/z values for all peaks that are at least 5% of the height of the largest peak. To speed the search process, a much shorter version of the spectrum is normally examined (e.g., only one peak in every fourteen mass units). 

The range of compounds from which electron ionization spectra may be obtained using the particle-beam interface is, like the moving-belt interface, extended when compared to using more conventional methods of introduction, e.g. the solids probe, or via a GC. It is therefore not unusual for specffa obtained using this type of interface not to be found in commercial libraries of mass spectra. 

SFC-based methods still need to show their potential, in spite of past great promise. pSFC-APCI-MS is a powerful method for identification of polymer additives, provided that a library of mass spectra of polymer additives using this technique is available. SFC-MS appears less performing than originally announced nevertheless, SFE-SFC-EIMS is an interesting niche approach to additive analysis. On the other hand, we notice the lack of real breakthrough in SFE-SFC-FTIR. 

Electron ionization (earlier called electron impact) (see Chapter 2, Section 2.1.6) occupies a special position among ionization techniques. Historically it was the first method of ionization in mass spectrometry. Moreover it remains the most popular in mass spectrometry of organic compounds (not bioorganic). The main advantages of electron ionization are reliability and versatility. Besides that the existing computer libraries of mass spectra (Wiley/NIST, 2008) consist of electron ionization spectra. The fragmentation mles were also developed for the initial formation of a radical-cation as a result of electron ionization. 

The best-known and the most commonly used hyphenated method is GC-MS more specifically, and most commonly, capillary column GC combined with quadrupole MS. This type of instrumentation is controlled by computer and data collected and analyzed by dedicated computer programs. The mass spectra produced by the analytes can be compared to those in a library of mass spectra of known compounds using a computer search algorithm. The computer program finds known compounds that best match the spectra of the analytes of interest. 

Different capillary columns are available for organic acid separation and analysis. In our laboratory, the gas chromatography column in all GC-MS applications is crosslinked 5% phenyl (poly)methyl silicone, 25 m internal diameter 0.20 mm stationary phase film thickness 0.33 pm (Agilent HP-5, DB-5, or equivalent). Several instrument configurations are commercially available, which allow for positive identification of compounds by their mass spectra obtained in the electron impact ionization mode. A commercially available bench-top GC-MS system with autosampler (Agilent 6890/5973, or equivalent) is suitable. Software for data analysis is available and recommended. The use of a computer library of mass spectra for comparison and visualization of the printed spectra is required for definitive identification and interpretation of each patient specimen. 

The conventional approach is to extract from the TIC profile the mass spectra of all peaks above a predetermined intensity and to perform either manual or computer-assisted [39] identification of each mass spectrum. Analysis of mass spectra should be carried out only by properly trained technologists, under the supervision of a qualified laboratory director. Libraries of mass spectra should be available for identification of peaks that are not readily recognized. This library should be user-created, indexed by retention time and molecular weight, and have the capacity to be expanded and edited. 

Misidentification is a potential risk when the library of mass spectra is relatively incomplete. Lacking the availability of a comprehensive, commercially available library, laboratories resort to make their own and it could take several years to develop a comprehensive tool, although hardly ever complete. Lack of reference spectra could lead to incorrect identification of isovalerylglycine (pivalic acid conjugates),... 

Figure 2.13—Detection by mass spectrometry. TIC chromatogram obtained with a mass spectrometer as a detection system. The instrument is capable of obtaining hundreds of spectra per minute. The above chromatogram corresponds to the total ion current at each instant of the elution profile. It is possible to identify each of the components using its mass spectrum. In many instances, compounds can be identified with the use of a library of mass spectra. (Chromatogram of a mixture of 71 volatile organic compounds (VOCs), reproduced by permission ofTekmarand Restek, USA.)...

Identification can also be achieved using a library of mass spectra. A library containing a large number of spectra will lead, in favourable cases, to successfully finding the mass spectrum of the molecule in question. 

Electron ionisation is still the most widely used technique for the analysis of volatile molecules. It is considered to be a hard ionisation process, which leads to reproducible spectra that can be compared to a library of mass spectra for compound identification. In this technique, ionisation occurs in the ion source by the collision of the sample molecules with electrons that are emitted from a filament by a thermoionic process (Fig. 16.15). 

Two prerequisites are necessary for inclusion of GC/MS in clinical chemistry The laboratories involved must consider the above problems as part of their responsibility, and the presently available apparatus should be improved, including simplification of operation, and cost. The development of libraries of mass spectra, such as presently found at the National Institutes of Health in Bethesda, Maryland, will also be necessary for widespread application. 

As with PDA detection and the construction of UV libraries, computerized data systems are used for data collection and processing with mass spectral detection. Unlike UV spectra, however, mass spectra are much less dependent on experimental conditions. Thus, it is possible to purchase commercial libraries of mass spectra for spectral matching. Mass spectral data systems range from systems that record the spectra and produce conventional relative abundance bar charts for subsequent analysis to those... 

