Magnetite/Ceria-Codecorated Titanoniobate Nanosheet: A 2D Catalytic Nanoprobe for Efficient Enrichment and Programmed Dephosphorylation of Phosphopeptides

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.

In Situ Controllable Fabrication of Two-Dimensional Magnetic Fe3O4/TiO2@Ti3C2Tx Composites for Highly Efficient Phosphopeptides Enrichment

Highly efficient enrichment of phosphopeptides is of great significance for phosphoproteomics-related biological and pathological processes research, but it remains challenging due to the lack of affinity materials which hold high enrichment efficiency and capacity. Ti₃C₂T_x MXene, a novel two-dimensional material with outstanding physicochemical properties, has attracted wide research interests for application in various fields. However, there are few reports on the use of MXene-derived materials for phosphopeptides separation in the biomedical field. In this work, we proposed a facile one-pot method that in situ oxidation and modification of Ti₃C₂T_x MXene, to prepare two-dimensional (2D) magnetic Fe₃O₄/TiO₂@Ti₃C₂T_x composites for potential application in phosphopeptides enrichment. Benefiting from the outstanding magnetic responsiveness and multiaffinity sites (Ti-O, Fe-O, and NH₂ groups), the Fe₃O₄/TiO₂@Ti₃C₂T_x composites possessed excellent enrichment performance with high sensitivity (0.1 fmol μL^-1), excellent selectivity (β-casein: bovine serum albumin = 1:5000, molar ratio), good repeatability (5 times), and high enrichment capacity (200 mg g^-1). Moreover, the results of selective enrichment of phosphopeptides from nonfat milk, human saliva, human serum, and rat brain lysates indicated the great potential of Fe₃O₄/TiO₂@Ti₃C₂T_x composites in low-abundance phosphopeptides enrichment from complex biological samples. This work has put forward a versatile method to prepare magnetic MXene composites and promoted the use of MXene composites in phosphoproteome in biomedicine.

Engineering of nanomaterials for mass spectrometry analysis of biomolecules

Mass spectrometry (MS) based analysis has received intense attention in diverse biological fields. However, direct MS interrogation of target biomolecules in complex biological samples is still challenging, due to the extremely low abundance and poor ionization potency of target biological species. Innovations in nanomaterials create new auxiliary tools for deep and comprehensive MS characterization of biomolecules. More recently, growing research interest has been directed to the compositional and structural engineering of nanomaterials for enriching target biomolecules prior to MS analysis, enhancing the ionization efficiency in MS detection and designing biosensing nanoprobes in sensitive MS readout. In this review, we mainly focus on the recent advances in the engineering of nanomaterials towards their applications in sample pre-treatment, desorption/ionization matrices and ion signal amplification for MS profiling of biomolecules. This review will provide a toolbox of nanomaterials for researchers devoted to developing analytical methods and practical applications in the biological MS field.

Flexible and hierarchical metal-organic framework composite as solid-phase media for facile affinity-tip fabrication to selectively enrich glycopeptides and phosphopeptides

Micro-tip-based solid-phase microextraction is considered as one of the green and powerful analytical sample preparation techniques, but its efficiency is severely hampered by some basic issues such as tedious fabrication, instability of sorbent bed, and blocking of the tip, especially for biological samples due to low permeability. These issues are tackled by introducing a flexible and hierarchical substrate in the microtip, having good mechanical strength and specific functionality to capture the desired biomolecules. Considering the well-ordered and flexible structure of melamine foam, it was used as a substrate and for hydrophilic interaction chromatography (HILIC). Metal-organic framework, due to its excellent characteristics, was grafted on its surface anchored by self-assembling polydopamine. The resulting material was characterized and packed in the tip by just pressing the material in the conical structure of the tip. This affinity tip established good and tunable permeability and was used to selectively enrich glycopeptides as well as phosphopeptides. The affinity tip demonstrated excellent performance to enrich glycopeptides and phosphopeptides with a low limit of detection up to 0.5 fmol μL^-1 from tryptic digests of horseradish peroxidase and β-Casein, respectively, and was stable up to 5 rounds of enrichment. Moreover, this affinity-tip also exhibited high selectivity up to up to 1:1000 (HRP digest to BSA digest) for glycopeptides and 1:200 (β-Casein digest to BSA digest) for phosphopeptides and demonstrated several other fascinating characteristics such as; excellent size exclusion effect for the omission of large-sized proteins, modest backpressure, reproducibility, reusability, smooth enrichment, and successfully applied to a human saliva sample.

