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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Numbers of peptides assigned to a proteins #850

Open yanisZirem opened 11 months ago

yanisZirem commented 11 months ago

Hello,

How do you decide whether you want to work with one unique peptide or multiple peptides? I searched the DIA-NN output matrices and found the "proteotypic" column, which provides information about whether the peptide is unique or not, but there is no information about the number of peptides per protein ?

Best regards,

Yanis

vdemichev commented 11 months ago

Hi Yanis,

Depends on the downstream application, usually OK to use non-proteotypic peptides and rely on protein grouping. You can count the numbers of unique peptides per protein easily in R or Python, e.g. with the table() function in R.

Best, Vadim

yanisZirem commented 11 months ago

Hi Vadim,

Thank you for your response

I'm using Python, R, and MATLAB... to open the TSV files and conduct statistical analyses However, when I open the TSV files, I encounter an issue regarding the calculation of the number of unique or non-unique peptides for each protein. It appears that there is only one peptide per protein, and we determine if it is unique or not based on the prototypic columns, there is no information about the number of peptides per each protein and the estimated coverage !

Thank you for your assistance

Yanis