Other species detected in mass spec results
Posted 14 February 2013 - 10:15 AM
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!
Posted 14 February 2013 - 11:35 AM
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.
Posted 14 February 2013 - 11:49 AM
Posted 22 February 2013 - 06:20 AM
When cutting tissue, use a sandwich protocol and discard the outer section.