Mass Spec Identifications of GAPDH - Why are we seeing GAPDH? (Aug/25/2009 )

Hi All,
I need everyone to put on their thinking caps for this!
I am a Sr. Staff Scientist and "old" PhD Protein Chemist for OSU and work as a protein scientist in their Mass Spec and Proteomics Department.

In the past year, we have identified various immunoprecipitated proteins as Glyceraldehyde 3-Phosphate Dehydrogenase! We have identified off of a matching gel of a client's western blot with a positive ID of GAPDH. So far, five labs looking for a specific protein from their specific pull-downs have had their proteins identified by MALDI and Orbitrap as GAPDH!

Is anybody else seeing their antibodies identifying GAPDH? Is this an artifact that has gone unnoticed??

Need Help!

Thanks so much,
Biokmst

We get cytokeratins rather than GAPDH.

Is there some contamination of your MS?

bob1 on Aug 25 2009, 04:55 PM said:

Keratins are a popular contaminant and makes sense. GAPDH is more unusual and seems to come from gels that were western blot identified and IP samples, so it can't be a contaminant. Samples have been run between the identified runs on the orbitrap and showed no GAPDH!!