To optimize protein desalting, consider the following factors:

Timing of Desalting: Determine when to desalt your protein sample or change the buffer. This step is crucial when salt might interfere with subsequent processes or when the sample requires a different buffer. Desalting can be performed before, during, or after purification, or before analysis.

Consider the following instances for performing desalting:

• Performing desalting before purification ensures the sample is in a suitable buffer so that your target protein binds to the column. 
• Performing desalting between purification stepsdecreases ionic strength before ion exchange chromatography, enabling proteins to bind to the column.
• Performing desalting after purification adjusts the conditions of the final purified protein or neutralizes the pH of antibodies eluted from an affinity chromatography column.
• Performing desalting before analysis removes excess salt and prevents issues such as poor labeling efficiency in Western blotting and streaking or wavy lanes during electrophoresis. 

Sample Loading: The sample-to-resin volume ratio is critical for effective desalting. To minimize dilution while maintaining good separation, it's recommended not to exceed a sample volume of 30% of the total bed volume.

Choose the Right Column: Consider factors such as the molecular weight of your protein, the volume of your sample, desired throughput, and the equipment or technique you plan to use when selecting a prepacked column or plate.