Common Mode Analysis background

In addition, due to lack of MS/MS capability, SIM has been more commonly performed on single quadrupole MS, while SRM has been broadly adapted on triple quadrupole (Figure 13-4) and ion-trap mass spectrometers. The increase in sensitivity and selectivity of SRM stem from the ion-chromatogram (i.e., LC-MS/MS) obtained by specific precursor-to-product ion transition for an analyte of interest (Figure 13-4). Conversely, in an SIM mode, the relative background noise due to the presence of other isobaric species (i.e., ions with a same m/z as the analyte of interest) can result in a lower signal-to-noise ratio for the analyte. Due to the widespread acceptance of SRM in quantitative analysis, the remaining part of this section focuses on a description of tandem-mass spectrometry (MS/MS), which is utilized in SRM (or MRM) experiments. 

Different methods for correction are possible the choice of method depends on the availability of spectra resulting from specific modes of spectral storage for different instruments. Ideally, all spectra are retained for an analysis, but because of processing and storage constraints, many instruments offer a mode of acquisition where spectra are stored only during the elution of a peak. Peak spectra can be limited to just the apex spectrum, or to a number of additional spectra across the peak, most commonly acquired at the baseline and the inflection points. If only apex spectra are available, no background correction is possible. For all other cases, the quality of background correction will depend on the availability of suitable baseline spectra. 

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