In hematopoiesis, co-expression of Sca-1 and c-Kit defines cells (LS+K) with long-term reconstituting potential. In contrast, poorly characterised LS-K cells fail to reconstitute lethally-irradiated recipients. Relative quantification mass spectrometry and transcriptional profiling were employed to characterise LS+K and LS-K cells. This approach yielded data on >1200 proteins. Only 32% of protein changes correlated to mRNA modulation demonstrating post-translational protein regulation in early hematopoietic development. LS+K cells had lower expression of protein synthesis proteins but did express proteins associated with mature cell function. Major increases in erythroid development proteins were observed in LS-K cells, based on this assessment of erythroid potential we showed them to be principally erythroid progenitors demonstrating effective use of discovery proteomics for definition of primitive cells.