It is clear that the methods chosen for sample preparation have a major impact on both the amount of sample required and the overall success of a microsequencing project. Tris buffer is commonly used for protein purification. These compounds are not volatile and leave a highly viscous residue. Triton X-100, Brij, and Tween solutions often contain aldehydes, oxidants and other contaminates that can inhibit Edman degradation. Large quantities of SDS can cause instrument malfunction and may lead to the loss of sample from the filter.
Dialysis tubing is often a source of contaminants and other interfering substances.
Avoid dialysis as a last step in sample preparation or use thoroughly cleaned, high-quality tubing. Always dialyzed against a salt counterion or dilute acid to prevent the protein and contaminates that may be present from sticking to the tubing. Avoid molecular biology grade reagents. Always wear gloves and work in a clean dust free area. Dust and finger prints are a major source of contaminating amino acids present in sequencing samples.