Library searches mass spectra

Some differences are also seen in the El spectra for the same type of compound but generated from a different initial monosaccharide. However, these differences are sometimes more difficult to interpret, as the identifications rely on mass spectral library searches. The spectrum for tri-TMS 1,6-anhydroglucopyranose was shown in Figure... 

Once a mass spectrum from an eluting component has been acquired, the next step is to try to identify the component either through the skill of the mass spectroscopist or by resorting to a library search. Most modem GC/MS systems with an attached data station include a large library of spectra from known compounds (e.g., the NIST library). There may be as many as 50,000 to 60,000 stored spectra covering most of the known simple volatile compounds likely to be met in analytical work. Using special search routines under the control of the computer, one can examine... 

Once the peaks have been collected and stored, the computer can be asked to work on the data to produce a mass spectrum and print it out, or it can be asked to carry out other operations such as library searching, producing a mass chromatogram, and making an accurate mass measurement on each peak. Many other examples of the use of computers to process mass data are presented in other chapters of this book. 

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). 

When a mass spectrum has been acquired by the spectrometer/computer system, it is already in digital form as m/z values versus peak heights (ion abundances), and it is a simple matter for the computer to compare each spectrum in the library with that of the unknown until it finds a match. The shortened search is carried out first, and the computer reports the best fits or matches between the unknown and spectra in the library. A search of even 60,000 to 70,000 spectra takes only a few seconds, particularly if transputers are used, thus saving the operator a great deal of time. Even a partial match can be valuable because, although the required structure may not have been found in the library, it is more than likely that some of the library compounds will have stractural pieces that can be recognized from a partial fit and so provide information on at least part of the structure of the unknown. 

However, the two levels may become obvious if the instrument operator tries, for example, to conduct a library search while the computer is trying to acquire input from another mass spectrum the library search has to wait. Acquiring the data is a foreground task. Other functions such as library searching are background tasks. 

Figure 16.2 is the mass spectrum of propylene glycol and shows the presence of an abundant m/z 45 ion. A library search will provide strong evidence that this compound is propylene glycol. Preparation of a TMS derivative will confirm this assignment. 

Library searching The use of a computer to compare a mass spectrum to be identified with large numbers of reference spectra. 

Once a mass spectrum has been obtained, it is possible to perform a library search, in different databases installed in the local computer or in remote servers through the Internet that can help in identification of unknowns. 

Mass spectra obtained by El are highly reproducible on different instrumentation and over the time. This allows mass spectra libraries to be built in which an unknown mass spectrum can be searched by using an algorithm. Indeed, a lot of El mass spectra libraries containing hundreds of thousands of mass spectra, such as the NIST/EPA/NIH... 

To record a mass spectrum it is necessary to introduce a sample into the ion source of a mass spectrometer, to ionize sample molecules (to obtain positive or negative ions), to separate these ions according to their mass-to-charge ratio (m/z) and to record the quantity of ions of each m/z. A computer controls all the operations and helps to process the data. It makes it possible to get any format of a spectrum, to achieve subtraction or averaging of spectra, and to carry out a library search using spectral libraries. A principal scheme of a mass spectrometer is represented in Fig. 5.2. To resolve more complex tasks (e.g., direct analysis of a mixture) tandem mass spectrometry (see below and Chapter 3) may be applied. 

Initially the substance at Rt 19.95 was identified as 2-nonen-l-ol based on mass spectrum library search. The comparison with a commercial 2-nonen-l-ol standard indeed revealed a high degree of similarity between the mass spectra, but a distinct deviation regarding the retention time suggesting a similar molecule with a chain length greater than 2-nonen-l-ol. The substance Rt 20.95 was tentatively identified as 6,10-dimethyl-5,9-undecadien-2-one which corresponds with the authentic standard regarding mass spectra and retention time. 

The El source has been the most widely used ion source over the past 60 years and continues to be the method of choice for the analysis (either qualitative or quantitative) of small- to medium-sized volatile organic compounds. The inherent reproducibility of the mass spectra has enabled the assembly of large spectral libraries. Computers associated with current generation instruments can efficiently (in a few seconds) search an unknown mass spectrum against tens of thousands of reference spectra in order to aid in the identification of an analyte. The general scheme of an El source includes the introduction of the vaporized analyte molecules into the ionization chamber, exposure of those molecules... 

