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.