**Preparation of the Cell Lysates: 1. Centrifuge the positive and negative cell lysates at 17,500 × g for 1 h at 4 °C. Discard the pellets. 2. Divide the supernatants (soluble fractions) from step 1 into 10 µL aliquots and store at -80 °C. 3. Perform SDS-PAGE with the positive cell lysate to ensure the target protein is in the soluble fraction. 4. Measure the total protein concentration in both positive and negative cell lysates using the BCA protein assay kit according to the manufacturer’s instructions. PAUSE POINT: Store cell lysates at -80 °C for up to two months. Capillary Preconditioning and Library Preparation: 5. Rinse each new capillary with approximately four capillary volumes of 100 mM HCl, 100 mM NaOH, ddH₂O, and RB, in that order. Repeat before and after every CE run. 6. Prepare 10 µL of 500 µM naive DNA library in SB. Heat to 94 °C and cool to 20 °C at 0.5 °C/s in a thermal cycler. Use this treatment for all future DNA library and aptamer samples. 7. Prepare a 100 µM solution of the temperature-treated DNA library (from step 6) in 100 µL SB. Determination of Library and Fluorescein Migration Times: 8. Prepare a 10 µL equilibrium mixture with 10 µM DNA library and 100 µM each masking DNA. Incubate for 10 minutes at room temperature. 9. Inject 150 nL of the mixture from step 8 into the capillary and perform NECEEM in RB at 375 V cm⁻¹ (normal polarity, positive electrode at injection end) for 60 min to observe the free DNA component. 10. Determine the migration time of the DNA library to the end of the capillary (free DNA component). 11. Perform NECEEM with the same equilibrium mixture plus 100 nM fluorescein (collection window migration marker). 12. Determine the migration time of fluorescein to the end of the capillary and its relative elution time to the free DNA.