Fig. 11.4. Electron ionization mass spectrum of nonanal. Unlike the previous example (toluene, Fig. 11.3), this 9-carbon alkyl aldehyde displays extensive fragmentation and a very low abundance molecular ion at mlz 142. The extensive degree of fragmentation exhibited by many compounds under El conditions makes manual interpretation complex and tedious. Consequently, computerized searches of spectral libraries find extensive use in compound identification.

Fig. 19.8. Electron ionization mass spectrum of toluene (top panel) from GC-MS analysis, and library search match (bottom panel) against the NIST library.

The importance of an appropriate transformation of mass spectra has also been shown for relationships between the similarity of spectra and the corresponding chemical structures. If a spectra similarity search in a spectral library is performed with spectral features (instead of the original peak intensities), the first hits (the reference spectra that are most similar to the spectrum of a query compound) have chemical structures that are highly similar to the query structure (Demuth et al. 2004). Thus, spectral library search for query compounds—not present in the database—can produce useful structure information if compounds with similar structures are present. 

Electronic databases of the mass spectral fragmentation patterns of known molecules can be rapidly searched by computer. The pattern and intensity of fragments in the mass spectrum is characteristic of an individual compound so comparison of the experimental mass spectrum of a compound with those in a library can be used to positively identify it, if its spectrum has been recorded previously. 

In Figure 8.14, the Cold El mass spectrum of corticosterone in methanol solution is shown in the upper trace, and is compared with the standard NIST 98 El library mass spectrum shown in the lower trace. Note the similarity of the library mass spectrum to that obtained with the SMB apparatus. All the major high mass ions of m/z 227, 251, 269, and 315 are with practically identical relative intensity and thus good library search results are enabled with the NIST library-matching factor of 829, and the reversed matching factor of 854% and 86.5% confidence level (probability) in corticosterone identification. In addition, the molecular ion at m/z 346 is now clearly observed while it is practically missing in the library (very small in the shown mass spectrum and absent in the other three replicate mass spectra). 

In the past, PTRC screening was mainly based on gas chromatography-mass spectrometry (GC-MS) [116]. The choice of GC-MS was based on a number of good reasons (separation power of GC, selectivity of detection offered by MS, inherent simplicity of information contained in a mass spectrum, availability of a well established and standardized ionization technique, electron ionization, which allowed the construction of large databases of reference mass spectra, fast and reliable computer aided identification based on library search) that largely counterbalanced the pitfalls of GC separation, i.e., the need to isolate analytes from the aqueous substrate and to derivatize polar compounds [117]. 

Modem mass spectral databases allow the automated searching of very extensive mass spectral libraries.6 This has made the identification of compounds by mass spectrometry a far more straightforward task. One must understand, however, that such databases are no substitute for the careful analysis of each mass spectrum and that the results of database matchup are merely suggestions. 

The third of the three adjacent peaks (29.207 minutes) is readily identified as 2-hydroxybenzaldehyde (salicylaldehyde) by comparison of the MS or IR spectrum with library data. It should be noted that the automated search routine in the MS software picked 3-and 4-hydroxybenzaldehyde as better matches than the 2-hydroxy compound, even though the 76 ion in the spectrum of the unknown is present only in the mass spectrum of the 2-hydroxy compound. However, the IR search routine correctly identified the 2-isomer. This illustrates that casual operators who rely on automated search routines for compound identification are much less likely to make errors when they have access to both IR and MS searching. 

Volatile profiles of raw and cooked-beef flavor samples, prepared by the procedures of Figure 1, were obtained after capillary GC and FPD. Although the identification of these sulfur containing compounds is as yet incomplete, the chromatograms demonstrated that there were a number of new sulfur compounds produced on cooking that were not present in the raw beef. Three prominent sulfur compounds were identified as markers in subsequent meat flavor deterioration experiments, namely, methional (13.2 min), methyl sulfone (13.8 min), and benzothiazole (25.3 min). Each compound produced an adequate mass spectrum for spectral library search and positive identification. 

To many, mass spectrometry is synonymous with El mass spectrometry. This view is understandable for two reasons. First, historically, El was universally available before other ionization methods were developed. Much of the early work was El mass spectrometry. Second, the major libraries and databases of mass spectral data, which are relied upon so heavily and cited so often, are of El mass spectra. Some of the readily accesible databases contain El mass spectra of over 390,000 compounds and they are easily searched by efficient computer algorithms. The uniqueness of the El mass spectrum for a given organic compound, even for stereoisomers, is an almost certainty. This uniqueness, coupled with the great sensitivity of the method, is... 

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