Protein ID in ESI QTOF - Protocol - (Dec/23/2014 )

Hi everyone,

When we need to identify a protein in a spot, we usually send it to another institute where they have a good old MALDI-TOF, which is arguably the best way to go for single protein IDs. 

However, we would like to do it ourselves. We don't have a MALDI, but we do have an ESI microTOF-Q II from Bruker that was acquired for a different purpose. 

I intend to digest the spot with trypsin, extract the peptides, purify them with a ZipTip, elute them in maybe 20 uL and inject them directly into the mass spec.

Does anyone work with an ESI microTOF-Q for protein identification? Any protocol (drying gas temp, flow rate from the syringe, parameters in the software...) would be much appreciated.

Thanks!

EDIT: I also want to add that the ion source is ESI, not nanoESI. 

I have not worked with ESI microTOF-Q but have worked extensively with MALDI TOF TOF. To my experience, I know thats the best instrument for protein identification. sometimes  we used to use ESI MS from applied biosystems, but somehow it used to give better results for small molecules identification but not for proteins.