Tandem mass spectrometry data processing

Benton, H.P. et al., XCMS(2) Processing tandem mass spectrometry data for metabolite identification and structural characterization, Anal. Chem., 80(16), 6382, 2008. 

To record a mass spectrum it is necessary to introduce a sample into the ion source of a mass spectrometer, to ionize sample molecules (to obtain positive or negative ions), to separate these ions according to their mass-to-charge ratio (m/z) and to record the quantity of ions of each m/z. A computer controls all the operations and helps to process the data. It makes it possible to get any format of a spectrum, to achieve subtraction or averaging of spectra, and to carry out a library search using spectral libraries. A principal scheme of a mass spectrometer is represented in Fig. 5.2. To resolve more complex tasks (e.g., direct analysis of a mixture) tandem mass spectrometry (see below and Chapter 3) may be applied. 

Despite the fact that direct analysis methods exclude a cost-intensive separation step overall analysis cost may still be high, namely by the need for more sophisticated instrumentation (allowing for a physical rather than chemical separation of components) or extensive application of chemometric techniques. The wide variety of additives that are commercially available and employed complicate spectroscopic data analysis. For multicomponent analysis some kind of physical separation of additive signals is often quite helpful, e.g. based on mobility (as in LR-NMR or NMRI), diffusion coefficient (as in DOSY NMR), thermal behaviour (as in a thermal analysis and pyrolysis techniques) or mass (as in tandem mass spectrometry). The power of signal processing techniques (such as multi-wavelength techniques, derivative spectrophotometry) is also used to the fullest extent. 

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