Epitaxial Growth of Guanidyl-Functionalized Magnetic Metal-Organic Frameworks with Multiaffinity Sites for Selective Capture of Global Phosphopeptides

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.

Multifunctional SERS Substrate for Simultaneous Detection of Multiple Contaminants and Photothermal Removal of Pathogenic Bacteria

In this work, a boric-acid-modified Fe3O4@Au@BA-MOF composite material as a multifunctional SERS substrate was ingeniously constructed for detecting both pathogens and antibiotics as well as photothermally inactivating the pathogens. Through improving the dispersity and stability of gold nanoparticles (Au NPs), leveraging the specificity of boric acid (BA) groups in recognizing cis-diol structures, and the ability of SERS technology to provide unique fingerprint spectra of targets, the sensitive and stable detection of pathogens and antibiotics was achieved. Compared with Au NPs and Fe3O4@Au, the SERS enhancement factor of Fe3O4@Au@BA-MOF was 4.31 × 106, which was about 400 times and 16 times higher than the former two, respectively. Among the existing work, the limit of detection for pathogens was lower or comparable, and it exhibited good stability, maintaining consistent performance for 23 days. Additionally, this substrate achieved efficient photothermal inactivation of pathogens under both near-infrared light and natural light excitation. Within 8 min of near-infrared light irradiation, the bactericidal rates for Staphylococcus aureus and Escherichia coli reach 100% and 99.3%, respectively.

Polyoxometalate functionalized magnetic metal-organic framework with multi-affinity sites for efficient enrichment of phosphopeptides

The reasonable design of metal-organic framework (MOF)-derived nanomaterial has important meaning in increasing the enrichment efficiency in the study of protein phosphorylation. In this work, a polyoxometalate (POM) functionalized magnetic MOF nanomaterial (Fe3O4@MIL-125-POM) was designed and fabricated. The nanomaterial with multi-affinity sites (unsaturated metal sites and metal oxide clusters) was used for the enrichment of phosphopeptides. Fe3O4@MIL-125-POM had high-efficient enrichment performance towards phosphopeptides (selectivity, a mass ratio of bovine serum albumin/α-casein/β-casein at 5000:1:1; sensitivity, 0.1 fmol; satisfactory repeatability, ten times). Furthermore, Fe3O4@MIL-125-POM was employed to enrich phosphopeptides from non-fat milk digests, saliva, serum, and A549 cell lysate. The enrichment results illustrated the great potential of Fe3O4@MIL-125-POM for efficient identification of low-abundance phosphopeptides.

Cobalt Phthalocyanine-Modified Magnetic Metal-Organic Frameworks for Specific Enrichment of Phosphopeptides

For mass spectrometry (MS)-based phosphoproteomics studies, sample pretreatment is an essential step for efficient identification of low-abundance phosphopeptides. Herein, a cobalt phthalocyanine-modified magnetic metal-organic framework (MOF) (Fe3O4@MIL-101-CoPc) was prepared and applied to enrich phosphopeptides before MS analysis. Fe3O4@MIL-101-CoPc exhibited an excellent magnetic response (74.98 emu g-1) and good hydrophilicity (7.75°), which were favorable for the enrichment. Fe3O4@MIL-101-CoPc showed good enrichment performance with high selectivity (1:1:5000), sensitivity (0.1 fmol), reusability (10 circles), and recovery (91.3%). Additionally, the Fe3O4@MIL-101-CoPc-based MS method was able to successfully detect 827 phosphopeptides from the A549 cell lysate, demonstrating a high enrichment efficiency (89.3%). This study promotes the application of postfunctionalized MOFs for phosphoproteomics analysis.

Progress in Core-Shell Magnetic Mesoporous Materials for Enriching Post-Translationally Modified Peptides

Endogenous peptides, particularly those with post-translational modifications, are increasingly being studied as biomarkers for diagnosing various diseases. However, they are weakly ionizable, have a low abundance in biological samples, and may be interfered with by high levels of proteins, peptides, and other macromolecular impurities, resulting in a high limit of detection and insufficient amounts of post-translationally modified peptides in real biological samples to be examined. Therefore, separation and enrichment are necessary before analyzing these biomarkers using mass spectrometry. Mesoporous materials have regular adjustable pores that can eliminate large proteins and impurities, and their large specific surface area can bind more target peptides, but this may result in the partial loss or destruction of target peptides during centrifugal separation. On the other hand, magnetic mesoporous materials can be used to separate the target using an external magnetic field, which improves the separation efficiency and yield. Core-shell magnetic mesoporous materials are widely utilized for peptide separation and enrichment due to their biocompatibility, efficient enrichment capability, and excellent recoverability. This paper provides a review of the latest progress in core-shell magnetic mesoporous materials for enriching glycopeptides and phosphopeptides and compares their enrichment performance with different types of functionalization methods.

