Ti(IV) carrying polydopamine-coated, monodisperse-porous SiO 2 microspheres with stable magnetic properties for highly selective enrichment of phosphopeptides

In Vitro Synergistic Photodynamic, Photothermal, Chemodynamic, and Starvation Therapy Performance of Chlorin e6 Immobilized, Polydopamine-Coated Hollow, Porous Ceria-Based, Hypoxia-Tolerant Nanozymes Carrying a Cascade System

A synergistic therapy agent (STA) with photothermal, photodynamic, chemodynamic, and starvation therapy (PTT, PDT, CDT, and ST) functions was developed. Hollow, mesoporous, and nearly uniform CeO2 nanoparticles (H-CeO2 NPs) were synthesized using a staged shape templating sol-gel protocol. Chlorin e6 (Ce6) was adsorbed onto H-CeO2 NPs, and a thin polydopamine (PDA) layer was formed on Ce6-adsorbed H-CeO2 NPs. Glucose oxidase (GOx) was bound onto PDA-coated Ce6-adsorbed H-CeO2 NPs to obtain the targeted STA (H-CeO2@Ce6@PDA@GOx NPs). A reversible photothermal conversion behavior with the temperature elevations up to 34 °C was observed by NIR laser irradiation at 808 nm. A cascade enzyme system based on immobilized GOx and intrinsic catalase-like activity of H-CeO2 NPs was rendered on STA for enhancing the effectiveness of PDT by elevation of ROS generation and alleviation of hypoxia in a tumor microenvironment. Glucose-mediated generation of highly toxic hydroxyl radicals (·OH) was evaluated for CDT. The effectiveness of PDT on glioblastoma T98G cells was markedly enhanced by O2 generation started by the decomposition of glucose. A similar increase in cell death was also observed when ST and CDT functions were enhanced by photothermal action. The viability of T98G cells decreased to 10.6% by in vitro synergistic action including ST, CDT, PDT, and PTT without using any antitumor agent.

Novel 3D-Printed Microfluidic Magnetic Platform for Rapid DNA Isolation

This study presents a novel miniaturized device as a 3D-printed microfluidic magnetic platform specifically designed to manipulate magnetic microparticles in a microfluidic chip for rapid deoxyribonucleic acid (DNA) isolation. The novel design enables the movement of the magnetic particles in the same or opposite directions with the flow or suspends them in continuous flow. A computational model was developed to assess the effectiveness of the magnetic manipulation of the particles. Superparamagnetic monodisperse silica particles synthesized in-house are utilized for the isolation of fish sperm DNA and human placenta DNA. It was demonstrated that the proposed platform can perform DNA isolation within 10 min with an isolation efficiency of 50% at optimum operating conditions.

Biobased Tannic Acid-Chitosan Composite Membranes as Reusable Adsorbents for Effective Enrichment of Phosphopeptides

High-performance reusable materials from renewable resources are rare and urgently required in bioseparation. Herein, a series of tannic acid-chitosan composite membranes for the enrichment of phosphopeptides were fabricated by the freeze casting method. First, a tannic acid-chitosan composite membrane was acquired via the multiple hydrogen bonds between tannic acid and chitosan, which had a long-range aligned three-dimensional microstructure. Second, a covalent-hydrogen bond hybrid composite was also fabricated, with stable and aligned honeycomb-like microstructures that formed by the synergy of covalence and hydrogen bonding. Besides, a ternary composite membrane was "one-pot" synthesized by the copolymerization of tannic acid, chitosan, and Ti4+ ions, indicating the feasibility of involving metal ions in the composition of the polymer skeleton in place of additional modification steps. The as-prepared chitosan composite membranes exhibited excellent performance in the enrichment of phosphopeptides from β-casein tryptic digest and human serum. Benefitting from the long-range aligned honeycomb-like structure coordinated by hydrogen bonds and covalent bonds, and a large number of pyrogallol functional groups provided by tannic acid, the covalent-hydrogen bond hybrid membrane showed excellent reusability and could be reused up to 16 times in phosphopeptide enrichment, as far as we know, which is the best reported result to date.