Ionic liquid modification of metal-organic framework endows high selectivity for phosphoproteins adsorption

Zr-based metal-organic framework, UiO-66-NH₂, provides favorable adsorption capacity to phosphoproteins, however, it exhibits obvious nonspecific adsorption to other proteins. In the present work, we report a facile strategy to reduce the nonspecific adsorption of nonphosphoproteins by modifying UiO-66-NH₂ with imidazolium ionic liquids (ILs). With respect to bare UiO-66-NH₂, the modified counterpart, UiO@IL, exhibits much improved selectivity to phosphoproteins while maintains comparable adsorption performance. The surface of UiO@IL presents a strong hydrophilicity due to the modification of ILs. Hydrophobic and electrostatic interaction between the absorbent and nonphosphoprotein is significantly reduced. In addition, the interaction between imidazole group of ILs moiety and phosphate group in phosphoprotein ensures the favorable adsorption capacity of UiO@IL for phosphoproteins. Anionic moieties of ILs, i.e., Cl^-, Br^-, BF₄^-, CF₃SO₃^-, play negligible effect in the adsorption process. As a representative, phosphoprotein β-casein (β-ca) is selectively enriched at a mass ratio of BSA:β-ca = 100:1. UiO@IL was further applied for the selective enrichment of phosphoprotein in milk.

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.

High catalytic efficiency from Er3+-doped CeO2-x nanoprobes for in vivo acute oxidative damage and inflammation therapy

Cerium oxide nanoparticles (NPs) due to their advanced catalytic performance have been widely used to treat oxidative damage. However, Ce2O3 NPs have not been further investigated in the treatment of acute oxidative injury in vivo. It is meaningful to improve the efficiency for treatment of acute oxidative injury with NPs in vivo. In this report, we designed Er3+-doped Ce2O3 (Er/Ce2O3) NPs with a size of 7.9 nm, which were used to treat acute liver injury. Er/Ce2O3 NPs realized high-efficiency catalysis of hydrogen peroxide (H2O2) at room temperature. An acute liver damage model was established through intraperitoneal injection of lipopolysaccharide (LPS) in C57 mice. By analyzing histopathological and biochemical indexes, Er/Ce2O3 NPs showed a significant improvement in LPS-induced acute liver injury. Acute liver oxidative damage can be treated within 24 hours, which proved the high catalytic efficiency of Er/Ce2O3 NPs in vivo. The activities of SOD, GPx and CTA increased and production of ROS decreased with Er/Ce2O3 NP treatment in comparison with LPS-induced injury, indicating that the mechanism of Er/Ce2O3 NPs in the treatment of acute oxidative damage of liver was mainly via catalysis of ROS products. Moreover, the protein expression levels of TNF-α, CD45 and IL-1β in liver decreased in the Er/Ce2O3 NPs-treated group, which indicated that Er/Ce2O3 NPs have the function of anti-inflammation property. Therefore, Er/Ce2O3 NPs can be applied to treat and prevent diseases caused by acute oxidative damage.

PAMAM–PMAA brush-functionalized magnetic composite nanospheres: a smart nanoprobe with tunable selectivity for effective enrichment of mono-, multi-, or global phosphopeptides

A novel PAMAM–PMAA brush functionalized magnetic composite nanosphere was successfully prepared for selective enrichment of mono-, multi-, or global phosphopeptides by modulating buffer polarity and acidity.

