Minimizing the peptide/protein loss due to interactions with custom consumable materials for proteomic study of protein samples at very low concentrations

Liquid chromatography-mass spectrometry (LC-MS) proteomics is challenged by the detection limit of current mass analyzers for low concentration – low quantity samples (e.g., single cell proteomics and tissue microdissection proteomics) but also especially by material losses during sample preparation steps. The binding of peptides and proteins to the surfaces of consumables significantly reduces the effective concentration in the solution, which further drastically decreases proteomic performance when the concentration of the starting material decreases. In addition to the optimization of the experimental protocols for the preparation of the samples and the technical evolution of the mass analyzers, the nature of the polymeric surface of consumables is crucial. We have therefore designed microvials suitable for proteomic low concentration sample preparation that can be molded in different polymeric materials. A comparative study has shown that the nature of the polymer material has a strong influence on proteomic performances for low concentration samples ranging from 1.5 to 10 ng/µl of proteins (injected quantity is less than 10ng). The nature of the vial has less impact on protein concentrations above 10ng/µl. Peptide loss due to surface interaction is not homogeneous with respect to peptide hydrophobicity, hydrophobic peptides being more impacted on commonly used vials. A polar polymer surface should therefore reduce hydrophobic interactions with peptides. Some polymer materials show promising behaviors for low concentration to single cell proteomic samples, leading to a 20% increase in identification compared to commercially available vials commonly used for proteomics.