Mass and charge selective protein fractionation for the differential analysis of T-cell and CD34+ stem cell proteins from cord blood

Studying biological processes through protein expression is difficult due to the dynamic flux of the proteome, the extreme diversity and heterogeneity, the wide range of cellular protein expression, and the limited detection range of technology. Fractionating complex biological mixtures can help overcome these issues but it can be a challenging process particularly when fractionating rare samples (≤ 10⁶ cells), due to the absolute limits in protein copy number and abundance. In this study, partitioning by charge and mass using the Microflow MF10 has been applied to CD34⁺ haematopoietic stem/progenitor cells and CD4⁺/CD8⁺ T-cells to separate proteins restricted by cell number. Less than 10 µg total proteins per fraction was used for comparative analysis using SDS-PAGE and identification of silver stained bands by LC-MS/MS revealed differentially expressed proteins between the 3 cell populations, which may be involved in cell differentiation.