Flavor chemists have traditionally relied on mass spectrometry in conjunction with gas chromatography (GC/MS) to identify the structures of volatile flavor components in heated food systems. Mass spectrometry provides the molecular weights of fragment ions, which are useful for deducing-molecular structure. The MS detection limit is on the order of 1CT g, however detection limits for target compound analysis or chemical class detection via selected ion monitoring can be much lower. Extensive libraries of mass spectra are available even so, many new flavor compounds can often not be identified from MS data alone. 

Database, which contains as much data on CWC-related chemicals as possible. Since on-site analysis in particular by MS is planned for future verification activities, library of mass spectra is mandatory. Retention times of chemicals are collected for chromatography analyses. Although NMR spectroscopy is not suitable for on-site analysis, it is nevertheless considered an essential technique (as may be also IR) for laboratories specialized in the detection and identification of CW agents and related chemicals. Qualified laboratories from all parts of the world were therefore asked to submit their mass, NMR, and IR spectra and retention time data to be included in the OCAD. 

Coupling the column from the GC to a mass spectrometer provides a very powerful combination, GC-MS, which can identify and quantify almost all the compounds in a complex mixture, such as an essential oil or perfume, by reference to libraries of mass spectra of known compounds. Careful investigation of the mass spectrum can be used deductively to determine a possible structure for an unknown material using fragmentation theories to identify sub-structural components of the molecule. Recent developments in benchtop mass spectrometers have brought a range of specialized MS techniques into the realm of GC-MS machines techniques such as chemical ionization and MS-MS are now available, which provide more information on individual sample components and allow better identification of unknown compounds. 

To circumvent this phenomenon it is possible to lower the energy of the electron beam that is used (from 70 eV to, say, 20 eV). This procedure is often used in cases where we know the substrate in order to enhance the intensity of the molecular ion. In the case of unknowns, however, it is a less widely practised procedure. The reason for this lies in the fact that if we lower the ionisation energy, we wiU he in a situation where we will not know to which extent we are allowing other reactions to occur. Furthermore, for comparative purposes it would be very difficult to maintain an effective library of mass spectra if the conditions used to record them varied between each substrate. One of the first advantage that comes to mind about mass spectrometry is the existence of extensive hbraries of spectra that were recorded under electron impact conditions over the years. These hbraries are available to anyone and the fact that specific conditions were kept while recording the spectra allows for their use in comparative work. 

The fragmentation pattern often exhibits peaks corresponding to loss of specific groups in the molecule, for example, —CO2 or —NH, which lends further credence to the presence of a given molecule or which can be used to gain structural information about a molecule. Manufacturers of mass spectrometers provide computer libraries of mass spectra of thousands of compounds, and spectral computer searches can be made to match an unknown spectrum. 

As is true with infrared and nuclear magnetic resonance spectroscopy, large libraries of mass spectra (>150,000 entries) are available in computer-compatible formats,- Most commercial mass spectrometer computer systems have the ability to rapidly search all or pari of such files for spectra that match or closely match the spectrum of an analyte. 

El spectra using 70 eV electrons are very reproducible and form the basis of many libraries of mass spectra available as an option with most data systems. There are some drawbacks. The technique is not suitable for involatile molecules, or compounds which are thermally unstable. Often the molecular ion is very weak or not detected. However, it is an excellent technique to analyse the eluent from Gas Chromatographs and many commercial GC/MS systems utilising El are available. 

D. Ehrenstorfer, Library of Mass Spectra, Dr. Ehrenstorfer GmbH Augsburg, Germany 2000. 

A library of mass spectra with the corresponding compounds represented as molecular graphs is needed for the development of MS classifiers. To construct an MS classifier... 

Thus, the mass spectrum for peak 1 is consistent with the structure of methyl benzoate. We could further confirm our identification by consulting a library of mass spectra. If we had any pure methyl benzoate around, we could also prepare a standard and use both the GC retention time and the mass spectrum of the standard as a means of confirming the compound identification. 

Terpenoids can be analyzed by the usual methods. For the volatile members of the family, gas chromatography-mass spectrometry (gc-ms) is a particularly useful tool. In laboratories (e.g., those in the major fragrance companies), which are accustomed to analyzing mixtures of volatile terpenoids, gc-ms is the major analytical technique employed and such laboratories will have extensive libraries of mass spectra of terpenoids to assist in this. However, the mass spectral fragmentation patterns of closely related terpenoids are often so similar as to render definitive identification by ms alone, impossible. For these materials and those for which there is no reference (e.g., compounds newly isolated from nature), nuclear magnetic resonance (nmr) spectroscopy is the analytical tool of choice. Physical techniques, e.g., density, refractive index, and optical rotation, are relatively inexpensive and prove useful in quality control. 

In those cases where a laboratory is routinely handling natural products that have been seen before in the same laboratory, a self-constructed library of mass spectra is a valuable aid to identification. Such a system is particularly useful in the GC/MS analysis of body fluids (in biomedical research and clinical diagnosis) and in the perfume and flavor industries e.g. terpene identification). Metabolic profiling by GC/MS 48) of the components of urine or serum provides an instance where computer techniques are a necessity and have become quite sophisticated. 

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