An introductory review on advanced multifunctional materials

This review summarizes the applications of some of the advanced materials. It included the synthesis of several nanoparticles such as metal oxide nanoparticles (e.g., Fe₃O₄, ZnO, ZrOSO₄, MoO_3-x, CuO, AgFeO₂, Co₃O₄, CeO₂, SiO₂, and CuFeO₂); metal hydroxide nanosheets (e.g., Zn₅(OH)₈(NO₃)₂·2H₂O, Zn(OH)(NO₃)·H₂O, and Zn₅(OH)₈(NO₃)₂); metallic nanoparticles (Ag, Au, Pd, and Pt); carbon-based nanomaterials (graphene, graphene oxide (GO), graphitic carbon nitride (g-C₃N₄), and carbon dots (CDs)); biopolymers (cellulose, nanocellulose, TEMPO-oxidized cellulose nanofibers (TOCNFs), and chitosan); organic polymers (e.g. covalent-organic frameworks (COFs)); and hybrid materials (e.g. metal-organic frameworks (MOFs)). Most of these materials were applied in several fields such as environmental-based technologies (e.g., water remediation, air purification, gas storage), energy (production of hydrogen, dimethyl ether, solar cells, and supercapacitors), and biomedical sectors (sensing, biosensing, cancer therapy, and drug delivery). They can be used as efficient adsorbents and catalysts to remove emerging contaminants e.g., inorganic (i.e., heavy metals) and organic (e.g., dyes, antibiotics, pesticides, and oils in water via adsorption. They can be also used as catalysts for catalytic degradation reactions such as redox reactions of pollutants. They can be used as filters for air purification by capturing carbon dioxide (CO₂) and volatile organic compounds (VOCs). They can be used for hydrogen production via water splitting, alcohol oxidation, and hydrolysis of NaBH₄. Nanomedicine for some of these materials was also included being an effective agent as an antibacterial, nanocarrier for drug delivery, and probe for biosensing.

Recent advances in development of functional magnetic adsorbents for selective separation of proteins/peptides

Nowadays, proteins separation has attracted great attention in proteomics research. Because the proteins separation is helpful for making an early diagnosis of many diseases. Magnetic nanoparticles are an interesting and useful functional material, and have attracted extensive research interest during the past decades. Because of the excellent properties such as easy surface functionalization, tunable biocompatibility, high saturation magnetization etc, magnetic microspheres have been widely used in isolation of proteins/peptides. Notably, with the rapid development of surface decoration strategies, more and more functional magnetic adsorbents have been designed and fabricated to meet the growing demands of biological separation. In this review, we have collected recent information about magnetic adsorbents applications in selective separation of proteins/peptides. Furthermore, we present a comprehensive prospects and challenges in the field of protein separation relying on magnetic nanoparticles.

Robust Dual-Biomimetic Titanium Dioxide-Cellulose Monolith for Enrichment of Phosphopeptides

Metal oxide affinity chromatography (MOAC) is considered to be one of the most effective methods for phosphopeptide enrichment. However, most of the materials used in the method are powder; frequent centrifugation is necessitated during the enrichment process, and potential risks of loss of peptides and materials and clogging of the column employed for liquid chromatography-mass spectrometry (LC-MS) arise. Moreover, the reusability of these materials to achieve sustainability was hardly investigated. To overcome these limitations, herein, inorganic titanium dioxide (TiO₂) was coated onto the skeletal surface of the organic cellulose monolith (CM) material with a coral-like structure via a sol-gel method. This produced an organic-inorganic hybrid TiO₂-CM material, which contained a combination of organic and inorganic substances, making it mimic the mollusk shell in terms of composition. The prepared TiO₂-CM material as monolith exhibited excellent mechanical strength and did not break during the enrichment process; thus, the tedious implementation of multiple centrifugation cycles was prevented, thereby streamlining the experimental procedure and avoiding the loss of peptides and materials. Moreover, a large amount of TiO₂ was introduced onto the surface of the CM material, and thus, the resultant TiO₂-CM material exhibited a large surface area. As a result, the fabricated TiO₂-CM material was successfully applied to the enrichment of phosphopeptides obtained from the tryptic digests of a BSA/β-casein (mass ratio, 500/1) mixture. The results were superior to those achieved for commercial TiO₂ beads, confirming that TiO₂-CM has excellent selectivity for phosphopeptides and reusability. Furthermore, 9287 unique phosphopeptides derived from the 2661 phosphoproteins were successfully identified from two milligrams of tryptic digests of Hela cell exosomes obtained through five independent replications after enriching using the TiO₂-CM material. The results indicated that the material has good application prospects in the analysis of protein phosphorylation. Furthermore, TiO₂-CM consists of green and cheap cellulose as the skeleton, and its synthesis process is environment-friendly, simple, and inexpensive.