Multilayered Fe3O4@(ZIF-8)3 combined with a computer-vision-enhanced immunosensor for chloramphenicol enrichment and detection

The misuse and overuse of chloramphenicol poses severe threats to food safety and human health. In this work, we developed a magnetic solid-phase extraction (MSPE) pretreatment material coated with a multilayered metal-organic framework (MOF), Fe3O4 @ (ZIF-8)3, for the separation and enrichment of chloramphenicol from fish. Furthermore, we designed an artificial-intelligence-enhanced single microsphere immunosensor. The inherent ultra-high porosity of the MOF and the multilayer assembly strategy allowed for efficient chloramphenicol enrichment (4.51 mg/g within 20 min). Notably, Fe3O4 @ (ZIF-8)3 exhibits a 39.20% increase in adsorption capacity compared to Fe3O4 @ZIF-8. Leveraging the remarkable decoding abilities of artificial intelligence, we achieved the highly sensitive detection of chloramphenicol using a straightforward procedure without the need for specialized equipment, obtaining a notably low detection limit of 46.42 pM. Furthermore, the assay was successfully employed to detect chloramphenicol in fish samples with high accuracy. The developed immunosensor offers a robust point-of-care testing tool for safeguarding food safety and public health.

Enrichment of Phosphopeptides Based on Zirconium Phthalocyanine-Modified Magnetic Nanoparticles

Highly selective extraction of phosphopeptides is necessary before mass spectrometry (MS) analysis. Herein, zirconium phthalocyanine-modified magnetic nanoparticles were prepared through a simple method. The Fe-O groups on Fe3O4 and the zirconium ions on phthalocyanine had a strong affinity for phosphopeptides based on immobilized metal ion affinity chromatography (IMAC). The enrichment platform exhibited low detection limit (0.01 fmol), high selectivity (α-/β-casein/bovine serum albumin, 1/1/5000), good reusability (10 circles), and recovery (91.1 ± 1.1%) toward phosphopeptides. Nonfat milk, human serum, saliva, and A549 cell lysate were employed as actual samples to assess the applicability of the enrichment protocol. Metallo-phthalocyanine will be a competitive compound for designing highly efficient adsorbents and offers a new approach to phosphopeptide analysis.

Dual-ligand hydrogen-bonded organic framework: Tailored for mono-phosphopeptides and glycopeptides analysis

Hydrogen-bonded organic frameworks (HOFs) have emerged as a promising class of materials for applications of separation and enrichment. Utilizing multiple-ligands to construct HOFs is a promising avenue towards the development of structurally stable and functionally diverse frameworks, offering opportunities to create customized binding sites for selective recognition of biomolecules. In recent years, due to the crucial role that protein post-translational modifications (PTMs) play in maintaining protein function and regulating signaling pathways, and the growing recognition of the extensive cross-talk that can occur between PTMs, simultaneous analysis of different types of PTMs represents a requirement of a new generation of enrichment materials. Here, for the first attempt, we report a dual-ligand HOF constructed from borate anion and guanidinium cation for the simultaneous identification of glycopeptides and phosphopeptides, especially mono-phosphopeptides. According to theoretical calculations, the HOF functional sites display a synergistic "matching" effect with mono-phosphopeptides, resulting in a stronger enrichment effect for mono-phosphopeptides as compared to multi-phosphopeptides. Also, due to its high hydrophilicity and boronate affinity, this material can efficiently capture glycoproteins. HOF is set to become an active research direction in the development of highly efficient simultaneous protein enrichment materials, and offers a new approach for comprehensive PTMs analysis.

Effective Enrichment of Phosphopeptides Using Magnetic Polyoxometalate-Based Metal-Organic Frameworks

In this study, magnetic polyoxometalate-based metal-organic frameworks (Fe3O4-POMOFs) were designed and applied to the enrichment of phosphopeptides. Thanks to the abundant metal oxide and metal ion sites, the material had a strong affinity for phosphopeptides. Simultaneously, the high amount of amino and guanidyl groups provided hydrophilicity and positive charge for phosphopeptide capture. By coupling with MS detection, the established platform possessed good reusability, high sensitivity (0.01 fmol), and high selectivity (α-casein/β-casein/bovine serum albumin = 1:1:5000). Furthermore, the method was successfully used for the detection of phosphopeptides in nonfat milk, human serum, saliva, and A549 cell lysate, showing great potential for practical application.

