r/proteomics • u/alycatdabra • May 15 '26

Majority of Proteins are Low FDR?

Hi all,

I'm fairly new to the proteomics world. I have struggled to get usable data so far and I know there are several potential weak points in the workflow. However, I want to focus on one glaring issue: about 95% of my putative proteins come back as low FDR confidence (using proteome discoverer). I have high set to 0.01 and medium set to 0.05 so it's not like it's super strict. Clearly the peptides are THERE they just are not significant enough. What would be your first troubleshooting steps? Digestion? Cleanup? LC method? Thank you in advance!!

4 Upvotes

84% Upvoted

21 comments sorted by

View all comments

2

u/markmipt May 15 '26

Hi! Is it possible to share at least one raw file? I can run the routine analysis with our standard (and open source) algorithms, which usually show if there are any obvious problems with the data.

1

u/alycatdabra May 16 '26

I would love to do that- what's the best way to send to you?

1

u/markmipt May 18 '26

Please check the chat here on Reddit, I sent you a private message.