Partial-, Double-Enzymatic Dephosphorylation and EndoGluC Hydrolysis as an Original Approach to Enhancing Identification of Casein Phosphopeptides (CPPs) by Mass Spectrometry

The identification of phosphopeptides is currently a challenge when they are part of a complex matrix of peptides, such as a milk protein enzymatic hydrolysate. This challenge increases with both the number of phosphorylation sites on the phosphopeptides and their amino acid length. Here, this paper reports a four-phase strategy from an enzymatic casein hydrolysate before a mass spectrometry analysis in order to enhance the identification of phosphopeptides and phosphosites: (i) the control protein hydrolysate, (ii) a two-step enzymatic dephosphorylation of the latter, allowing for the almost total dephosphorylation of peptides, (iii) a one-step enzymatic dephosphorylation, allowing for the partial dephosphorylation of the peptides and (iv) an additional endoGluC enzymatic hydrolysis, allowing for the cleavage of long-size peptides into shorter ones. The reverse-phase high-pressure liquid chromatography–tandem mass spectrometry (RP-HPLC-MS/MS) analyses of hydrolysates that underwent this four-phase strategy allowed for the identification of 28 phosphorylation sites (90%) out of the 31 referenced in UniprotKB/Swiss-Prot (1 June 2021), compared to 17 sites (54%) without the latter. The alpha-S2 casein phosphosites, referenced by their similarity in the UniProt database, were experimentally identified, whereas pSer148, pThr166 and pSer187 from a multiphosphorylated long-size kappa-casein were not. Data are available via ProteomeXchange with identifier PXD027132.

Yolk-shell ZnO@C-CeO2 ternary heterostructures with conductive N-doped carbon mediated electron transfer for highly efficient water splitting

Herein, carbon-incorporated yolk-shell ZnO@C-CeO₂ ternary heterostructures are employed as visible light responsive photocatalyst for highly efficient photoelectrochemical (PEC) water splitting. Compared to conventional ZnO/CeO₂ semiconductors, introduction of a thin PDA shell layer assures the generation of a conductive N-doped graphitic carbon layer after a calcination post-treatment with mesoporous hollow morphologies. The evaluation of PEC water splitting performance of ZnO@C-CeO₂ photoanodes reveals the maximum photocurrent density as 7.43 mA/cm² at 1.18 V RHE under light whereas almost no response is recorded at dark. These superior PEC H₂ evolution performance strongly implies efficient charge separation, facilitated charge transfer between photoanode and electrolyte interface as well as within the semiconductor bulk by means of rapid electron transfer ability of N-doped graphitic carbon layer and prolong life time of light inside yolk-shell structure. Furthermore, considerable depression in PL intensity of ZnO@C-CeO₂ photoanodes compared to ZnO clearly reveals a higher photon absorption due to the reflection of light in hollow region and increase in electron hole separation efficiency. Moreover, plausible Z-scheme charge transfer mechanism using ZnO@C-CeO₂ photoanodes under visible light illumination is verified using radical trapping experiments and X-ray photoelectron spectroscopy (XPS) methods, suggesting new generation of heterostructures for sufficient conversion of sunlight to H₂ fuels.

Recent trends in sorbents for bioaffinity chromatography

Isolation or enrichment of biological molecules from complex biological samples is mostly a prerequisite in proteomics, genomics, and glycomics. Different techniques have been used to advance the efficiency of the purification of biological molecules. Bioaffinity chromatography is one of the most powerful technique that plays an important role in the isolation of target biological molecules by the specific interactions with ligands that are immobilized on different support materials. This review examines the recent developments in bioaffinity chromatography particularly over the past 5 years in the literature. Also properties of supports, immobilization techniques, types of binding agents, and methods used in bioaffinity chromatography applications are summarized.

