Duplicate peptides in phosphoproteomics data

[LJMHiggins]

Firstly, thank you for putting together this useful resource.

I have been accessing the phoshphoproteomics data for some analyses, and have found what looks like peptide duplication.

I am using cptac Version: 1.5.14

I found the duplication by running the following:

luad = cptac.Luad()
test = luad.get_phosphoproteomics("bcm")
flat_columns = ['_'.join(map(str, col)) for col in test.columns]
duplicates = pd.Series(flat_columns).duplicated()
len(pd.Series(flat_columns)[duplicates])
`
Giving 61807 duplicates.

Inspection of a specific peptide confirmed duplication:

test.loc[:, [col for col in test.columns if "SCPIKEDSFLQRYSS" in col]]

Not sure if this is present in other tumour types at this stage. Do you know why I could be seeing this?

Many thanks