Journal
PROTEOMICS
Volume 10, Issue 16, Pages 3040-3044Publisher
WILEY
DOI: 10.1002/pmic.201000103
Keywords
Artifacts; Bioinformatics; Cell culture; MS; SILAC
Funding
- European Commission [HEALTH-F4-2007-200767/APOSYS]
- ProteoRed (the Spanish Proteomics Network)
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Cell culture is a fundamental tool in proteomics where mammalian cells are cultured in vitro using a growth medium often supplemented with 5-15% FBS. Contamination by bovine proteins is difficult to avoid because of adherence to the plastic vessel and the cultured cells. We have generated peptides from bovine serum using four sample preparation methods and analyzed the peptides by high mass accuracy LC-MS/MS. Distinguishing between bovine and human peptides is difficult because of a considerable overlap of identical tryptic peptide sequences. Pitfalls in interpretation, different database search strategies to minimize erroneous identifications and an augmented contaminant database are presented.
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