Proteolabels 1.0 User Guide


Peptides

Peptide scoring


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.

Peptide quantification

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.


Experiment Design
Proteins