Design of reversibly charge-changeable rhodamine B modified magnetic nanoparticles to enrich phosphopeptides

In the present study, by employing ethylenediaminetetraacetic acid (EDTA), tetraethylene pentaamine (TEPA), and rhodamine B (Rb), we designed and synthesized a magnetic adsorbent (Fe₃O₄@EDTA@TEPA@Rb) on the basis of reversible charge change of Rb and applied to capture phosphopeptides. Rb existing in open planarized zwitterion form when stimulated by acidic loading buffer adsorbs negative phosphopeptides via electrostatic interaction. Under the stimulation of alkalic eluent, ring-closed structure of Rb is formed to elute the enriched phosphopeptides. TEPA containing rich amino groups is used as a crosslinking agent, which is also protonated in acidic loading buffer to bond phosphopeptides. Then phosphopeptides are eluted when TEPA deprotonates in alkalic eluent. Coupled with matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) detection, phosphopeptide signals originated from 0.4 fmol/μL β-casein digests were successfully detected. In addition, Fe₃O₄@EDTA@TEPA@Rb can also efficiently enrich phosphopeptides from skimmed milk, human serum and saliva samples (26, 4, 39 phosphopeptides, respectively), opening a new gallery for phosphopeptides-related analysis. In general, the developed adsorbent has the great potential for further application in the near future.

Construction of hierarchically porous metal-organic framework HP-UiO-66-30% for sensitive determination of benzoylurea insecticides

Due to widespread application of benzoylurea insecticides (BUs) and its persistence in environment, the effective capture of benzoylurea insecticides residues in environment is an important issue of environmental safety monitoring. To obtain excellent adsorption performance, creating defective structure in metal-organic frameworks (MOFs) can be employed as the method for adjusting its properties. Zirconium(Ⅳ)-based MOF termed as UiO-66-30% was constructed with 2-aminoterephthalic acid (NH₂-BDC) and terephthalic acid (H₂BDC) as building blocks. After calcination and removal of thermal-sensitive ligand (NH₂-BDC), hierarchically porous UiO-66-30% (HP-UiO-66-30%) with multistage pore structure and good stability was obtained. The unique structure of HP-UiO-66-30% endowed it to achieve instantaneous equilibrium (within 2 min) when it was used as a dispersed solid phase extraction (d-SPE) adsorbent to extract BUs from environmental samples, greatly reducing the operation time. A wide linear range (0.05-200 ng mL^-1), good linearity (R² ≥ 0.9980), low detection limits (0.01-0.03 ng mL^-1) and quantification limits (0.05-0.1 ng mL^-1) were obtained for BUs. In addition, the HP-UiO-66-30% material possessed the good reusability and the adsorption capacity did not change significantly over 16 adsorption-desorption cycles. Finally, the established dispersed solid phase extraction-high performance liquid chromatography-diode array detector (d-SPE-HPLC-DAD) method was successfully applied to determination of BUs residues in environmental soil samples. The results demonstrated that HP-UiO-66-30% was an excellent sorbent for extraction BUs from environmental samples.

An alkali-resistant zirconium-biligand organic framework with dual-metal centers for highly selective capture of phosphopeptides

The stability of MOFs plays one of the most important roles in material applications, while the delicate structure of MOFs suffers from the limitation of poor alkali tolerance. A new biligand Zr-MOF (biUIO-66-NH₂NO₂) with alkali-resistance performance and active functional groups has been synthesized in this study. The biUIO-66-NH₂NO₂ demonstrated a much better stability in 1% NH₃·H₂O solution than its parent material, UIO-66-NH₂. Following further immobilization of Zr⁴⁺ ions, the biDZMOF consisting of dual-zirconium centers was prepared and was further applied in global enrichment of phosphopeptides by avoiding the instability of enrichment materials in the essential alkali elution procedure for the phosphopeptide enrichment workflow. The alkali-resistant elution of phosphopeptides from the biDZMOF can be directly coupled to a tandem mass spectrometry system for peptide analysis without desalting treatment. 425 phosphopeptides in total in 3 independent samples were identified from 10 μL human saliva after enrichment with biDZMOF. The improvement in alkali resistance and successful post-modification of biUIO-66-NH₂NO₂ suggest an efficient strategy to develop new types of MOF materials for application.