Efficient extraction of low-abundance peptides from digested proteins and simultaneous exclusion of large-sized proteins with novel hydrophilic magnetic zeolitic imidazolate frameworks

Magnetic mesoporous carbon nanocomposites derived from bimetallic metal-organic frameworks for enrichment of low-abundance peptides

Mesopore-structured cobalt and nickel metal-organic frameworks (Co/Ni-ZIF) were synthesized by a self-assembly method using Co and Ni as bimetallic centers and 2-methylimidazole as the organic ligand at room temperature. The resulting rhombic dodecahedral nanocomposites possessing rich mesopores with an average diameter of 4 nm were collected centrifugally and then carbonized under a nitrogen atmosphere to generate bimetallic magnetic porous carbon nanocomposites (Co/Ni-MCNs). After thorough characterization, the as-prepared Co/Ni-MCNs decorated with a graphite shell layer with pyridinic nitrogen were utilized in magnetic separation and enrichment of low-abundance peptides through hydrophobic and π-π stacking interactions. This is the first attempt to prepare mesoporous carbon materials having plentiful holes with bimetal MOFs as precursors, in which partial nickel-containing components served as sacrificial templates. Owing to the ordered structure, abundant mesopores, rich interaction sites, excellent magnetic properties and good compatibility with biological tissues, this proposed magnetic affinity probe has been successfully used in the identification of endogenous peptides in human urine and serum in combination with matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS).

From Nanozymes to Multi-Purpose Nanomaterials: The Potential of Metal-Organic Frameworks for Proteomics Applications

Metal-organic frameworks (MOFs) have the potential to revolutionize the biotechnological and medical landscapes due to their easily tunable crystalline porous structure. Herein, the study presents MOFs' potential impact on proteomics, unveiling the diverse roles MOFs can play to boost it. Although MOFs are excellent catalysts in other scientific disciplines, their role as catalysts in proteomics applications remains largely underexplored, despite protein cleavage being of crucial importance in proteomics protocols. Additionally, the study discusses evolving MOF materials that are tailored for proteomics, showcasing their structural diversity and functional advantages compared to other types of materials used for similar applications. MOFs can be developed to seamlessly integrate into proteomics workflows due to their tunable features, contributing to protein separation, peptide enrichment, and ionization for mass spectrometry. This review is meant as a guide to help bridge the gap between material scientists, engineers, and MOF chemists and on the other side researchers in biology or bioinformatics working in proteomics.

Copper Nanowire/Polydopamine-Modified Sodium Alginate Composite Films with Enhanced Long-Term Stability and Adhesion for Flexible Organic Light-Emitting Diodes

Copper nanowire (CuNW), with combined advantages of high conductivity and cost-effectiveness, is considered a promising material for the development of next-generation transparent conductive films (TCFs) in the field of flexible optoelectronics. However, the practical application of CuNW TCFs is hindered by some limitations, such as conductivity degradation and poor adhesion. Here, we demonstrate a stable CuNW composite film by embedding CuNWs into a polydopamine (PDA)-modified sodium alginate (NaAlg) matrix without sacrificing the optoelectronic properties of the CuNW network. The introduction of the PDA modifier significantly enhances the antiaging capability of the NaAlg layer, providing strengthened protection of the embedded CuNWs against moisture and oxygen, thereby resulting in minimal degradation of the conductivity of CuNWs for up to 9 months under ambient conditions. Simultaneously, the interface adhesion between the CuNW network and the substrate is further enhanced due to the abundance of catechol structures in PDA, allowing for the maintenance of the electrical conductivity of the CuNW network even under cyclic external bending stress and tape-peeling forces. In addition, embedding CuNWs into the polymer binding layer produces a CuNW composite film with a very smooth surface. A flexible OLED based on the PDA-modified NaAlg/CuNW TCF is successfully fabricated, exhibiting performance comparable to that of a traditional rigid indium tin oxide-based device, while also demonstrating remarkable mechanical durability. The modification strategy can promote practical applications of the CuNW network in flexible optoelectronic devices.

