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Quantification
rmillikin edited this page Aug 31, 2017
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- MetaMorpheus uses FlashLFQ to extract MS1 intensity and quantify peptides identified by MS2 identifications below a 0.01 Q-value.
- Quantification occurs after identification. All MS1 peaks around the identifying MS2 spectrum within the retention time window are checked for an expected isotopic distribution. FlashLFQ's peakfinding algorithm is used to find MS1 peaks that meet the expected isotopic distribution.
- Peptides are quantified by apex intensity, meaning that the most intense peak that meets the quantification criteria will be reported as the intensity (rather than integrated peak intensity).
- Because modified peptides can ionize at different efficiencies than unmodified peptides, and can thus affect the intensity of the detected ion, peptide intensity should only be compared to the same peptide with the same mods across runs. Make sure you're comparing apples to apples.
- Protein label-free quantification is also handled by FlashLFQ. Peptides that are shared between multiple protein groups have their intensity evenly split between those groups. Protein quantification is currently the sum of all the protein group's peptide intensities, ignoring peptides that were ambiguously quantified in any run.