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Quantification
Robert Millikin edited this page Aug 6, 2018
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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 isotopic envelope that meets the quantification criteria will be reported as the intensity (rather than integrated peak intensity).
- Protein label-free quantification is also handled by FlashLFQ. See the FlashLFQ page for a description of how protein quantification is handled.