Tandem MS data

Stage, there is no indication from Figure 13.13a whether the ions observed represent one or more isobaric compounds. However, careful analysis of the tandem MS data can identify multiple components or yield valuable structural information. For example, the MS/MS spectrum of m/z 456 (Figure 13.13b) shows five main ions m/z 438, 396, 378, 352, 338, and 254). By then conducting MS/MS/MS experiments (Figure 13.13c-f) it can be deduced that the ion peak at m/z 456 represents two compounds and, further, that derivatization appears to occur at either of two positions on the C-9 esterifying acid [35]. 

Limitations of GMF approaches are related to the data that comes in to the algorithms. Since tandem MS data is not as information rich as a set of multiple-stage MS spectra, it may not be possible to distinguish between two structures based on the one spectrum alone. In fact, it is often the case that supplemental evidence is required to make a confident assertion that structures have been assigned correctly. 

Commercially, Agilent Technologies produces chips for both direct infusion into a mass spectrometer and for HPLC-MS applications. The chips accommodate nanoflow rates with an electrospray ionisation source, are about the size of a credit card and are rensable. The infusion chip is for collecting direct MS or tandem MS data. The protein HPLC chip has both a sample enrichment and CIS separation column on the chip, as well as the connections and spray nozzles for electrospray. There are also a small molecule chip and a glycan chip. The chip being used is placed in a Chip Cube MS interface which positions the sprayer tip perpendicular to the MS inlet (Figure 10.7). 

The ability to translate these experimentally observed differences reliably into chemical structures is stiU in its infancy. For CGA derivatives, we have over the last decade made a very good start. We have clearly shown that tandem MS data can be reliably used for full stmcture elucidation. The method is, in most cases, superior to NMR spectroscopy because of the latter s unfavorable signal overlaps and issues of conformation. At least for the class of CGAs, MS has complemented and in many cases even replaced NMR as the structure elucidation tool of choice for many research groups. 

Acquiring tandem MS data for a specific parent ion across the tissue section can provide more specific images because a specific parent ion/product ion transition can be mapped. The image thus generated would be a tandem MS image. As has been shown previously (6), performing tandem MS on a ion trap provides the... 

The ability to separate isobaric ions using tandem MS in imaging tissue has been shown previously (6), but the characterization of the many isobaric ions present has not been fully explored. For example, Cha and Yeung (18) showed the characterization of cerebrosides and PCs using graphite-assisted laser desorption and the separation of isobars including cerebrosides, but not across the entire tissue. In the current study, tandem MS data were collected across the entire tissue from over 40 different ions. The full-scan tandem mass spectra were then analyzed for possible isobaric species present see Table 12.2 for a list of all the tandem MS experiments. In addition, to help characterize the isobars, MS was performed on selected MS/MS daughter ions to elucidate the structure of the PL species present see Table 12.2). 

METLIN [10, 11] is a metabolomics database, which is a repository of metabolite information as well as tandem MS data. The METLIN database was developed and is maintained by Dr Siuzdak laboratory at The Scripps Research Institute. The METLIN metabolite database is available to the public online (http //metlin.scripps.edu) for metabolite searches. 

In addition to the parent residues, detection and characterization of metabolites of these drugs are also possible with the use of hybrid analyzers like QTOP. Evaluation of both single and tandem MS data has enabled identification of several plausible metabolites of enrofloxacin, some not previously observed in milk [71]. 

HPLC-APCI-MS data are found to be most useful when the chemical identity of additives in a polymer is already known (verification) otherwise tandem MS... 

Several algorithms are available for the analysis of MS/MS spectra including SEQUEST, MASCOT, and X Tandem among others. Note that additional secondary quality control of assessment of MS/MS data has recently been implemented to assess identification probabilities and false positivity rates. The MS/MS spectra from an experiment can be interrogated against a concatenated forward and reverse database and an assessment of the intrinsic error rate of the data set can be made. Other approaches for secondary analysis of matching scores for peptide sequencing data include XCorr score normalization routines that are independent of peptide and database size.33... 

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