When considering the desire to automate the selection process coupled with the overall time required to develop new recognition binders against a target of interest, the bacterial display is uniquely advantageous. The bacterial display technology offers an alternate strategy for generating tailor-made CT99021 affinity ligands in a short time period, since one round of selection or screening can be performed in one day with bacterial cells. In this method, cellular machinery is used to generate billions of diverse polypeptide molecules that can be screened with high throughput methods to identify unique polypeptide sequences for a desired target. Briefly, the fifteen amino acid, random polypeptide sequences are displayed on the surface of the E.coli during arabinose induction on a circularly permutated derivative of the outer membrane protein, OmpX, referred to as eCPX. The eCPX enables better peptide display off of the membrane surface, and is a biterminal display scaffold, displaying both the random peptide as a flexible linear sequence at the Nterminus and an expression tag sequence at the C-terminus for expression normalization. Bacterial display libraries using either the OmpX or eCPX have been used previously to isolate polypeptide binding reagents to streptavidin, vascular endothelial growth factor, adult neural stem cells, protease activated pro-domains, and classification of breast tumor subtypes. To isolate the bacterial clones which express peptide sequences with high affinity to the target, conventional approaches require multiple rounds of magnetic separation for pre-enrichment followed by fluorescence activated cell-sorting. FACS sorting is limited to at most 108 cells in one session, whereas magnetic sorting can accommodate 109 to 1010 clones per sort with more rapid results and greater recovery. Although this hybrid approach has proven to be effective over manual magnetic sorting, it is labor-intensive, and the sorting results are known to be operator-dependent. Furthermore, the high capital and maintenance cost of FACS instruments limit its accessibility. Another limitation of FACS for both medical and DoD applications is the potential for generating an aerosolized biohazard at the nozzle when dealing with infectious pathogens; additional steps need to be taken to reduce this hazard, such as adding an aerosol management unit, further increasing cost. To address the need for a rapid, safe, efficient, cost effective, and reproducible affinity ligand selection, we have developed a semiautomated magnetic bacterial cell sorting system, the micromagnetic cell sorter, equipped with disposable microfluidic cartridges. As an alternative to glass MMS cartridges these low cost, highly reproducible and disposable polypropylene cartridges are autoclavable and limit any aerosolization of potential biohazards during library sorting, since all the fluid management, mixing, and sorting is accomplished within the card. The ability to perform semi-automated sorting in a disposable, selfcontained microfluidic cartridge with reproducible results is critical for the DoD since any new defense threats could be safely sorted in a native state ahead of any available recombinant form.