Databases, mass spectra

If PMF and sequence homology searches fail using available protein and EST databases, mass spectrum data can, in principle, be used to search genome databases (GenBank http //www.ncbi.nlm.nih.gov/). However, only a small percentage of large genomic sequences code for proteins such that bioinformatics still needs to accurately define exon-intron structures (Andersen and Mann, 2000). 

Multivariate data analysis usually starts with generating a set of spectra and the corresponding chemical structures as a result of a spectrum similarity search in a spectrum database. The peak data are transformed into a set of spectral features and the chemical structures are encoded into molecular descriptors [80]. A spectral feature is a property that can be automatically computed from a mass spectrum. Typical spectral features are the peak intensity at a particular mass/charge value, or logarithmic intensity ratios. The goal of transformation of peak data into spectral features is to obtain descriptors of spectral properties that are more suitable than the original peak list data. 

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. 

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 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]. 

Mass spectrum for Problem 22-14 from NIST/EPA/ NIH Mass Spectral Database.8... 

Every organic chemical has a mass spectrum, which is a combination of ions with different masses and different intensities (abundances). To identify a compound, its mass spectrum is compared to the mass spectra of standards, analyzed under the same instrument settings, and to the EPA/National Institute for Standards and Technology (NIST) mass spectra library. The EPA/NIST library is stored in the database of the computer that operates the instrument. A comparison to the library spectra is possible only if there is consistency in the compound spectra generated by different GC/MS systems at hundreds of environmental laboratories. To achieve such consistency, the EPA methods for GC/MS analysis include the mass... 

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. 

FIGURE 7.44 MALDI mass spectra from on-CD analysis of the phosphopeptide-con-taining sample, (a) Peptide mass spectrum after concentration/desalting. A database search showed that the sample contained bovine protein disulfide isomerase. (b) Phosphopeptide enrichment by IMAC. Two phosphopeptides at m/z 964 and 2027 were recognized (c) Phosphopeptide enrichment followed by enzymatic on-column dephosphorylation using alkaline phosphatase. Two phosphopeptides at m/z 884 and 1947 were recognized from the mass shifts of 80 Da from (B), which were resulted from dephosphorylation [794]. Reprinted with permission from the American Chemical Society. 

Figure 5.10. Sample spectra retrieval from SDBS. (a) 13C-NMR spectrum in DMSO-d6. (b) -NMR (400 MHz) spectrum in DMSO-d6. (c) Mass spectrum, (d) Infrared spectrum in KBr. Sample spectra (including spectral analysis) of uracil are retrieved from Spectral Database Systems. The structure of uracil (molecular weight = 112) is represented with the number corresponding to the position of carbons and the alphabet denoting the position of protons to facilitate NMR assignments ...

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... 

The Schedule 3 list contains only 17 discrete chemicals, of which four represent toxic chemicals. One of them is too simple (HCN) to produce an informative mass spectrum and some of the precursors (chlorinating chemicals) cannot be analyzed by GC/MS. Mass spectra are contained in the OPCW Analytical Database and in commercially available databases. The mass spectrum of trichloroni-tromethane (chloropicrin, CAS 76-06-2) is almost identical to that of trichloromethane (chloroform), apart from a peak at mlz 30. Not scanning this low... 

Figure 4.4. Protein identification by MALDI-TOF. Steps in protein identification by MALDI-TOF are shown. Prior separation by gel or liquid chromatography to a single protein is needed prior to enzymatic digestion with trypsin. Digested peptides are spotted onto a MALDI target with an appropriate matrix that assists desorption of peptides upon activaton by laser. Peaks from the resulting mass spectrum represent peptide ions that can be searched in a database to match a theoretical tryptic digest from known proteins. The more proteins that are matched, the greater the statistical confidence in assignment of a protein identification.

The standard low-resolution mass spectrum (Fig. 30.3) is computer generated, which allows easy comparison with known spectra in a computer database for identification. The peak at the highest mass number is the molecular ion (M ), the mass of the molecule minus an electron. The peak at RA = 100%, the base peak, is the most abundant fragment in the spectrum and the computer automatically scales the spectrum to give the most abundant ion as 100%. The mass spectrum of a compound gives the following information about its chemical structure ... 

In both techniques the separated compounds from the chromatograph are sampled automatically and the mass spectrum of each compound is recorded. Comparison of the mass spectra with a library in an on-board database permits identification of the components of the mixture. 

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