interpretation of freequant outputs

[weiranheng]

Hello,
I'm a freshman in proteomics, I 've tried philosopher pipeline ，and it work well. Smooth tool
I still got a question in interpreting results, so ,seeking help.
In freequant outputfile" combined_protein.tsv", I found a column with a name “coverage ” ,is it standing for abundance of protein?
Thanks

best regards,
Chen

[sarah-haynes]

Hi Chen, protein coverage is the percentage of the total protein sequence length found in the identified peptides. You can find a guide to the other columns, including intensity if you ran freequant, here.

Sarah

[weiranheng]

Thank you Sarah,it helps .
However, if it's what it means, I feel more confused
In file "combined_protein.tsv", I found many proteins with "Total insensity","Total spectral count" presenting 0 !
(only "Unique Stripped Peptides"and some "coverage" are non-zero items).
It detected proteins with zero intensity ,how could that happen ?

Best regards,
Chen

[sarah-haynes]

Hi Chen, a new version will come out soon that should have a fix for that, it will be posted on this page: https://github.com/nesvilab/philosopher/releases/latest

Cheers,
Sarah

[weiranheng]

Hi Sarah,
Thank you very much.
I 'll follow up on this link.
Wish you happy everyday!

Best,
Chen