Neutral loss searching

The package uses fragment as well as neutral loss searching yielding hit lists useful for determining possible chemical structures for an unknown compound even when the compound is clearly not in the reference database. A limit of 500 spectra from the users own mass spectrometry database is currently in place for the basic package but this can be overcome with an upgrade. 

Maximum benefit from Gas Chromatography and Mass Spectrometry will be obtained if the user is aware of the information contained in the book. That is, Part I should be read to gain a practical understanding of GC/MS technology. In Part II, the reader will discover the nature of the material contained in each chapter. GC conditions for separating specific compounds are found under the appropriate chapter headings. The compounds for each GC separation are listed in order of elution, but more important, conditions that are likely to separate similar compound types are shown. Part II also contains information on derivatization, as well as on mass spectral interpretation for derivatized and underivatized compounds. Part III, combined with information from a library search, provides a list of ion masses and neutral losses for interpreting unknown compounds. The appendices in Part IV contain a wealth of information of value to the practice of GC and MS. 

Even though a good fit is not obtained, the library search may indicate the structural type. Review the characteristic fragment pathways of the suspected structural type in Part II of this book, and check Part III to determine if the ions observed and neutral losses correspond to the suggested structural type. 

The ability of MS/MS to search for classes of compounds in a mixture will be as valuable in food and flavor analyses as it is in other complex mixture analyses, such as the pharmaceutical or environmental fields. Flavors are complex mixtures, but often consist of groups of chemically similar compounds. It is precisely the identification of these groups for which parent ion and neutral loss MS/MS experiments are particularly adept. This is a characteristic that is patently not available with GC/MS, which has been the usual method of analyses of these mixtures. 

Increasing speed in data-acquisition on newer instruments enables more advanced DDA experiments to be performed. The use of automated DDA-MS-MS of multiple precursor ions on an ion-trap instrument is combined with a postacquisition search through the complete data set for specific neutral losses or common fragment ions. The method is applied to search for metabolites of MEN 15916 [42] and revealed both mono-, di-, and trihydroxy-metabohtes, as well as some unexpected metabolites (a carboxylic acid, a A-dealkylated metabolite, and its hydroxy-analog). 

For the neutral loss scan, the first mass analyzer (Qj) scans all the masses (Figure 7(d)). The second mass analyzer (Q3) also scans, but at a fixed offset from the first mass analyzer. This offset corresponds to a neutral loss that is commonly observed for a particular class of compounds for example, the loss of 44 u (C02) from [M — H] ions will be indicative of carboxylic acids. Alkyl loss (C H2b+i) will be seen in the loss of 15, 29, or 43, etc. and the loss of 18 u (H20) will be indicative of a primary alcohol. A comprehensive table of common neutral fragments may be found in McLafferty and Turecek.32 The mass spectrum is then a record of all precursor ions that lose the specified neutral fragment. Again, neutral loss scans cannot be performed with trap-type MS instruments or with ToF analyzers. However, postacquisition analysis software can be used to search for the specified neutral loss. 

Frequently, organisms will produce several members (factors) within a family of compounds. Product-ion MS/MS spectra can often be used to propose new structures within these series of natural product factors. For example, LC-MS/MS can provide both the molecular weight and product-ion MS/MS spectra of the unknowns. Database searches using these spectra may produce a match to a known natural product in the sample, which can be conlirmed as previously described. In addition, the correlation of product ions and neutral losses from the MS/MS spectra with the structure of these known compounds can often be used to propose structures for the other related factors in the sample. An example of this correlation was shown by Janota et al. [84], who used this approach to propose several structures within the roridin family. 

Finally, a double synchronized scanning of both mass analysers is made with a pre-programmed shift between them, corresponding to a given neutral mass (e.g. a neutral fragment such as CO or C2 H2). Thus, all precursor ions present in the ion source, that undergo the same neutral loss, are detected (search for neutrals). 

It is evident from this chapter that there are many examples of methods for the analysis of antibiotic residues in food that utilize mass spectrometry. As a result, the fragmentation patterns for different classes of antibiotics have been proposed and described in several multi-residue methods, as well as in procedures for specific groups of compounds. Table 6.4 and Figure 6.14 provide examples of the common product ions and expected neutral losses seen in MS/MS spectra for major classes of antibiotics. Specific examples, along with relevant citations, are also provided. As MS methods begin to search for and identify more non-targeted analytes, it will become more important to be familiar with the fragmentation patterns of common analytes. 

Neutral loss masses from the M-r peak are also used via a special tool for spectral searching. 

The CNL approach is utilized to search for metabolites, which exhibit a characteristic loss of a neutral fragment such as a fragment of the parent drug or typical neutral loss of phase II metabolites. Characteristic PI and CNL of parent drug are determined from its MS/MS spectrum and then used in the survey scan to search for drug-related metabolites. For example, the acetyl or... 

GSH adducts can be readily detected by LC—ESI/MS/MS in the positive ion mode with either the full-scan mode to search for anticipated conjugates or the constant neutral loss scanning for 129 Da ( -glutamyl moiety) to detect GSH-derived metabolites followed by collision induced dissociation (CID) and MS/ MS analysis of MH (Baillie and Davis, 1993 Levsen et al., 2005 Nikolic et al., 1999). More recently, negative ion ESI methodology in combination with the... 

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