Other species detected in mass spec results - (Feb/14/2013 )

Hi,
I used bovine (cow) tissue to do an IP, which was then submitted for mass spec analysis. The database used was SwissProt57.1. The weird thing was that the results contained sequences from all kinds of species, including mouse and human. Some of the peptides from mouse and human sequences are present in the bovine sequence. That would make sense if the results contained only those conserved sequences. But some peptides are unique to mouse/human only! How is that possible when the starting material was bovine? Any thoughts or input would be appreciated. Thanks!

First off - does your lab work with mice at all?

If so, then there's your answer - mouse protein in dust from the air. This is especially common for keratins. The same reasoning applies to human samples found in your mass spec.

Also, I'm not sure that the full bovine genome has been published, let alone the proteome, so those sequences that appear to be specific for mouse or human, may well not be, it's just that they aren't in the database yet as also present in Bos.

Thanks. I knew to expect contamination from Keratin from all kinds of species but I was surprised to see the specific protein of interest from other species too. I guess you may be right- "mouse protein in the air". And yes, I should take into the consideration that the bovine proteome is not as complete as that of mouse and human. I hope the reviewers would accept that. Thanks for your help!

You may also check your tissue for DNA of these other species. Maybe cells were deposited at your tissue during storage or cutting of the tissue. If you can´t do the PCR there are service labs, e.g. www.multiplexion.de.
When cutting tissue, use a sandwich protocol and discard the outer section.