Understanding how quantification results are calculated - Proteome Discoverer Software - Understanding how quantification results are calculated - Proteome Discoverer Software - Proteome Discoverer Software

Procedure

1. It calculates the raw quantification values and associates them with the PSMs identified by Sequest HT, Mascot, or other search engines. The quantification values are peak areas or heights for precursor ion quantification, and intensities or S/N values of the mass or reporter tags in reporter ion quantification.
2. It sums the quantification channel values linked to the PSMs to the peptide groups and proteins. PSMs that do not meet the criteria set by the method, such as minimum S/N threshold or isolation purity, are not included in this sum. Otherwise, this methodology aggregates all contributing signals of the protein, irrespective of the charge and modification state of the peptides. The result is quantification channel abundance values for all channels from all files for the peptides and proteins.
3. It optionally normalizes the abundance values according to the selected normalization method in the consensus workflow.
4. It optionally scales the normalized abundance values for each protein and peptide so that the average abundance is 100. For instance, if you select a TMT 6plex quantification method, the application scales the calculated abundance values of each protein so that their sum is 600 (100 x 6). If the abundances are equal, each one is 100.
5. It groups the optionally normalized and scaled abundance values according to the sample grouping that you specified when you set up the analysis. Grouping in this case means effectively taking the median of the abundance values of all replicates.
6. It calculates the quantification ratios from the grouped abundance values according to the ratios selected when you set up the analysis.