ZrO2 Nanofiber as a Versatile Tool for Protein Analysis

A review of intact glycopeptide enrichment and glycan separation through hydrophilic interaction liquid chromatography stationary phase materials

Protein glycosylation, one of the most important biologically relevant post-translational modifications for biomarker discovery, faces analytical challenges due to heterogeneous glycosite, diverse glycans, and mass spectrometry limitations. Glycopeptide enrichment by removing abundant hydrophobic peptides helps overcome some of these obstacles. Hydrophilic interaction liquid chromatography (HILIC), known for its selectivity, glycan separations, intact glycopeptide enrichment, and compatibility with mass spectrometry, has seen recent advancements in stationary phases like Amide-80, glycoHILIC, amino acids or peptides for improved HILIC-based glycopeptide analysis. Utilization of these materials can improve glycopeptide enrichment through solid-phase extraction and separation via high-performance liquid chromatography. Additionally, using glycopeptides themselves to modify HILIC stationary phases holds promise for improving selectivity and sensitivity in glycosylation analysis. Additionally, HILIC has capability to assess the information about glycosites and structural information of glycans. This review summarizes recent breakthroughs in HILIC stationary materials, highlighting their impact on glycopeptide analysis. Ongoing research on advanced materials continues to refine HILIC's performance, solidifying its value as a tool for exploring protein glycosylation.

Negatively Charged Composite Nanofibrous Hydrogel Membranes for High-Performance Protein Adsorption

Nanofibrous materials are considered as promising candidates for fabricating high-efficiency chromatography media, which are urgently needed in protein pharmaceuticals purification and biological research, yet still face several bottlenecks. Herein, novel negatively charged composite nanofibrous hydrogel membranes (NHMs) are obtained by a facile combination of electrospinning and surface coating modification. The resulting NHMs exhibit controllable morphologies and chemical structures. Benefitting from the combined effect of the stable framework of silicon dioxide (SiO₂) nanofiber and the function layer of negatively charged hydrogel, as well as good pore connectivity among nanofibers, NHMs exhibit a high protein adsorption capacity of around 1000 mg g^-1, and are superior to the commercial cellulose fibrous adsorbent (Sartobind^®) and the reported nanofibrous membranous adsorbents. Moreover, due to their relatively stable physicochemical and mechanical properties, NHMs possess comprehensive adsorption performance, favorable resistance to acid and solvents, good selectivity, and excellent regenerability. The designed NHMs composite adsorbents are expected to supply a new protein chromatography platform for effective protein purification in biopharmaceuticals and biochemical reagents.

Titanium dioxide-functionalized dendritic mesoporous silica nanoparticles for highly selective isolation of phosphoproteins

Selective isolation of phosphoproteins is of great significance in biological applications. Herein, titanium dioxide-functionalized dendritic mesoporous silica nanoparticles are prepared via a post-grafting method for selective capture of phosphoproteins. The fabricated nanoparticles possess a unique central-radial pore structure with a surface area of 666.66 m² /g and a pore size of 22.2 nm. The high-binding affinity of TiO₂ with the phosphate groups facilitates the selective adsorption of phosphoproteins. Moreover, the open central-radial pore structure endows the dendritic mesoporous nanoparticles with better adsorption performance toward phosphoproteins with respect to the commercial titanium dioxide nanoparticles and titanium dioxide-functionalized conventional mesoporous silica nanoparticles by providing more accessible affinity sites. At pH 2, an adsorption capacity of 157.2 mg/g is derived for β-casein. The feasibility of the as-prepared dendritic material in real biological sample assay is demonstrated by the selective isolation of phosphoproteins from defatted milk, as illustrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis assay.

