Evaluation of binding preference of different microtubes for nanoproteomics sample preparation

Non-specific binding of protein and plastics is a main cause of sample loss in proteomics sample preparation. In the nanoproteomics, researchers often adopt low binding plasticware to minimize the sample loss. However, there has been little discussion in the scientific literature on the differences of microtube performance in reducing protein/peptide binding. Therefore, the exact impact of sample loss during the sample preparation is not well studied. Here, we applied qualitative and quantitative approaches to investigate the protein/peptide loss during the nanoproteomics experiment process. Our results clearly showed that there are significant differences in non-specific binding among all the tested microtubes, with a protein recovery rate ranging from less than 10% to over 90% for different microtubes. We found that storage temperature is also one of the key factors that contribute to protein recovery from the plastic. In addition, we further investigated the binding preferences of different microtubes by the physical characteristics of protein and peptides, such as isoelectric point, hydrophobicity, length, and charge. Our findings contribute to a better understand-ing of protein/peptide loss in proteomics sample preparation and provide further guidance for researchers in choosing proper containers for their precious sample.