Metal Organic Framework Nanomaterial-Based Extraction and Proteome Analysis of Membrane and Membrane-Associated Proteins

Membrane proteins (MPs) play a key role in various biological processes, while difficulties still exist in the extraction because of their inherent low abundance and poor solubility caused by high hydrophobicity. Metal organic framework (MOF) materials with good hydrophobic properties have the ability to absorb MPs, especially zeolitic imidazolate framework (ZIF) materials. Here, two MOF materials (ZIF-8 and ZIF-67) were compared for MP extraction, and our results revealed that higher yield was obtained with ZIF-67. After method development, the optimal enrichment effect was obtained when the mass ratio of proteins and ZIF-67 reached 1:20 with 100 mM NaCl in 20% ethanol at 4 °C and pH 9.0. When compared with a commercial kit, the extraction yield increased by 88.11% and the average number of identified MPs elevated by 29.17% with the developed ZIF method. Normal lung cell MRC5 was employed to verify the effectiveness of the ZIF method. Results showed 45.13% increase in yield and 22.88% increase in average number of identified MPs by the ZIF method. Our method was further applied to the enrichment of MPs for high-metastatic (95D) and low-metastatic (95C) human lung cancer cells. A total of 1732 (95D) and 1711 (95C) MPs were identified, among which 710 MPs were dysregulated significantly; 441 upregulated MPs in 95D cells were found to be closely related to the growth, proliferation, and migration of lung cancer cells. Our results collectively demonstrated that ZIF-67 was an ideal material for MP extraction, which might be helpful for analysis of cancer proteomics and discovery of cancer migration associated MPs.

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.

Material-assisted mass spectrometric analysis of low molecular weight compounds for biomedical applications

Low molecular weight compounds play an important role in encoding the current physiological state of an individual. Laser desorption/ionization mass spectrometry (LDI MS) offers high sensitivity with low cost for molecular detection, but it is not able to cover small molecules due to the drawbacks of the conventional matrix. Advanced materials are better alternatives, showing little background interference and high LDI efficiency. Herein, we first classify the current materials with a summary of compositions and structures. Matrix preparation protocols are then reviewed, to enhance the selectivity and reproducibility of MS data better. Finally, we highlight the biomedical applications of material-assisted LDI MS, at the tissue, bio-fluid, and cellular levels. We foresee that the advanced materials will bring far-reaching implications in LDI MS towards real-case applications, especially in clinical settings.

Core-shell magnetic zeolite imidazolate framework-8 as adsorbent for magnetic solid phase extraction of brucine and strychnine from human urine

Core-shell magnetic zeolite imidazolate framework-8 (Fe3O4@PAA@ZIF-8) was successfully synthesized and first employed as adsorbent of magnetic solid-phase extraction (MSPE) for the determination of brucine and strychnine in human urine sample coupled with high performance liquid chromatography. The as-prepared Fe3O4@PAA@ZIF-8 was characterized by transmission electron microscopy, Fourier-transform infrared spectrometry, X-ray diffraction, vibrating sample magnetometer and zeta potential analysis. Main parameters affecting the MSPE efficiency, including amount of adsorbent, sample solution pH, extraction time, ionic strength, desorption solvent, desorption time and desorption volume were further optimized. Under the optimized conditions, the proposed method provided good linearity (5.0-1000.0 μg L-1) with determination coefficients between 1.0000 and 0.9998, low limits of detection in the range of 1.1-1.2 μg L-1, and excellent reproducibility with relative standard deviations of less than 7.7%. The intra-day and inter-day precision were 1.5-3.2% and 2.1-7.2%, respectively. Satisfactory spiked recoveries were between97.2% and 115.4% with the relative standard deviations less than 6.3%. The results demonstrated that Fe3O4@PAA@ZIF-8 composite was a promising magnetic adsorbent for the preconcentration of brucine and strychnine in human urine sample.

