The omega display is a measure of peptide frequency for a single protein identification. It comes in two forms, giving information for both the peptide (ω) and protein (Ω) level.
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The peptide omega score ("ω-score") for a peptide is the amount of peptide identifications for a single protein which are accounted for by a specific residue sequence in a specific charge state; the same peptide in two different charge states will have two different ω-scores.
For example, looking at the protein.pl page for an identification of ENSP00000295546 (Collage alpha-3(IV) chain precursor) in result file GPM10100095769 (link to file), the frequencies for the peptides are displayed in the rightmost column.
The first peptide, TMFSLDTYST K, is doubly charged and has a ω-score of 0.0019. This means that the total number of identifications of this peptide in a doubly charged state account for 0.19% of the peptide identifications in this observation of ENSP00000295546. The second distinct peptide sequence, MKPLDGSALY TGSALDFVR, is also doubly charged, but has a ω-score of 0.0072. This means that 0.72% of the doubly charged peptides identified in this observation of ENSP00000295546 are of this residue.
One immediate conclusion is that the second peptide is identified almost four times as often as the first in this protein.
Peptides are counted with respect to charge state, across all peptides identified and submitted for inclusion in The GPM. The ω-score for a specific peptide in a specific charge state is the ratio of the total number of identifications of that peptide in that charge state, divided by the sum of identifications of all peptides in that protein in the same charge state. E.g., peptide ABCDE at z=2 has been identified a total of 300 times in GPMDB. Protein X has three peptides with z=2: ABCDE (300 total identifications), DEFG (100 total identifications), and MNPQRS (200 total identifications). The total identifications for doubly-charge peptides in protein X is 600 (300 + 100 + 200). Peptide ABCDE has ω=0.5 (300/600). Peptide DEFG has ω=0.17 (100/600). Peptide MNPQRS has ω=0.33 (200/600).
The omega display for proteins ("Ω-score") is a measure of peptide coverage with respect to charge state. It is made up of a delimited list of ratios, rounded to two decimal places, denoting what share of the peptides in a particular charge state for a single protein were seen in a single protein identification:
Ω = 01|.532|.443 (taken from an enzyme identification in GPMDB)
The superscripts denote the charge state for the preceding number. In this instance, this specific identification contained less than one half of one percent of the singly charged peptides, roughly 53% of the double charged peptides, and roughly 44% of the triply charged peptides. Charge states higher than three are not included in the calculations.