Detecting Peptides
Typically, peptide signals are detected at the MS1 level and distinguished from chemical noise through their characteristic isotopic pattern. These patterns are then tracked across the retention time dimension and used to reconstruct a chromatographic elution profile of the mono-isotopic peptide mass. The total ion current of the peptide signal is then integrated and used as a quantitative measurement of the original peptide concentration. For each detected peptide, all isotopic peaks are first found and the charge state is then assigned.
While the first method, introduced above, has problems due to the identity of the peptide precursor ion that is being measured which, in high-throughput studies, could easily be a completely different peptide happening to display a similar m/z ratio and elutes at the same time or overlapping with other peptides.
The second method has problems due to the fact that the peptides are identified thus making it necessary to run an additional MS/MS scan which takes time and therefore reduces the resolution of the experiment.
Read more about this topic: Label-free Quantification
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