Fragments, definition identification

Unfortunately, not all molecular species are detected with equal efficiency by MS. The detection of an individual phospholipids is dependent both upon radyl chain saturation and length with a greater intensity of response being determined for more unsaturated species, but a lower response being found as the chain length increased. In addition the detection of the different lipid classes is affected by solvent since this can alter the nature of the adduct formation and thus simplify or make more complex the spectra. The CID fragmentation of lipids in most cases permits the definitive identification of individual species. 

Although elution time from a LC separation provides valuable information for a particular species, definitive identification of the lipid species has to be performed based on its product-ion mass spectrum. For those researchers who are using LC-MS for identification and quantification of lipid species, familiar with the fragmentation patterns of lipid classes, therefore deriving the product-ion mass spectra of individual lipid species, is very important although a few databases and/or libraries (see Chapter 5) can be used to aid the identification. Resolving complex biological lipids into a... 

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. 

Definition of Ej and E2 eonformations of the a subunit of Na,K-ATPase involves identification of cleavage points in the protein as well as association of cleavage with different rates of inactivation of Na,K-ATPase and K-phosphatase activities [104,105]. In the Ei form of Na,K-ATPase the cleavage patterns of the two serine proteases are clearly distinct. Chymotrypsin cleaves at Leu (C3), Fig. 3A, and both Na,K-ATPase and K-phosphatase are inactivated in a monoexponential pattern [33,106]. Trypsin cleaves the E form rapidly at Lys ° (T2) and more slowly at Arg (T3) to produce the characteristie biphasic pattern of inactivation. Localization of these splits was determined by sequencing N-termini of fragments after isolation on high resolution gel filtration columns [107]. 

The potential for the preservation of lipids is relatively high since by definition they are hydrophobic and not susceptible to hydrolysis by water, unlike most amino acids and DNA. A wide range of fatty acids, sterols, acylglycerols, and wax esters have been identified in visible surface debris on pottery fragments or as residues absorbed into the permeable ceramic matrix. Isolation of lipids from these matrices is achieved by solvent extraction of powdered samples and analysis is often by the powerful and sensitive technique of combined gas chromatography-mass spectrometry (GC-MS see Section 8.4). This approach has been successfully used for the identification of ancient lipid residues, contributing to the study of artifact... 

The fate of the free acyl radical 68 and radical 74 is not known. Most probably it is a constituent of polymer deposits on the wall of the irradiation vessel which hitherto have not been identified more definitely.29 Moreover, the identification of methane and carbon monoxide among the gaseous products of the photolysis of 4-methylphenyl acetate (55) provides evidence for the existence of the acetyl fragment. This intermediate is expected to decarbonylate to give carbon monoxide and a methyl radical, which in turn abstracts hydrogen from the solvent.34... 

Precise definition of the host-protection epitope(s) of the Taenia and Echinococcus vaccine antigens would be valuable if it were to lead to the development of a synthetic vaccine or provide reagents to assist with quality control of vaccine production. Identification of a limited number of host-protective fragments may allow the recombinant antigen to be replaced by synthetic peptides. This would have significant advantages in the production... 

Melanine, ammelide and cyanuric acid were not detected in the HCOOH extracts and the identification of s-triazines previously reported does not prove that s-triazines are indigenous. This kind of compound can easily be formed during the experimental and analytical procedures. Nevertheless, this last conclusion is not definitive. As pointed out by Stoks and Schwartz33, the carbonaceous chondrites are far from homogenous. Important variations from sample to sample exist, even if all these samples are fragments of the same chondrite. Moreover, and as previously reported, the sample treatment is of prime importance. It can lead to the formation of secondary products or liberate molecules unobservable after milder treatment. To conclude, it seems clear that nitrogen heterocycles are present in carbonaceous chondrites and that pyrimidine derivatives are less abundant than purine derivatives. 

An earlier off-odor problem that surfaced was the presence of 4-phenyl-cyclohexene in styrene-butadiene coated paper (Koszinowski et al. 1980). This compound was created by a Diels-Alder condensation reaction involving a molecule of styrene and butadiene and is differentiated by its odor from the isomeric 3 and 1-phenyl-cyclohex-ene compounds which cannot be formed by such a condensation reaction. The recognition threshold of this compound in the headspace over an aqueous solution lies around a concentration of 10 pg/kg (10 ppb). The typical odor of this compound at concentrations of 4-phenyl-cyclohexene in paper over 4 mg/kg (4 ppm) is easily identified. AGC determination in this concentration range is also possible without difficulty and its identification with MS using the relative molecular mass of 158 and one of the retro Diels-Alder decomposition product fragments at m/e = 104 (styrene) and mJe = 54 (butadiene) is definitely possible. 

In RmL the analysis of the structural features of the lid is simplified by the availability of structures of both native and complexed molecules this allows for clear identification of the mobile fragments. The lid is created by a long surface loop made up by residues 80—109. This fragment defies a classical definition of an H loop (Leszczynski and Rose, 1986) in that it exhibits well-defined secondary structure in its central helical fragment. Residues 82-96 (which include a short helix) directly obscure the entrance to the active site in the native enzyme. It is notable that between Arg-80 and Val-95 this fragment is not involved in any hydrogen bonds with any other parts of the molecule. Thus, the lid interacts with the main body of the protein only through hydrophobic interactions. 

Definitive confirmation of pesticide residues was obtained by comparison of parent and fragment ion intensities and mass numbers of eluted pesticides and reference pesticides. Table I lists the residues encountered and the mass numbers and intensities of the characteristic fragments employed for identification in the adipose tissue sample. The mass spectral fragmentation patterns for all the compounds included in Table I with the exception of -HCH have been adequately discussed by other investigators (7). 

Since ABA is a minor component in crude extracts of plant material, extensive purification is necessary prior to identification and quantification [8,31]. The definitive method for identifying ABA as its methyl ester. Me-ABA, is combined gas chromatography-mass spectrometry (GC-MS). Negative chemical ionization causes very little fragmentation, so that the molecular ion is the base peak. This technique has been used extensively in studies with 0-labeled ABA to determine the location of the atoms within the ABA molecule [32]. GC-selected ion monitoring (SIM) is a very sensitive method for quantifying ABA, but requires ABA labeled with a stable isotope, usually H, as internal standard to compensate for losses. 

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