Layer-by-layer assembled magnetic bimetallic metal-organic framework composite for global phosphopeptide enrichment

A Ti/Nb-functionalized COF material based on IMAC strategy for efficient separation of phosphopeptides and phosphorylated exosomes

In this work, on the basis of an immobilized metal ion affinity chromatography enrichment strategy, a new kind of covalent organic framework (COF) material for enrichment of phosphorylated peptides and exosomes was successfully prepared in a facile method, and Ti⁴⁺ and Nb⁵⁺ were used as dual-functional ions (denoted as COF-S-S-COOH-Ti⁴⁺/Nb⁵⁺). With the advantage of unbiased enrichment towards phosphopeptides, COF-S-S-COOH-Ti⁴⁺/Nb⁵⁺ shows ultra-high selectivity (maximum molar ratio of β-casein: BSA is 1:20,000) and low limit of detection (0.2 fmol). In addition, the material has an excellent phosphopeptide loading capacity (100 μg/mg) and reusability (at least seven times). Furthermore, applying the material to the actual sample, 4 phosphopeptides were selectively extracted from the serum of renal carcinoma patients. At the same time, exosomes with an intact structure in the serum of renal carcinoma patients were successfully isolated rapidly using this strategy. All experiments have shown that COF-S-S-COOH-Ti⁴⁺/Nb⁵⁺ exhibits exciting potential in practical applications.

Preparation of Magnetic Metal-Organic Frameworks@Molecularly Imprinted Nanoparticles for Specific Extraction and Enrichment of Bisphenol A in Food

Metal-organic frameworks (MOFs) with systematically tailored structures have been suggested as promising precursors to the preparation of diverse functional materials. Herein, a facile and versatile layer-by-layer strategy without any special surface modifications has been proposed for the preparation of magnetic metal-organic frameworks (MMOFs) supported molecularly imprinted polymer nanoparticles (MMOFs@MIP), which are based on a magnetically susceptible core conjugated with an imidazole-derived self-assembled layer and a silane-based imprinted shell. The obtained MMOFs@MIPs, which integrated the advantages of Fe₃O₄, MOFs, and MIPs, were characterized and exhibited good magnetic properties, a rapid mass transfer rate, and an excellent adsorption selectivity as well as capacity for the targeted molecular - bisphenol A (BPA). Moreover, the MMOFs@MIPs were employed as adsorbents in magnetic solid phase extraction (MSPE) to selectively bind and rapidly separate BPA from real samples with satisfactory recoveries ranging from 88.3% to 92.3%. More importantly, the desirable reusability of MMOFs@MIP was also evaluated, and the recoveries still maintained above 88.0% even after five re-use cycles. Furthermore, combined with high-performance liquid chromatography (HPLC) analysis, a novel MSPE-HPLC method was developed, enabling the highly selective and sensitive detection of BPA in a wide linear range of 0.5–5000 μg L⁻¹ with a low limit of detection (LOD) of 0.1 μg L⁻¹. This work contributes a promising method for constructing various functional nanoparticles @MOFs@MIP hybrid materials for applications in many different fields.

Ag nanoparticles supported on a magnetic NiFe2O4/MIL-101(Fe) metal–organic framework nanocomposite for the room temperature rapid catalytic reduction of nitrophenols and nitroanilines

A novel Ag@NiFe2O4/MIL101(Fe) ternary magnetic nanocomposite was synthesized for the room temperature rapid catalytic reduction of nitrophenols and nitroanilines.

Removal of adsorption sites on the external surface of mesoporous adsorbent for eliminating the interference of proteins in enrichment of phosphopeptides/nucleotides

