Abstract
HPLC-MS/MS analysis of various human cell lines shows the presence of a major amount of bovine protein contaminants. These likely originate from fetal bovine serum (FBS), typically used in cell cultures. If evaluated against a human protein database, on average 10% of the identified human proteins will be misleading (bovine proteins, but indicated as if they were human). Bovine contaminants therefore may cause major bias in proteomic studies of cell cultures, if not considered explicitly.
Highlights
Identification and quantitation of proteins in human cell lines are typical objectives of proteomics and are mostly performed by HPLC-MS1
We have downloaded and analyzed HPLC-MS/MS results of the various cell lines listed above from the Pride database (Table 1), corresponding to research performed by Geiger et al In this paper we have performed a comparative analysis of these results, with the objective of identifying bovine contaminants in human cell lines and estimating its influence on human proteome studies
Bovine serum components were found to be common, abundant contaminants of human cell lines. These are the remains of fetal bovine serum (FBS), a generally used cell culture media
Summary
Identification and quantitation of proteins in human cell lines are typical objectives of proteomics and are mostly performed by HPLC-MS1. It is a reasonable assumption that these impurities come from fetal bovine serum (FBS), a universally used component of cell culture media[3, 4] This observation prompted us to examine whether this is a common problem or if it was related to a particular sample only. We have downloaded and analyzed HPLC-MS/MS results of the various cell lines listed above from the Pride database (Table 1), corresponding to research performed by Geiger et al In this paper we have performed a comparative analysis of these results, with the objective of identifying bovine contaminants in human cell lines and estimating its influence on human proteome studies. Qualitative analysis of peptides and proteins studied by LC-MS/MS as described above were evaluated by Byonic[7] (version 2.15.7, Protein Metrics Inc., Cupertino, CA, USA), Andromeda[8] and Mascot[9] (version 2.5.1, www.matrixscience.com) softwares. Only proteins with at least two peptide hits were considered
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