Novel electroblowing synthesis of submicron zirconium dioxide fibers: effect of fiber structure on antimony(v) adsorption

Both stable and radioactive antimony are common industrial pollutants. For antimonate (Sb(v)) removal from industrial waste water, we synthesized submicron zirconium dioxide (ZrO₂) fibers by electroblowing and calcination of the as-electroblown fibers. The fibers are amorphous after calcination at 300 and 400 °C and their average diameter is 720 nm. The fibers calcined at 500 to 800 °C have an average diameter of 570 nm and their crystal structure transforms from tetragonal to monoclinic at the highest calcination temperatures. We investigated Sb(v) adsorption capacity of the synthesized ZrO₂ fibers as a function of pH, adsorption isotherm at pH 6 and adsorption kinetics at pH 7. The tetragonal ZrO₂ fibers calcined at 500 °C exhibited the best potential for Sb(v) remediation with Sb(v) uptake of 10 mg g^-1 at pH 2 and a maximum Sb(v) uptake of 8.6 mg g^-1 in the adsorption isotherm experiment. They also reached 30% of 7 days' Sb(v) uptake in only a minute. The adsorption kinetics followed the Elovich model.

Amorphous TiO2 Nanotubes as a Platform for Highly Selective Phosphopeptide Enrichment

This work reports highly selective phosphopeptide enrichment using amorphous TiO₂ nanotubes (TiO₂NTs) and the same material decorated with superparamagnetic Fe₃O₄ nanoparticles (TiO₂NTs@Fe₃O₄NPs). TiO₂NTs and TiO₂NTs@Fe₃O₄NPs materials were applied for phosphopeptide enrichment both from a simple peptide mixture (tryptic digest of bovine serum albumin and α-casein) and from a complex peptide mixture (tryptic digest of Jurkat T cell lysate). The obtained enrichment efficiency and selectivity for phosphopeptides of TiO₂NTs and TiO₂NTs@Fe₃O₄NPs were increased to 28.7 and 25.3%, respectively, as compared to those of the well-established TiO₂ microspheres. The enrichment protocol was extended for a second elution step facilitating the identification of additional phosphopeptides. It further turned out that both types of amorphous TiO₂ nanotubes provide qualitatively new physicochemical features that are clearly advantageous for highly selective phosphopeptide enrichment. This has been confirmed experimentally resulting in substantial reduction of non-phosphorylated peptides in the enriched samples. In addition, TiO₂NTs@Fe₃O₄NPs combine high selectivity and ease of handling due to the superparamagnetic character of the material. The presented materials and performances are further promising for applications toward a whole range of other types of biomolecules to be treated in a similar fashion.

A magnetic nanofiber-based zwitterionic hydrophilic material for the selective capture and identification of glycopeptides

High-performance affinity materials are highly required in the sample preparation process in mass spectrometry-based glycoproteomics studies. In this research, a novel magnetic nanofiber-based zwitterionic hydrophilic material is prepared for glycopeptide enrichment and identification. The one-dimensional hydroxyapatite nanofiber (HN) acted as the supporting substance for immobilizing both Fe3O4 nanoparticles and Au nanoparticles, following the surface modification with a zwitterionic tripeptide l-glutathione (GSH) via the affinity interactions between the thiol group in GSH and both Au and Fe3O4 to form the magHN/Au-GSH nanofiber. Owing to the unique structural features, excellent hydrophilicity, abundant zwitterionic molecules, and strong magnetic responsiveness, the as-prepared magHN/Au-GSH nanofiber possesses satisfactory specificity for glycopeptide enrichment. As a result, the magHN/Au-GSH nanofiber demonstrated great detection sensitivity (2 fmol), satisfying enrichment recovery (89.65%), large binding capacity (100 mg g-1), and high enrichment selectivity (1 : 100) toward glycopeptides. Furthermore, 246 N-glycosylated peptides corresponding to 104 N-glycosylated proteins were identified from only 1 μL human serum, revealing the great potential of this affinity nanofiber for glycopeptide enrichment and glycoproteomics research.

Submicron fibers as a morphological improvement of amorphous zirconium oxide particles and their utilization in antimonate (Sb(v)) removal

Zirconium oxide was formed into submicron fibers to improve the Sb(v) separation performance compared to a conventional aggregate material.