Efficient separation of phosphopeptides employing a Ti/Nb-functionalized core-shell structure solid-phase extraction nanosphere

A strategy for effectively enriching global phosphopeptides was successfully developed by using ammonia methyl phosphate (APA) as a novel chelating ligand and Ti⁴⁺ and Nb⁵⁺ as double functional ions (referred to as Fe₃O₄@mSiO₂@APA@Ti⁴⁺/Nb⁵⁺). With the advantage of large specific surface area (151.1 m²/g), preeminent immobilized ability for metal ions (about 8% of total atoms), and unbiased enrichment towards phosphopeptides, Fe₃O₄@mSiO₂@APA@Ti⁴⁺/Nb⁵⁺ displays high selectivity (maximum mass ratio β-casein to BSA is 1:1500), low limit of detection (LOD, as low as 0.05 fmol), good relative standard deviation (RSD, lower than 7%), recovery rate of 87% (¹⁸O isotope labeling method), outstanding phosphopeptide loading capacity (330 μg/mg), and at least five times re-use abilities. In the examination of the actual sample, 24 phosphopeptides were successfully detected in saliva and 4 phosphopeptides were also selectively extracted from human serum. All experiments have shown that Fe₃O₄@mSiO₂@APA@Ti⁴⁺/Nb⁵⁺ exhibits exciting potential in view of the challenge of low abundance of phosphopeptides. Graphical abstract.

Monodisperse-porous cerium oxide microspheres as a new support with appreciable catalytic activity for a composite catalyst in benzyl alcohol oxidation

Monodisperse porous ceria microspheres as a support with individual catalytic activity, facile post-functionalization and high surface area for heterogeneous catalysis.

Hydrophilic polydopamine-derived mesoporous channels for loading Ti(IV) ions for salivary phosphoproteome research

Salivary phosphoproteome holds great promise in clinic diagnosis. For profiling of salivary phosphoproteome, it is essential to develop efficient enrichment methods prior to mass spectrum (MS). Among developed enrichment strategies, immobilized metal ions affinity chromatography (IMAC) has exhibited outstanding performance. In this work, we report a coherent approach where polydopamine (PDA) is first utilized to form mesoporous structure through soft templating method, then chelated with Ti⁴⁺ to construct hydrophilic polydopamine-derived magnetic mesoporous nanocomposite (denoted Fe₃O₄@mPDA@Ti⁴⁺). In virtue of the merits including ordered mesoporous channels, appropriate superparamagnetism, and abundant Ti⁴⁺, the enrichment strategy based on Fe₃O₄@mPDA@Ti⁴⁺ combined with MS is employed for accurate identification of phosphopeptides in β-casein digest and human saliva. As expected, Fe₃O₄@mPDA@Ti⁴⁺ revealed a great selectivity (1:200) and a low detection limit (0.1 fmol μL^-1) toward phosphopeptides. More importantly, the further successful capture of phosphopeptides from human saliva indicated the prominent potential of this method for seeking phosphopeptide biomarkers in further analysis.

An Integral Recognition and Signaling for Electrochemical Assay of Protein Kinase Activity and Inhibitor by Reduced Graphene Oxide-Polydopamine-Silver Nanoparticle-Ti4+ Nanocomposite

A novel electrochemical biosensing method for protein kinase (PKA) activity was demonstrated by using a reduced graphene oxide-polydopamine-silver nanoparticle-Ti4+ (rGO-PDA-AgNPs-Ti4+) nanocomposite. The obtained nanocomposite possessed an integral capability for phosphopeptide recognition and signal readout. The polydopamine modified reduced graphene oxide (rGO-PDA) was firstly prepared based on a self-polymerization method of dopamine. The silver ions were adsorbed onto polydopamine (PDA) layer and directly reduced into silver nanoparticles (AgNPs), which was used for electrochemical signal reporting. Then, the Ti4+ cations were attached onto the PDA layer for phosphopeptide recognition according to the strong coordination ability of PDA with Ti4+ and phosphate group. The prepared rGO-PDA-AgNPs-Ti4+ nanocomposites were characterized with different methods. The developed rGO-PDA-AgNPs-Ti4+ nanocomposites were then employed for electrochemical analysis of PKA-catalyzed kemptide phosphorylation. The sensitive detection toward PKA activity was realized with an experimental detection limit of about 0.01 U/mL. It may be also extended for the inhibitor evaluation. Thus, it provided a facile and sensitive means for electrochemical analysis of PKA activity and inhibitor screening.

