A reference database of electrophoretic migration patterns for human proteins in a set of cell lines.

Protein denaturing electrophoresis based on sodium dodecyl sulfate (SDS-PAGE) is a technique widely applied for studying proteins, either alone or in combination with specific antibody-based detection. Despite its popularity, SDS-PAGE and western blotting are poorly reproducible and can give different results depending on experimental factors affecting electrophoresis but also on the characteristics of the antibodies used for detection. We reasoned that a reference database of accurately determined migration patterns for human proteins would be very useful for the community. Using mass spectrometry and an internal calibration strategy, we have constructed a database of migration patterns for thousands of proteins in five commonly used human cell lines and one mouse cell line. We show that the electrophoretic molecular weights determined are accurate and, for a large portion of the proteome, highly reproducible across replicates and cell lines. Data exploration highlighted numerous known protein processing events that can be mapped by combining migration patterns and the sequence coverage observed. The information is freely available in a website and should constitute a useful reference for investigators trying to validate western blot results and protein migrations in general.