Protein coverage calculation

[apsteinberg]

Hi all,

I had a quick question regarding how the calculation of protein coverage is performed in the protein.tsv report. I was trying to compute protein coverage by using the results that are in the peptide.tsv -- basically, I was taking the Protein Start and Protein End positions listed for each peptide related to a given protein in the peptide.tsv file, and using these to compute protein coverage. I am finding there is a slight discrepancy between the values. Does the protein coverage listed in the protein.tsv report include some additional peptides?

Thanks, Asher

[fcyu]

Hi Asher,

It is calculated by ProteinProphet. If I remember it correctly, it uses all peptides from all samples/input files.

Best,

Fengchao

[anesvi]

I though we were even going to remove that column, Fengchao? Yes I think it is from ProteinProphet which uses peptides with a weight of 0.5 and above. But philosopher is using a modified razor assignment logic so the set of peptides assigned as razor peptides to each protein is different. But I have to check to see what we are really printing in that column.

[apsteinberg]

Hi Fengchao and Alexey,

Thanks for the quick response. If I am understanding correctly, the peptides in the peptide.tsv are slightly different than those used for the protein coverage calculation that is included in the protein.tsv output?

Best, Asher

[fcyu]

That's correct. The protein coverage calculation was not well implemented in Philosopher. We need to change that.

Best,

Fengchao

[apsteinberg]

Got it. Thank you both, this is super helpful!

Best, Asher