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the signal analysis consists of extracting the intensity of the signal at a specific
coordinate on the LC-MS map and giving the corresponding XIC.
Figure 4: Extraction of the MS signal of a peptide previously identified using a search engine
The first approach is more exhaustive than the latter as it can find quantitative information
on peptides that may not have been fragmented by the mass spectrometer. About the
second approach, we can only assume that knowing the peptide’s exact monoisotopic mass
should reduce the probability of making mistakes in the quantification, but no study to our
knowledge has proved it so far. In a comparative quantitation analysis, both approaches
require the matching of the extracted signals (cf. figure 5). To do this, the LC-MS Maps
have to be previously aligned in order to correct the variability coming from the peptide’s
chromatographic elution. Indeed the difference for the elution time of a given peptide in
two LC-MS analysis may reach tens of seconds. Even if a peptide mass can be precisely
measured, it is still possible that peptides with very close m/z elute at the same time frame.
Figure 3 shows how important the density of the measures is. Therefore, comparing LCMS maps without aligning their time scale would generate many matching errors.
Figure 5: Matching of the detected peptides on several LC-MS maps