Evaluation of the Binding Preference of Microtubes for Nanoproteomics Sample Preparation

Nonspecific binding between the protein and the container is an often-neglected cause of sample loss in large-scale proteomics sample preparation. In nanoproteomics, due to the small sample size, this absorption loss is no longer negligible, and researchers often adopt low binding plasticware to minimize the sample loss. However, there has been little discussion in the scientific literature on the differences in microtube performance on reducing protein/peptide binding. Therefore, the exact impact of sample loss during the sample preparation is not well understood. Here, we investigated the protein/peptide loss during the nanoproteomics experiment process. Our results showed that there are significant differences in nonspecific binding among the tested microtubes, with a protein recovery rate ranging from less than 10% to over 90% for different microtubes. Interestingly, we found that the storage temperature could also be one of the key factors that contribute to protein recovery from the plastic container. In addition, we investigated the binding preferences of different microtubes by the physical characteristics of the identified proteins and peptides, such as isoelectric point, hydrophobicity, length, and charge. Our findings help to better understand protein/peptide loss in proteomics sample preparation and provide further guidance for researchers in choosing proper containers for their precious sample.