Regulating metal-organic frameworks as stationary phases and absorbents for analytical separations

Metal-organic frameworks (MOFs) are highly ordered framework systems composed of metal centers and organic linkers formed through coordination bonds. The diversity of metal elements and easily modified organic ligands, together with controllable synthetic approaches, gives rise to the designability of various MOF structures and topologies and the capability of MOFs to be functionalized. Their structural diversity provides MOFs with many unique properties, such as permanent porosity, flexible structures, thermostability, and high adsorption capacity, leading to great practicability in technical applications. In this review, we concentrate on the applications of MOFs in the field of gas chromatography, high-performance liquid chromatography, and the enrichment of biomolecules, based on rational arrangements in the structures and functions of MOFs. Moreover, we emphasize the importance of structural and chemical regulations for the improvement of separation efficiency.

Metal-Organic Frameworks for Liquid Phase Applications

In the last two decades, metal-organic frameworks (MOFs) have attracted overwhelming attention. With readily tunable structures and functionalities, MOFs offer an unprecedentedly vast degree of design flexibility from enormous number of inorganic and organic building blocks or via postsynthetic modification to produce functional nanoporous materials. A large extent of experimental and computational studies of MOFs have been focused on gas phase applications, particularly the storage of low-carbon footprint energy carriers and the separation of CO2-containing gas mixtures. With progressive success in the synthesis of water- and solvent-resistant MOFs over the past several years, the increasingly active exploration of MOFs has been witnessed for widespread liquid phase applications such as liquid fuel purification, aromatics separation, water treatment, solvent recovery, chemical sensing, chiral separation, drug delivery, biomolecule encapsulation and separation. At this juncture, the recent experimental and computational studies are summarized herein for these multifaceted liquid phase applications to demonstrate the rapid advance in this burgeoning field. The challenges and opportunities moving from laboratory scale towards practical applications are discussed.

Metal-organic frameworks as advanced materials for sample preparation of bioactive peptides

Development of novel affinity materials and separation techniques is crucial for the progress of modern proteomics and peptidomics. Detection of peptides and proteins from complex matrices still remains a challenging task due to the highly complicated biological composition, low abundance of target molecules, and large dynamic range of proteins. As an emerging area of analytical science, metal-organic framework (MOF)-based separation of proteins and peptides is attracting growing interest. This minireview summarizes the recent advances in MOF-based affinity materials for the sample preparation of proteins and peptides. Some newly emerging MOF nanoreactors for the degradation of peptides and proteins are introduced. An update of MOF-based affinity materials for the isolation of glycopeptides, phosphopeptides and low-abundance endogenous peptides in the last two years is focused on. The separation mechanism is discussed along with the chemical structures of MOFs. Finally, the remaining challenges and future development of MOFs in analyzing peptides and proteins in complicated biological samples are discussed.

One-pot synthesis of trypsin-based magnetic metal-organic frameworks for highly efficient proteolysis

Immobilization of enzymes onto metal-organic frameworks (MOFs) through a biomimetic mineralization approach can preserve biological functionality in harsh environments. Despite the success of this approach, the alkaline environment of the reaction system, which is caused by the organic monomers of MOFs, makes it unsuitable for some pH-sensitive enzymes, especially for trypsin. Herein, we reported a facile approach for the one-pot synthesis of trypsin-immobilized magnetic zeolite imidazolate framework-8 (iron oxide@ZIF-8@trypsin), where the growth of ZIF-8 around the citric acid-modified iron oxide and immobilization of trypsin occurred simultaneously when the pH of the reaction system was changed to some extent. With a large specific surface area and a high enzyme loading capacity, the resultant iron oxide@ZIF-8@trypsin exhibited 2.6 times higher enzymatic activity than free trypsin. Moreover, it showed a favourable magnetic response (43 emu g^-1) which made the operation and recycling easy and convenient. In addition, iron oxide@ZIF-8@trypsin could be applied as an immobilized enzyme microreactor (IMER) to rapidly and efficiently digest proteins and complex human serum samples with satisfactory results, showing great promise for application in proteomic analysis.

