Dear colleagues,
I am currently performing mass-spec identification on some proteins (from a human cell line origin). Yet, from Mascot database search, some (but not all) instead showed matches to Bovine proteins specifically (quite high protein score of ~200 each, C.I. =100) but no match to any human proteins.
May I know what would be a possible reason for this? Would you mind sharing your experience (if you have encountered such a scenario before)?
P.S. My other samples (from various organisms) all showed a high score Mascot result, suggesting that the analysis workflow should have went alright.
Thank you.
Can you provide the name of the top 3 these bovine proteins? Check out this link:
http://www.thegpm.org/crap/
http://www.thegpm.org/crap/
One possibility is that the cell extract was contaminated from fetal bovine serum used in the growth medium.
The first thing I would do is double check the parameters of your search, e.g. did you specify a database with human sequences, are your mass tolerances OK, ...
Second, do an error tolerant search. This can point you towards potential problems with the digestion or unexpected modifications. Good luck!
Contamination is the most likely source. It may not only be in your sample, but also in the mass spectrometer components (LC column, etc.) You could check with your colleagues to see if they ran into similar problem on this system , and run some QC spectra (on calibration mixtures).
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