Proteomics (Q9UPP1) data versus Western Blot analysis

Recently a reviewer from one of our submitted manuscripts called our attention pointing at the big discrepancy between the expression levels of our target protein in an specific AML cell line detected by Western Blotting, compare to the expression levels of the same protein in the same cell line shown in DEPMap PROTEOMICS (Q9UPP1). Using Western Blotting we have very low protein expression close to zero compare with other AML cell lines whereas DepMap shows in their PROTEOMICS (Q9UPP1) a similar high expression level of our target protein in that particular cell line compare with the same other AML cells. Is it a logical way to explain this discrepancy?

many thanks in advance!!



The proteomics data that the portal shows was generated by the Gygi Lab and was published as part of the paper Quantitative Proteomics of the Cancer Cell Line Encyclopedia. I don’t know enough about the method, nor mass spec in general, that they used to be able to comment on the discrepancy. I can only share that I haven’t heard of any general issues with that dataset. I can only refer you to the original authors of the paper for specific questions.

Sorry I can’t be of more assistance.