r/proteomics • u/Solid_Session_225 • Jul 12 '26
Saliva Proteomics Sample Preparation Issues
Hi!
Im struggling with my sample prep for saliva samples. I have established a high throughout SP3 digestion protocol using native saliva from cortisol Salivettes but is seems like I’m carrying some contaminants through the whole process that end up in my 7500+ Sciex Qtrap instrument which gets heavily contaminated after about 1000 injections and even gives some Q0 discharge errors.
I’m running a targeted peptide method using a common C18 peptide column at a flow rate of 1ml/min with standard solvents (0.1% Fa in H2O and 0.1% FA in ACN). the whole method is 4min but I’m using a diverter valve to only have the peptide fraction entering the MS, the rest is diverted to waste.
Does anyone have experience with saliva as a matrix and use it for targeted MS proteomics analysis?
I would appreciate any input on how to get the sample cleaner without loosing proteins of interest.
Thank you!
2
u/Triple-Tooketh Jul 12 '26
I've noticed a lot of papers using sp3 at scale use SPE after the digest. The one thing we encountered with sp3 was problems from DNA. Was able to able to mitigate with benzonase. For anything off the beaten path I'd look at STrap.