Fly-ash as a low-cost material for isolation of phosphoproteins

Metal oxide affinity chromatography (MOAC) is one of the most commonly used techniques for selective isolation phosphoproteins and phosphopeptides. This technique is capable of capturing the phosphorylated biomolecules through the affinity of the phosphoryl group for metal oxides/hydroxides. Fly-ash (FA), a by-product of coal-combustion power plants, is primarily composed of oxides of silicon and metals, among which iron and titanium. A number of studies have demonstrated the potential of these metal oxides for phosphoprotein and phosphopeptide enrichment. FA is annually produced over hundred million tons worldwide and generally considered as hazardous waste. It is thus of great importance to enhance its utilization. Here we present the first demonstration of the utility of FA as a low-cost MOAC material for the enrichment of phosphoproteins. With an FA-microcolumn, phosphoproteins can be successfully sequestered from other proteins. FA-microcolumns are shown to be simple, cheap and selective devices for phosphoprotein enrichment from a small volume of mixtures.

Discrimination and highly selective adsorption of phosphoproteins and glycoproteins with arginine-functionalized polyhedral oligomeric silsesquioxane frameworks

The crosstalk between phosphoproteins and glycoproteins causes many difficulties in their selective isolation/enrichment from biological samples. This issue is of high significance in proteomics study, but thus far, it has not received proper attention. Herein, an arginine-functionalized polyhedral oligomeric silsesquioxane (POSS) framework, PP-x-Arg (x = 0, 1, 2, … denotes the amount of salt in preparation), was developed by combining salt-templated thermal polymerization of POSS and pyromellitic dianhydride (PMDA) with post-modification using arginine. PP-x-Arg possesses a porous nanostructure and abundant functional groups, namely, guanidine and zwitterionic groups, enabling the selective adsorption of phosphoproteins or glycoproteins via specific phosphate-guanidine affinity or hydrophilic interaction between PP-x-Arg and glycoproteins, respectively. In particular, the adsorption selectivity exhibited by PP-x-Arg can be easily regulated by adjusting the pH values of the adsorption medium. The PP-x-Arg framework was further employed for the discrimination and isolation of phosphoproteins and glycoproteins from biological samples.

Thermoresponsive Arrays Patterned via Photoclick Chemistry: Smart MALDI Plate for Protein Digest Enrichment, Desalting, and Direct MS Analysis

Sample desalting and concentration are crucial steps before matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) analysis. Current sample pretreatment approaches require tedious fabrication and operation procedures, which are unamenable to high-throughput analysis and also result in sample loss. Here, we report the development of a smart MALDI substrate for on-plate desalting, enrichment, and direct MS analysis of protein digests based on thermoresponsive, hydrophilic/hydrophobic transition of surface-grafted poly(N-isopropylacrylamide) (PNIPAM) microarrays. Superhydrophilic 1-thioglycerol microwells are first constructed on alkyne-silane-functionalized rough indium tin oxide substrates based on two sequential thiol-yne photoclick reactions, whereas the surrounding regions are modified with hydrophobic 1H,1H,2H,2H-perfluorodecanethiol. Surface-initiated atom-transfer radical polymerization is then triggered in microwells to form PNIPAM arrays, which facilitate sample loading and enrichment of protein digests by concentrating large-volume samples into small dots and achieving on-plate desalting through PNIPAM configuration change at elevated temperature. The smart MALDI plate shows high performance for mass spectrometric analysis of cytochrome c and neurotensin in the presence of 1 M urea and 100 mM NaHCO₃, as well as improved detection sensitivity and high sequence coverage for α-casein and cytochrome c digests in femtomole range. The work presents a versatile sample pretreatment platform with great potential for proteomic research.

