▲ 4 r/proteomics
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!!
u/alycatdabra — 7 days ago