This study aimed to provide a characterization of morphologically-altered red blood cells (RBCs) and to compare their properties to those of long-stored morphologically normal RBCs and to short-stored RBCs. For proteomics experiments, RBC concentrates stored in blood bank conditions were submitted to a CFSE staining protocol that allows specific sorting of morphologically-altered (CFSEhigh) and normal (CFSElow) RBC subpopulations. Proteome of erythrocytes and ghosts were analyzed at day 3-10 (short-stored, CFSElow RBC subpopulation) and day 40-44 (long-stored, CFSEhigh and CFSElow RBC subpopulations) of storage by a label free quantification approach.