High-resolution proteome/peptidome analysis of body fluids by capillary electrophoresis coupled with MS

The analysis of proteins and peptides in biological fluids is becoming more important as they are potential sources of diagnostic biomarkers of disease. The complexity of body fluids is such that no single technique can both identify and quantify all the constituents present. It therefore requires pre-concentration of the compounds of interest and hyphenated techniques like capillary electrophoresis (CE) or high-performance liquid chromatography (HPLC) coupled to a mass spectrometer (MS) to provide the separation, identification, and quantification of the proteins and peptides under investigation. Here we provide protocols for sample preparation of various body fluids, namely, urine, plasma, and cerebrospinal fluid, and how to obtain maximum sensitivity and selectivity of the small proteins and peptides under investigation by CE-MS.