Organic molecule-assisted synthesis of Fe3O4/graphene oxide nanocomposites for selective capture of low-abundance peptides and phosphopeptides

The iron oxide nanoparticles (Fe₃O₄) were prepared by organic molecule-assisted method in aqueous solution. The facile synthetic process of Fe₃O₄ nanoparticles was conducted only by mixing FeCl₂ and 2-methylimidazole (2-MIM) without any additives. A possible growth mechanism of the Fe₃O₄ nanocrystals was proposed for this mild reaction. Then, the Fe₃O₄ nanoparticles were anchored onto graphene oxide (GO) sheets in water by ultrasound-assisted method, forming an affinity probe with strong biocompatibility. Due to the hydroxy and carboxylic groups of GO sheets, Fe₃O₄/GO probe exhibits excellent performance for enriching low-abundance hydrophilic peptides, while the Fe₃O₄ nanoparticles endure the probe with specific affinity to phosphopeptides. The analytical protocol was developed for sequential enrichment of low-abundance peptides and phosphopeptides by the affinity probe. It exhibited the sequence coverage of 26% for capture of 17 low-abundance peptides from bovine serum albumin (BSA), as well as the selectivity of 1:1:100 for phosphopeptides from α-/β-casein/BSA, and low detectable concentration of 2.5 fmol and probe reusability of 5 times for capture of phosphopeptides from α-/β-casein. Consequently, the prepared Fe₃O₄/GO material possesses excellent feature as multifunctional affinity probe for low-abundance peptides including phosphopeptides from complex biological matrices detected by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Designed synthesis of a "One for Two" hydrophilic magnetic amino-functionalized metal-organic framework for highly efficient enrichment of glycopeptides and phosphopeptides

Highly efficient enrichment of glycopeptides or phosphopeptides from complex biological samples is indispensable for high-throughput mass spectrometry analysis. In this study, for the first time, a "one for two" hydrophilic magnetic amino-functionalized metal-organic framework (MOF) was designed and synthesized for selective enrichment of both glycopeptides and phosphopeptides. A well-known solvo-thermal reaction was adopted to prepare a magnetic core Fe₃O₄, followed by self- polymerization of dopamine, creating a polydopamine (PDA) onto Fe₃O₄. Thanks to the hydroxyl and amino group of PDA, Zr³⁺ was easily adhered to the surface, inducing the following one-pot MOF reaction with amino ligand. After characterization of the as-prepared MOFs (denoted as Fe₃O₄@PDA@UiO-66-NH₂), its ultrahigh surface area, excellent hydrophilicity and strong magnetic responsiveness were highly confirmed. Based on hydrophilic interaction, it was applied to glycopeptide enrichment, while based on strong binding between Zr and phosphopeptides, it was applied to phosphopeptide enrichment, both exhibiting excellent performance in standard proteins and human serum with high sensitivity and selectivity. These results showed the as-prepared MOFs had great potential in proteomics research.

Environmental implications and applications of engineered nanoscale magnetite and its hybrid nanocomposites: A review of recent literature

This review focuses on environmental implications and applications of engineered magnetite (Fe3O4) nanoparticles (MNPs) as a single phase or a component of a hybrid nanocomposite that exhibits superparamagnetism and high surface area. MNPs are synthesized via co-precipitation, thermal decomposition and combustion, hydrothermal process, emulsion, microbial process, and green approaches. Aggregation/sedimentation and transport of MNPs depend on surface charge of MNPs and geochemical parameters such as pH, ionic strength, and organic matter. MNPs generally have low toxicity to humans and ecosystem. MNPs are used for constructing chemical/biosensors and for catalyzing a variety of chemical reactions. MNPs are used for air cleanup and carbon sequestration. MNP nanocomposites are designed as antimicrobial agents for water disinfection and flocculants for water treatment. Conjugated MNPs are widely used for adsorptive/separative removal of organics, dyes, oil, arsenic, phosphate, molybdate, fluoride, selenium, Cr(VI), heavy metal cations, radionuclides, and rare earth elements. MNPs can degrade organic/inorganic contaminants via chemical reduction or catalyze chemical oxidation in water, sediment, and soil. Future studies should further explore mechanisms of MNP interactions with other nanomaterials and contaminants, economic and green approaches of MNP synthesis, and field scale demonstration of MNP utilization.

Low-cost iron oxide magnetic nanoclusters affinity probe for the enrichment of endogenous phosphopeptides in human saliva

Simple and low cost iron oxide magnetic nanoclusters (Fe₃O₄ MNCs) affinity material has been directly applied for phosphorylated peptides/proteins enrichment.