The erythrocyte cytoplasmic proteome is composed of 98% hemoglobin; the remaining 2% is largely unexplored. Here we used a combinatorial library of hexameric peptides as a capturing agent to lower the signal of hemoglobin and amplify the signal of low to very low abundance proteins in the cytoplasm of human red blood cells (RBCs). Two types of hexapeptide library beads have been adopted: amino-terminal hexapeptide beads and beads in which the peptides have been further derivatized by carboxylation. The amplification of the signal of low abundance and suppression of the signal of high abundance species were fully demonstrated by two-dimensional gel maps and nano-LC-MSMS analysis. The effect of this new methodology on quantitative information also was explored. Moreover using this approach on an LTQ-Orbitrap mass spectrometer, we could identify with high confidence as many as 1578 proteins in the cytoplasmic fraction of a highly purified preparation of RBCs, allowing a deep exploration of the classical RBC pathways as well as the identification of unexpected minor proteins. In addition, we were able to detect the presence of eight different hemoglobin chains including embryonic and newly discovered globin chains. Thus, this extensive study provides a huge data set of proteins that are present in the RBC cytoplasm that may help to better understand the biology of this simplified cell and may open the way to further studies on blood pathologies using targeted approaches. Molecular & Cellular Proteomics 7: 2254 -2269, 2008.Mature red blood cells (RBCs) 1 have a life span of approximately 120 days and are optimally adapted for oxygen and carbon dioxide as well as for proton transport. They consist of a plasma membrane that envelopes a viscous concentrated (33%) solution of proteins of which hemoglobin (Hb) constitutes approximately 98% of the global proteome. The absence of nucleus and the loss of cytoplasmic organelles allow the RBC passing through narrow capillaries, with a concomitant drastic shape change, to properly accomplish its most important biological tasks. A number of other vital functions present in RBCs are related to appropriate generation and expenditure of energy. These include the following: (a) initiation and maintenance of glycolysis, (b) cation pumping against electrochemical gradients, (c) synthesis of glutathione and other metabolites, (d) nucleotide catabolism reactions, (e) maintenance of Hb iron in its functional, reduced, ferrous state, (f) protection of enzymatic and structural proteins from oxidative denaturation, and (g) preservation of membrane phospholipid asymmetry.The structure of the RBC membrane (a thin layer that constitutes less than 0.1% of the cell thickness and only 1% of its weight) has been well elucidated in the past 35 years both from the normal and pathological metabolic points of view (1, 2) and, more recently, from a structural point of view via extensive proteomics mapping (3). Regarding the cytoplasmic content of the RBC, most studies have focused on a variety of rare ...