Phosphoproteomic strategies in cancer research: a minireview

Understanding the cellular processes is central to comprehend disease conditions and is also true for cancer research. Proteomic studies provide significant insight into cancer mechanisms and aid in the diagnosis and prognosis of the disease. Phosphoproteome is one of the most studied complements of the whole proteome given its importance in the understanding of cellular processes such as signaling and regulations. Over the last decade, several new methods have been developed for phosphoproteome analysis. A significant amount of these efforts pertains to cancer research. The current use of powerful analytical instruments in phosphoproteomic approaches has paved the way for deeper and sensitive investigations. However, these methods and techniques need further improvements to deal with challenges posed by the complexity of samples and scarcity of phosphoproteins in the whole proteome, throughput and reproducibility. This review aims to provide a comprehensive summary of the variety of steps used in phosphoproteomic methods applied in cancer research including the enrichment and fractionation strategies. This will allow researchers to evaluate and choose a better combination of steps for their phosphoproteome studies.

Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials

Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.

Effect of shell structure of Ti-immobilized metal ion affinity chromatography core-shell magnetic particles for phosphopeptide enrichment

Magnetic materials in sample preparation for shotgun phosphoproteomics offer several advantages over conventional systems, as the enrichment can be achieved directly in solution, but they still suffer from some drawbacks, due to limited stability and selectivity, which is supposed to be affected by the hydrophilicity of the polymeric supports used for cation immobilization. The paper describes the development of an improved magnetic material with increased stability, thanks to a two-step covering of the magnetic core, for the enrichment of phosphopeptides in biological samples. Four materials were prepared featuring a polymeric shell with tunable hydrophilicity, obtained by "grafting from" polymerization of glycidyl methacrylate with 0-8.3% of polyethylene glycol methacrylate (PEGMA), the latter used to modulate the hydrophilicity of the material surface. Finally, the materials were functionalized with iminodiacetic acid for Ti4+ ion immobilization. The materials were analyzed for their composition by a combination of CHN elemental analysis and thermogravimetric analysis, also hyphenated to gas chromatography and mass spectrometric detection. Surface characteristics were evaluated by water contact angle measurements, scanning electron microscopy and energy dispersive X-ray spectrometry. These materials were applied to the enrichment of phosphopeptides from yeast protein digests. Peptides were identified by proteomics techniques using nano-high performance liquid chromatography coupled to mass spectrometry and bioinformatics. Qualitatively the peptides identified by the four systems were comparable, with 1606-1693 phosphopeptide identifications and a selectivity of 47-54% for all materials. The physico-chemical features of the identified peptides were also the same for the four materials. In particular, the grand average of hydropathy index values indicated that the enriched phosphopeptides were hydrophilic (ca. 90%), and only some co-enriched non-phosphorylated peptides were hydrophobic (21-28%), regardless of the material used for enrichment. Peptides had a pI ≤ 7, which indicated a well-known bias for acidic peptides binding, attributed to the interaction with the metal center itself. The results indicated that the enrichment of phosphopeptides and the co-enrichment of non-phosphorylated peptides is mainly driven by interactions with Ti4+ and does not depend on the amount of PEGMA chains in the polymer shell.

Ni(II)-decorated porous titania microspheres as a stationary phase for column chromatography applications: Highly selective purification of hemoglobin from human blood

Titania (TiO₂)-based monodisperse-porous stationary phase/sorbent was synthesized by decoration of Ni(II) ions onto TiO₂ microspheres 4.2 µm in size, obtained by a staged-shape template hydrolysis and condensation protocol. Ni(II) ions were attached onto iminodiacetic acid-3-glycidoxypropyltrimethoxysilane (IDA-GPTMS) bound-titania microspheres by metal-chelate complex formation. The appropriate mean size, sufficiently high surface area and high porosity providing an appropriate column permeability make Ni(II)-decorated TiO₂ microspheres a good sorbent/stationary phase for batch/continuous-column chromatography applications. Ni(II)-decorated TiO₂ microspheres were investigated as a sorbent for purification of a typical histidine-rich protein, hemoglobin (Hb) via immobilized metal affinity chromatography (IMAC) in batch fashion, by including bovine serum albumin (BSA) as reference. The saturation capacities of batch adsorption runs performed with bovine Hb and BSA were determined as 137 ± 9 and 45 ± 3 mg/g, respectively. Human Hb with the purity of > 95% was recovered from whole blood by IMAC conducted in batch-fashion. Ni(II)-decorated microspheres were also evaluated as a stationary phase in a microfluidic-IMAC system, in which, human Hb was recovered from whole blood with a purity of 85%. The microfluidic-IMAC system constructed here, based on monodisperse-porous TiO₂ microspheres, is a promising tool for genomics/proteomics applications involving isolation of valuable biomolecules from low-volume samples.