Fluorescamine Labeling for Assessment of Protein Conformational Change and Binding Affinity in Protein-Nanoparticle Interaction

Protein adsorption alters the "biological identity" of nanoparticles (NPs) and could affect how biosystems respond to invading NPs. Study of protein-NP interaction can help understand how the physicochemical properties of NPs impact the interaction and thus potentially guide the design of safer and more effective NPs for biomedical or other applications. Binding affinity between proteins and NPs and the occurrence of protein conformational change upon binding to NPs are two important aspects to be learned, but few methods are currently available to assess both simultaneously in a simple way. Herein, we demonstrated that the fluorescamine labeling method developed by our group not only could reveal protein conformational change upon adsorption to NPs, owing to its capability to label the primary amines exposed on protein surface, but also could be applied to measure the binding affinity. By screening the interaction between a large number of proteins and four types of NPs, the present study also revealed that protein adsorption onto NPs could be strongly affected by structure flexibility. The proteins with high structure flexibility experienced high degrees of conformation change when binding to the polystyrene NPs, which could potentially influence protein function. Overall, we demonstrate that our assay is a quick, simple, and high-throughput tool to reveal potential impacts on protein activity and evaluate the strength of protein-NP binding.

Aptasensor Based on Hierarchical Core-Shell Nanocomposites of Zirconium Hexacyanoferrate Nanoparticles and Mesoporous mFe3O4@mC: Electrochemical Quantitation of Epithelial Tumor Marker Mucin-1

A novel nanostructured hierarchical core-shell nanocomposite of zirconium hexacyanoferrate (ZrHCF) and a mesoporous nanomaterial composed of Fe₃O₄ and carbon nanospheres (denoted as ZrHCF@mFe₃O₄@mC) was prepared and used as a novel platform for an aptasensor to detect the epithelial tumor marker mucin-1 (MUC1) sensitively and selectively. The prepared ZrHCF@mFe₃O₄@mC nanocomposite exhibited good chemical functionality, water stability, and high specific surface area. Therefore, large amounts of aptamer molecules resulted in high sensitivity of the developed electrochemical aptasensor toward traces of MUC1. The constructed sensor also showed a good linear relationship with the logarithm of MUC1 concentration in the broad range of 0.01 ng·mL^-1 to 1.0 μg·mL^-1, with a low detection limit of 0.90 pg·mL^-1. The fabricated ZrHCF@mFe₃O₄@mC-based aptasensor exhibited not only high selectivity because of the formation of aptamer-MUC1 complex but also good stability, acceptable reproducibility, and applicability. The proposed novel strategy based on a newly prepared hierarchical core-shell nanocomposite demonstrated outstanding biosensing performance and presents potential applications in biomedical fields.

Plasmonic nanodisc arrays on calcinated titania for multimodal analysis of phosphorylated peptides

A hybrid material of gold nanodiscs on a calcinated titania nanofilm that allows for selective quantitative and qualitative characterization of surface-enriched phosphopeptides has been designed and reported. Fabrication was realized through a combination of layer-by-layer deposition and high temperature calcination for the titania, and hole-mask colloidal lithography for the plasmonic nanostructures. The morphology of the resulting titania material was rigorously characterized, exhibiting substantially decreased surface roughness, which allows for lithographic fabrication of plasmonic nanostructures. Moreover, high specificity in adsorption and enrichment of phosphopeptides was exhibited, which was verified by LSPR shifts and matching peaks under mass spectrometric analysis. The construction of these biochips should inform other combinatorial nanofabrication techniques, in addition to allowing future phosphoproteomic analyses to be performed in a time and resource-efficient manner.

