This report describes an analysis of the red blood cell proteome by ion trap tandem mass spectrometry in line with liquid chromatography. Mature red blood cells lack all internal cell structures and consist of cytoplasm within a plasma membrane envelope. To maximize outcome, total red blood cell protein was divided into two fractions of membrane-associated proteins and cytoplasmic proteins. Both fractions were divided into subfractions, and proteins were identified in each fraction separately through tryptic digestion. Membrane protein digests were collected from externally exposed proteins, internally exposed proteins, "spectrin extract" mainly consisting of membrane skeleton proteins, and membrane proteins minus spectrin extract. Cytoplasmic proteins were divided into 21 fractions based on molecular mass by size exclusion chromatography. The tryptic peptides were separated by reverse-phase high-performance liquid chromatography and identified by ion trap tandem mass spectrometry. A total of 181 unique protein sequences were identified: 91 in the membrane fractions and 91 in the cytoplasmic fractions. Glyceraldehyde-3-phosphate dehydrogenase was identified with high sequence coverage in both membrane and cytoplasmic fractions. Identified proteins include membrane skeletal proteins, metabolic enzymes, transporters and channel proteins, adhesion proteins, hemoglobins, cellular defense proteins, proteins of the ubiquitin-proteasome system, G-proteins of the Ras family, kinases, chaperone proteins, proteases, translation initiation factors, and others. In addition to the known proteins, there were 43 proteins whose identification was not determined. Molecular & Cellular Proteomics 3:501-509, 2004.A human red blood cell (RBC) 1 is in residence in the human circulatory system for 120 days carrying oxygen from the lungs to all tissues within the body and carbon dioxide from the tissues back to the lungs. An RBC is an 8-m biconcave disk bounded by a plasma membrane. The major cytoplasmic constituent is hemoglobin, which is responsible for binding and releasing oxygen and carbon dioxide. On the cytoplasmic surface of the plasma membrane is a two-dimensional meshwork of proteins referred to as spectrin membrane skeleton. The spectrin membrane skeleton renders elasticity and flexibility to an RBC, allowing it to pass through vessels and capillaries that narrow to 1 m in diameter (1).Because of the ease in obtaining RBCs and because they lack internal organelles, the plasma membrane of this cell type has been studied extensively. The functions of hemoglobin are also well documented. Based on four decades of study, the identity, function, and topology of many RBC membrane proteins have been determined (1-3). With the advent of modern mass spectrometry (MS) and associated proteomic techniques, determination of the RBC proteome is now plausible. This kind of approach is a necessary first step in understanding how the RBC proteome becomes altered in various hematologic disorders. With this goal in mind, we utilized ion trap ...