Fluoroalcohol – Induced coacervates for selective enrichment and extraction of hydrophobic proteins

Improving identification of low abundance and hydrophobic proteins using fluoroalcohol mediated supramolecular biphasic systems with quaternary ammonium salts

In this study, a newly discovered Supramolecular Biphasic System (S-BPS) was used in bottom-up proteomics of the Saccharomyces cerevisiae strain of yeast. We took advantage of S-BPS in bottom-up proteomics of this strain of yeast as the protein sample, while the results were compared to routinely used solubilizing reagents, such as urea, and sodium dodecyl sulfate (SDS). With the S-BPS, we identified 3043 proteins as compared to 2653 proteins that were identified in the control system. Interestingly, of the additional 390 proteins characterized by the S-BPS, 300 proteins were low abundance (less than 4000 molecules/cell). Remarkably, the identification of proteins at very low abundance (less than 2000 molecule/cell) was improved by 106%. This suggests that the S-BPS is particularly advantageous for detecting low abundance proteins. Gene Ontology (GO) analysis was conducted to find fractionation pattern of proteins in our two-phase system, and in nearly every gene ontology category, the S-BPS provided greater coverage than the control experiment, i.e., coverage for integral membrane proteins and mitochondrial ribosome proteins are improved by 18% and 58%, respectively. The improvements in proteins coverage for low abundance and membrane proteins can be attributed to the strong solubilizing power of the amphiphile-rich phase of this S-BPS and its capability for concomitant extraction, fractionation, and enrichment of the complex proteomics samples. Each phase has selectivity towards specific yeast protein groups, this selectivity is generally based on pI and hydrophobicity of proteins. Therefore, more hydrophobic proteins and acidic proteins exhibit greater affinities for the amphiphile-rich phase due to the hydrophobic effect and electrostatic interactions.

Improved Protein Coverage in Bottom-Up Proteomes Analysis Using Fluoroalcohol-Mediated Supramolecular Biphasic Systems With Mixed Amphiphiles for Sample Extraction, Fractionation, and Enrichment

A new class of supramolecular biphasic systems containing fluoroalcohol-induced coacervates (FAiC) provides concomitant fractionation of complex protein mixtures, high solubilizing power for extraction of various types of proteins, especially those with high hydrophobicity (such as membrane proteins), and enrichment of low-abundance proteins. Subsequently, the use of FAiC biphasic systems (BPS) in the bottom-up proteomics workflow resulted in significantly higher coverage for the whole proteome, various subproteomes, especially those embedded or associated with membranes, post-translationally modified proteins, and low-abundance proteins (LAPs) as compared to the conventional methodologies. In this work, we used a new type of FAiC-BPS composed of mixed amphiphiles, a zwitterionic surfactant 3-(N,N-dimethylmyristyl ammonia) propane sulfonate (DMMAPS), a quaternary ammonium salt (QUATS), and hexafluoroisopropanol (HFIP) as the coacervator for extraction, fractionation, and enrichment of yeast proteome in bottom-up proteomics. The coverage of the lower-abundance proteins (abundance below 2000 molecules/cell) improved by more than 100% using DMMAPS and DMMAPS + QUATS systems as compared to the conventional methods using urea or detergent solutions for protein solubilization. Additionally, these coacervate systems show increased coverage of integral membrane proteins and proteins with α-helices by up to 24 and 555%, respectively.

Twenty years of supramolecular solvents in sample preparation for chromatography: achievements and challenges ahead

Supramolecular solvents (SUPRAS) have progressively become a suitable alternative to organic solvents for sample preparation in chromatographic analysis. The inherent properties of these nanostructured solvents (e.g. different polarity microenvironments, multiple binding sites, possibility of tailoring their properties, etc.) offer multiple opportunities for the development of innovative sample treatment platforms not approachable by conventional solvents. In this review, major achievements attained in the combination SUPRAS-chromatography in the last 20 years as well as the challenges that should be addressed in the near future are critically discussed. Among achievements, particular attention is paid to the theoretical and practical knowledge gained that has helped make substantial progress in the area. In this respect, advances in the understanding of the mechanisms involved in SUPRAS formation and SUPRAS-solute interactions driving extractions are discussed, with a view to the setting up of knowledge-based extraction procedures. Likewise, the strategies followed to improve the compatibility of SUPRAS extracts with liquid and gas chromatography and adapt SUPRAS-based extractions to different formats are presented. Ongoing efforts to apply SUPRAS in multicomponent extractions and synthesize tailored SUPRAS for the development of innovative sample treatments are highlighted. Among challenges identified, discussion is focused on the automation of SUPRAS-based sample treatment and the elucidation of SUPRAS nanostructures, which are considered essential for their acceptance in routine labs and the design of tailored SUPRAS with programmed functions. Graphical abstract.