Calculating PSM abundances - Proteome Discoverer Software - Calculating PSM abundances - Proteome Discoverer Software - Proteome Discoverer Software

A quantification value is the intensity, S/N, or area detected for a given quantification channel. For reporter ion quantification, a quantification channel is one of the mass or reporter tags, and for precursor ion quantification, it is one of the different possible labeling states of a PSM corresponding to the different heavy amino acids used in the cell cultures. “Intensity” refers to both the intensity of the reporter peaks in reporter ion quantification and to the apex intensity or areas detected in precursor ion quantification. The S/N corresponds to the intensity of the peak divided by the noise values calculated for each peak during acquisition.

You can set the following parameters to control this step:

• Use Single-Peak Quan Channels: Determines whether the application uses quantification channels identified with only a single peak for the precursor ion pattern for precursor quantification.
• Average Reporter S/N Threshold: Specifies the minimum average reporter signal-to-noise threshold value to use. The application ignores PSMs with quantification results below this threshold.
• Precursor Abundance Based On: For label-free or precursor ion quantification, you can choose the abundance associated with a PSM to be either the intensity at the apex of the chromatographic profile of the selected feature or the total peak area.
• Reporter Abundance Based On: For reporter ion quantification, the PSM abundance can be based on either S/N or peak intensity. The Automatic setting bases the abundance on S/N for quantification spectra acquired using Orbitrap MS and bases the abundance on intensity for quantification spectra acquired suing ion trap MS.

The following table lists some of the different circumstances that can arise in calculating quantification ratios for PSMs from the selected quantification values. The parameters in the table belong to the Reporter Ions Quantifier node.

The table does not include cases resulting from PSM uniqueness and protein grouping. It focuses on cases where some or all of the quantification channels are zero. In these cases, the application detects nothing on a channel because the spectrum does not contain one of the reporter peaks, the heavy or light isotope pattern is missing, a quantification value falls below a specified minimum threshold, or the calculated ratios are very high or very low.

The table also lists the different possible cases exemplified by arbitrary values. The values in the tables have [counts] as units if the cases are presented for reporter ion quantification. For precursor ion quantification, 114 and 115 are replaced by Light and Heavy and the quantification values have [counts × seconds] as units.