Urinary Proteomics Employing Capillary Electrophoresis Coupled to Mass Spectrometry in the Monitoring of Patients After Stem Cell Transplantation

Complex biological samples hold significant information on the health status and development of disease. Approximately 22,000 human genes give rise to more than 400,000 proteins as functional entities (Anderson and Anderson, Electrophoresis 19:1853–1861, 1998). Thus, the proteome provides a much richer source of information than the genome for describing the state of health or disease of humans. The composition of body fluids comprises a rich source of information on changes of protein and peptide expression. Here we describe the application of capillary electrophoresis (CE) coupled online to an electrospray-ionization time-of-flight mass spectrometer (ESI-TOF-MS) to analyze human urine for the identification of biomarkers specific for complications after allogeneic hematopoietic stem cell transplantation (Kaiser et al. Blood 104:340–349, 2004; Weissinger et al. Blood 109:5511–5519, 2007). In addition, we describe methods for the sequencing of native proteins/peptides, necessary for the identification of possible new therapeutic targets.