Flexible Hierarchical ZrO2 Nanoparticle-Embedded SiO2 Nanofibrous Membrane as a Versatile Tool for Efficient Removal of Phosphate

Functional nanoparticles modified silica nanofibrous materials with good flexibility, a hierarchical mesoporous structure, and excellent durability would have broad applications in efficient removal of contaminants, yet have proven to be enormously challenging to construct. Herein, we reported a strategy for rational design and fabricating flexible, hierarchical mesoporous, and robust ZrO₂ nanoparticle-embedded silica nanofibrous membranes (ZrO₂/SiO₂ NM) for phosphate removal by combining the chitosan dip-coating method with the electrospinning technique. Our approach allows ZrO₂ nanoparticles to be in situ firmly and uniformly anchored onto SiO₂ nanofibers to drastically enlarge the specific surface area and porosity of membranes. Therefore, the resultant ZrO₂/SiO₂ NM exhibited a prominent removal efficiency of 85% and excellent adsorption amount of 43.8 mg P g^-1 membranes in 30 min toward phosphates. Furthermore, the removal performance toward different types of phosphates revealed that the resultant membranes also could be used to remove phosphates in detergent and fertilizer water samples. More importantly, the membranes with good flexibility could directly be taken out from solution after use without any post-treatment. Such a simple and intriguing approach for fabricating nanofibrous membranes may provide a new platform for constructing membranes with superb phosphate removal performance.

Different Stationary Phase Selectivities and Morphologies for Intact Protein Separations

The central dogma of biology proposed that one gene encodes for one protein. We now know that this does not reflect reality. The human body has approximately 20,000 protein-encoding genes; each of these genes can encode more than one protein. Proteins expressed from a single gene can vary in terms of their post-translational modifications, which often regulate their function within the body. Understanding the proteins within our bodies is a key step in understanding the cause, and perhaps the solution, to disease. This is one of the application areas of proteomics, which is defined as the study of all proteins expressed within an organism at a given point in time. The human proteome is incredibly complex. The complexity of biological samples requires a combination of technologies to achieve high resolution and high sensitivity analysis. Despite the significant advances in mass spectrometry, separation techniques are still essential in this field. Liquid chromatography is an indispensable tool by which low-abundant proteins in complex samples can be enriched and separated. However, advances in chromatography are not as readily adapted in proteomics compared to advances in mass spectrometry. Biologists in this field still favour reversed-phase chromatography with fully porous particles. The purpose of this review is to highlight alternative selectivities and stationary phase morphologies that show potential for application in top-down proteomics; the study of intact proteins.

Scalable Fabrication of Electrospun Nanofibrous Membranes Functionalized with Citric Acid for High-Performance Protein Adsorption

Fabricating protein adsorbents with high adsorption capacity and appreciable throughput is extremely important and highly desired for the separation and purification of protein products in the biomedical and pharmaceutical industries, yet still remains a great challenge. Herein, we demonstrate the synthesis of a novel protein adsorbent by in situ functionalizing eletrospun ethylene-vinyl alcohol (EVOH) nanofibrous membranes (NFM) with critic acid (CCA). Taking advantage of the merits of large specific surface area, highly tortuous open-porous structure, abundant active carboxyl groups introduced by CCA, superior chemical stability, and robust mechanical strength, the obtained CCA-grafted EVOH NFM (EVOH-CCA NFM) present an excellent integrated protein (take lysozyme as the model protein) adsorption performance with a high capacity of 284 mg g(-1), short equilibrium time of 6 h, ease of elution, and good reusability. Meanwhile, the adsorption performance of EVOH-CCA NFM can be optimized by regulating buffer pH, ionic strength, and initial concentration of protein solutions. More importantly, a dynamic binding efficiency of 250 mg g(-1) can be achieved driven solely by the gravity of protein solution, which matches well with the demands of the high yield and energy conservation in the actual protein purification process. Furthermore, the resultant EVOH-CCA NFM also possess unique selectivity for positively charged proteins which was confirmed by the method of sodium dodecyl sulfate polyacrylamide gel electrophoresis. Significantly, the successful synthesis of such intriguing and economic EVOH-CCA NFM may provide a promising candidate for the next generation of protein adsorbents for rapid, massive, and cost-effective separation and purification of proteins.

Recent advances in electrospun metal-oxide nanofiber based interfaces for electrochemical biosensing

Synthesis of various electrospun metal-oxide nanofibers and their application towards electrochemical enzymatic and enzyme-free biosensor platforms has been critically discussed.