Doxorubicin-loaded Fe3O4-ZIF-8 nano-composites for hepatocellular carcinoma therapy

Hepatocellular carcinoma (HCC) is one of the most common and malignant cancers and has no effective therapeutic approaches. Chemotherapeutic drug doxorubicin (DOX) is widely used for HCC therapy, but its application is limited by the clinical toxicity. In the present study, an Fe3O4-ZIF-8 magnetic nano-composite was fabricated and used for DOX delivery for HCC therapy. The morphology, structure and property of Fe3O4-ZIF-8 nano-composites were evaluated by scanning electron microscopy, transmission electron microscopy and N2 adsorption-desorption isotherms studies. The drug release from DOX@Fe3O4-ZIF-8 was measured in pH 7.4 phosphate-buffered saline. The cellular uptake ability of DOX@Fe3O4-ZIF-8 into hepatocarcinoma cell line (MHCC97H) was visualized with a confocal laser scanning microscope. The effects of Fe3O4-ZIF-8, DOX and DOX@Fe3O4-ZIF-8 against MHCC97H cells were evaluated by CCK-8 assay and flow cytometry assay. Fe3O4-ZIF-8 nano-composites were synthesized and used as a nano-carrier for the delivery of DOX. Because of high drug loading property of ZIF-8, 1 mg Fe3O4-ZIF-8 nano-composites loaded 120 μg DOX when DOX@Fe3O4-ZIF-8 was synthesized in 30 mg/mL DOX solution. The cumulative DOX release curve showed a slow and sustained release pattern over time. The results of CCK-8 assay showed that Fe3O4-ZIF-8 was nontoxic to MHCC97H cells, and DOX@Fe3O4-ZIF-8 presented effective inhibiting effect on cell viability of MHCC97H cells. Cellular uptake assay showed that DOX@Fe3O4-ZIF-8 accumulated in both cytoplasm and nuclei. Moreover, because of valid drug accumulation, DOX@Fe3O4-ZIF-8 exhibited a good inducing effect on cell apoptosis of MHCC97H cells. In conclusion, based on the nontoxic and high drug loading capability of Fe3O4-ZIF-8, DOX@Fe3O4-ZIF-8 presented enhanced effects on HCC cells compared to free DOX, indicating its potential for the chemotherapy of HCC.

Preparation of a magnetic multiwalled carbon nanotube@polydopamine/zeolitic imidazolate framework-8 composite for magnetic solid-phase extraction of triazole fungicides from environmental water samples

A novel magnetic zinc-based zeolitic imidazolate framework (MMP/ZIF-8) has been prepared using a magnetic multiwalled carbon nanotube@polydopamine nanocomposite as the magnetic core and support. It was then used as an adsorbent for magnetic solid-phase extraction of triazole fungicides from environmental water samples. Successful synthesis of MMP/ZIF-8 was confirmed by material characterization, and the results showed that the synthetic composite has a high Brunauer-Emmett-Teller surface area (141.56 m2 g-1), large total pore volume (0.636 mL g-1), and high superparamagnetism with a saturation magnetization of 44.1 emu g-1. To evaluate the extraction performance of MMP/ZIF-8, the main parameters that affect the extraction efficiency were optimized. Under the optimal conditions, the developed method shows good linearity (R 2 ≥ 0.9915) in the concentration range 1-400 μg L-1. Low limits of detection (0.08-0.27 μg L-1, signal/noise = 3 : 1) and good precision (intraday relative standard deviation ≤ 7.73%, interday relative standard deviation ≤ 9.65%) are also achieved. The developed method was applied for analysis of triazole fungicides in environmental water samples.