- General Usage
On the peptide panel, the first aspect you may wish to explore is the Peptide Score. The Peptide Score is assigned to each pair/triplet, based on profiling the mass shift, retention time shift, chromatogram shape and drift time (where ion mobility data is available) for the features within the pair/triple. The Peptide score ranges from 0 (poor) to 100 (very reliable). Values above 50 are generally considered reliable for quantification. At this stage, you can explicitly remove peptides with a low score, using the boxes or slider on the left panel. However, the recommended protein quantification algorithm (weighted averaging), automatically downweights those peptides with a lower Peptide score in the final protein-level ratio. If you are only interested in quantifying peptides (e.g. in a phosphoproteomics study), you may wish to remove those peptides with Score < 50 at this stage.
You can explore peptide quantification values on this panel, with various options for selecting additional columns on the top banner and left panel. If you double click a given peptide, a panel will pop-up displaying further details about the peptide pair/triple, including chromatograms and isotope profiles in the aggregate spectrum.