thumb|LCQ Mass Spectrometer used in mass spectrometry. There are two mass spectrometry-based methods currently used for protein profiling. The more established and widespread method uses high resolution, two-dimensional electrophoresis to separate proteins from different samples in parallel, followed by selection and staining of differentially expressed proteins to be identified by mass spectrometry. Despite the advances in 2-DE and its maturity, it has its limits as well. The central concern is the inability to resolve all the proteins within a sample, given their dramatic range in expression level and differing properties. The combination of pore size, and protein charge, size and shape can greatly determine migration rate which leads to other complications.
thumb|LCQ Mass Spectrometer used in mass spectrometry There are two mass spectrometry-based methods currently used for protein profiling The more established and widespread method uses high resolution two-dimensional electrophoresis to separate proteins from different samples in parallel followed by selection and staining of differentially expressed proteins to be identified by mass spectrometry Despite the advances in 2-DE and its maturity it has its limits as well The central concern is the inability to resolve all the proteins within a sample given their dramatic range in expression level and differing properties The combination of pore size and protein charge size and shape can greatly determine migration rate which leads to other complications