Abstract
Mass spectrometric (MS) data of human cell secretomes are usually run through the conventional human database for identification. However, the search may result in false identifications due to contamination of the secretome with fetal bovine serum (FBS) proteins. To overcome this challenge, here we provide a composite protein database including human as well as 199 FBS protein sequences for MS data search of human cell secretomes. Searching against the human-FBS database returned more reliable results with fewer false-positive and false-negative identifications compared to using either a human only database or a human-bovine database. Furthermore, the improved results validated our strategy without complex experiments like SILAC. We expect our strategy to improve the accuracy of human secreted protein identification and to also add value for general use.
Highlights
The posterior error probability (PEP) value, which is known as the local false discovery rate and measures the probability of error for a single peptide spectrum matches (PSM), is plotted between HFDB and HuDB search results
We assessed the amount of residual fetal bovine serum (FBS) proteins remaining in cell culture media or on the surface of culture plates
The result of the FBS profiling was a list of about 200 proteins which was used to construct a composite database for secretome analysis
Summary
Mass spectrometric (MS) data of human cell secretomes are usually run through the conventional human database for identification. The search may result in false identifications due to contamination of the secretome with fetal bovine serum (FBS) proteins. To overcome this challenge, here we provide a composite protein database including human as well as 199 FBS protein sequences for MS data search of human cell secretomes. We expect our strategy to improve the accuracy of human secreted protein identification and to add value for general use. The main drawbacks of analyzing secretomes involve contamination by intracellular proteins and fetal bovine serum (FBS) proteins used in cell culture media [4].
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