Interpretation of mass spectra

TABLE 15.5. Nominal, Monoisotopic, and Average Mass for Some Elements and Molecules  

Element or Molecule Nominal Mass Monoisotopic Mass Average Mass 

Biomolecules such as proteins and oligonucleotides present mass spectra that are complicated by the presence of multiply charged families of ions. The parent species, for example, generated by a soft ionization method such as FAB of ESI, will yield several m/z peaks in which m is equal to a constant plus (protein) or minus (nucleic acid) a variable number of proton masses, while z is a variable. Egg white lysozyme, for example, yields ESI-mass spectra with fine parent peaks between m/z values of 1194 and 1791 the corresponding z values are 12-8 [see Fig. 15.9(a)]. 

Amino Acid Residues (from-to) Mass (Da) Sequence 

Larger analytes with more protonation-deprotonation sites yield larger families of peaks for each fragment, and the overlap of mlz ranges for different fragment families can further complicate the spectra of biomolecules. For this reason, soft ionization methods, that produce few fragments, are particularly useful for biomolecule MS. 

As mentioned previously (Chap. 2.2.2.4.1), the major purpose of the GC-MS analysis of a nitrobenzene or cupric oxide oxidation mixture is to verify the identity of the oxidation products established previously by GC or HPLC analysis, and to elucidate the structure of unknown constituents. For example, GC-MS analysis of the nitrobenzene oxidation mixture of milled bamboo lignin from Phyllostachys pubescence showed unequivocally that compounds (l)-(3) in the total ion chromatogram of the oxidation mixture (Fig. 6.2.2) are indeed p-hydroxybenzaldehyde, vanillin, and syringaldehyde, respectively (Tai et al. 1990) (see Chap. 9.1 for a discussion of the GC-MS technique). In addition, the unknown compound in the chromatogram was identified as p-hydroxyazobenzene (15) (Fig. 6.2.1), one of the phenolic reduction products of nitrobenzene. 

Nevertheless, procedures are recommended for deciphering information coded in a mass spectrum. (Certain users accuse experienced mass spectrometrists of having a criminological feel for the subject - and they are justified ) In this spectroscopic discipline, the experience of a frequently investigated class of 

The procedure shown in the following scheme has proved to be effective  

As all GC-MS systems are connected to very powerful computer systems, each interpretation process for El spectra should begin with a search through available spectral libraries (see Section 3.2.3). Spectral libraries are an inestimable source of knowledge, which can give information as to whether the substance belongs to a particular class or on the appearance of clear structural features, even when identification seems improbable. Careful use of the database spares time and gives important suggestions. The different search procedures especially the similarity search modes can all help. 

Is there an obvious isotope pattern, for example, for chlorine, bromine, silicon or sulfur The molecular ion shows all elements with stable isotopes in the compound. Is it possible to find out the maximum number of carbon atoms  

This is a typical limitation with residue analysis as usually it is not possible to detect C signal intensities with certainty. Also a noticeable absence of isotope signals, particularly with individual fragments, can be important for identifying the presence of phosphorus, fluorine, iodine, arsenic and other monoisotopic elements. Only the molecular or quasimolecular ions give complete information on all isotopes in the elemental formula. 

The amount of energy acquired during ionization and the structure of the analyte determine the complexity of the mass spectra obtained. Other features, including isotopic composition, the nitrogen rule, rings plus double bond considerations (see later), and accurate mass values, provide additional information. 

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McLafferty, F.W, Interpretation of Mass Spectra, University Science Books, 1996. 

Machine learning provides the easiest approach to data mining, and also provides solutions in many fields of chemistry quality control in analytical chemistry [31], interpretation of mass spectra [32], as well prediction of pharmaceutical properties [33, 34] or drug design [35]. 

The book is divided into four parts. Part I, The Fundamentals of GC/MS, includes practical discussions on GC/MS, interpretation of mass spectra, and quantitative GC/MS. Part II, GC Conditions, Derivatization, and Mass Spectral Interpretation of Specific Compound Types, contains chapters for a variety of compounds, such as acids, amines, and common contaminants. Also included are GC conditions, methods for derivatization, and discussions of mass spectral interpretation with examples. Part III, Ions for Determining Unknown Structures, is a correlation of observed masses and neutral losses with suggested structures as an aid to mass spectral interpretation. Part IV, Appendices, contains procedures for derivatization, tips on GC operation, troubleshooting for GC and MS, and other information which are useful to the GC/MS user. Parts I to III also contain references that either provide additional information on a subject or provide information about subjects not covered in this book. 

Budzikiewicz, H., Djerassi, C., and Williams, D. H. Interpretation of Mass Spectra of Organic Compounds. San Francisco Holden-Day, 1964. 

McLafferty, F. W., and Turecek, F. Interpretation of Mass Spectra (4th ed.). Mill Valley, CA University Science Books, 1993. 

Mass Spectra and Chemical Structure While there are a number of books (Refs 16, 30, 49 64) already referred to, which deal with details of the instrumentation and techniques of mass spectrometry, there are several concise introductory texts (Refs 10, 21 52) on the interpretation of mass spectra. Still other recent books deal comprehensively with organic structural investigation by mass spectrometry. One of these (Ref 63) discusses fundamentals of ion fragmentation mechanisms, while the others (Refs 7, 15, 20, 28 29) describe mass spectra of various classes of organic compounds. In the alloted space for this article methods of interpretation of mass spectra and structural identification can not be described in depth. An attempt is, therefore, made only to briefly outline the procedures used in this interpretation... 

McLafferty, Interpretation of Mass Spectra , 2nd Ed, W,A. Benzamin, Inc, Reading, Mass (1973) 64) W. McFadden, Techniques of... 

McLafferty, F.W. "Interpretation of Mass Spectra" University Science Books Mill Valley, CA, 1980. 

Computer programs have been developed that assist, at different levels, in the interpretation of mass spectra, the goal being identification... 

The mass spectrometer can be regarded as a kind of chemistry laboratory, especially designed to study ions in the gas phase. [1,2] In addition to the task it is usually employed for - creation of mass spectra for a generally analytical purpose - it allows for the examination of fragmentation pathways of selected ions, for the study of ion-neutral reactions and more. Understanding these fundamentals is prerequisite for the proper application of mass spectrometry with all technical facets available, and for the successful interpretation of mass spectra because Analytical chemistry is the application of physical chemistry to the real world. [3]... 

Even if the analyte is chemically perfectly pure it represents a mixture of different isotopic compositions, provided it is not composed of monoisotopic elements only. Therefore, a mass spectrum is normally composed of superimpositions of the mass spectra of all isotopic species involved. [11] The isotopic distribution or isotopic pattern of molecules containing one chlorine or bromine atom is listed in Table 3.1. But what about molecules containing two or more di-isotopic or even polyisotopic elements While it may seem, at the first glance, to complicate the interpretation of mass spectra, isotopic patterns are in fact an ideal source of analytical information. 

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