Various mesoporous adsorbents are of great promise for enriching small molecules from biological samples based on the size-exclusion effect. At present, the mesoporous adsorbents have adsorption sites distributed uniformly on the internal and external surfaces of mesopores. However, the adsorption sites on the external surface can adsorb proteins, interfering with the enrichment of small molecules. Herein, a novel immobilized-Ti⁴⁺ magnetic mesoporous adsorbent removing the adsorption sites on the external surface was facile prepared via the coupling chemistry of isocyanate with amine and consequent hydrolysis of urea linkage by urease. The adsorbent enables fast and selective enrichment of phosphopeptides and nucleotides from biological samples. In addition, sensitive detection methods for phosphopeptides and nucleotides in human serum are developed by coupling the magnetic solid-phase extraction with matrix-assisted laser desorption/ionization time of flight mass spectrometry and liquid chromatography-mass spectrometer, respectively. Under optimal conditions, response is linear (R² ≥ 0.9923), limits of detection are low (0.41-9.48 ng mL^-1), and reproducibility is acceptable (inter- and intra-day assay RSDs of≤15.0%) for six nucleotides. The developed strategy offers an effective method to eliminate the interference of proteins in the enrichment of small molecules from real biological samples.

Metal-Organic Framework-Derived Hollow and Hierarchical Porous Multivariate Metal-Oxide Microspheres for Efficient Phosphoproteomics Analysis

Pre-enrichment of the biological samples is a crucial step in phosphoproteomics research. At present, metal-oxide affinity chromatography (MOAC) is one of the most recognized enrichment strategy. Therefore, the design and preparation of a MOAC-based affinity material with better enrichment properties will be of great significance for the phosphoproteomics study. In this work, we obtained a novel multivariate metal-oxide microsphere (NiFe₂O₄@C@TiO₂) with a hollow and hierarchical porous structure through pyrolysis of TiO_2-modified Fe/Ni-based metal-organic frameworks (MOFs). After pyrolysis, the carbon matrix derived from the MOFs provided support and porous properties. Meanwhile, multivariate metal oxides endowed the microspheres with an excellent magnetic response property and superior enrichment performance for phosphorylated biomolecules. The unique hollow and hierarchical porous structure greatly enhanced the diffusion of phosphorylated biomolecules. Therefore, the microspheres exhibited excellent enrichment performance for phosphorylated biomolecules: a large adsorption capacity (124 μmol g^-1), excellent selectivity (α-casein/BSA, 1:5000, m/m), perfect size-exclusion performance (α-casein digests/α-casein/BSA, 1:500:500), and extremely low detection limit (2 fmol). Furthermore, the microspheres showed excellent enrichment performance in a series of real biological samples, such as nonfat milk, serum, saliva, rat brain tissue, and plasma exosomes of patients with esophageal cancer, which further demonstrated its huge application potential in MS-based phosphoproteomics research.

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.

A facile "one-material" strategy for tandem enrichment of small extracellular vesicles phosphoproteome

Small extracellular vesicles (SEVs), are cell-derived, membrane-enclosed nanometer-sized vesicles that play vital roles in many biological processes. Recent years, more and more evidences proved that small EVs have close relationship with many diseases such as cancers and Alzheimer's disease. The use of phosphoproteins in SEVs as potential biomarkers is a promising new choice for early diagnosis and prognosis of cancer. However, current techniques for SEVs isolation still facing many challenges, such as highly instrument dependent, time consuming and insufficient purity. Furthermore, complex enrichment procedures and low microgram amounts of proteins available from clinical sources largely limit the throughput and the coveage depth of SEVs phosphoproteome mapping. Here, we synthesized Ti⁴⁺-modified magnetic graphene-oxide composites (GFST) and developed a "one-material" strategy for facile and efficient phosphoproteome enrichment and identification in SEVs from human serum. By taking advantage of chelation and electrostatic interactions between metal ions and phosphate groups, GFST shows excellent performance in both SEVs isolation and phosphopeptide enrichment. Close to 85% recovery is achieved within a few minutes by simple incubation with GFST and magnetic separation. Proteome profiling of the isolated serum SEVs without phosphopeptide enrichment results in 515 proteins, which is approximately one-fold more than those otained by ultracentrifugation or coprecipitation kits. Further application of GFST in one-material-based enrichment led to identification of 859 phosphosites in 530 phosphoproteins. Kinase-substrate correlation analysis reveals enriched substrates of CAMK in serum SEVs phosphoproteome. Therefore, we expect that the low instrument dependency and the limited sample requirement of this new strategy may facilitate clinical investigations in SEV-based transportation of abnormal kinases and substrates for drug target discovery and cancer monitoring.

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.