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.

Membrane-protected magnetic covalent organic framework for efficient extraction of estrogens in dairy products

The presence of estrogens residues in dairy products is a growing concern due to their potential health risk. Herein, in this study, we have developed a membrane-protected magnetic solid-phase extraction (MP-MSPE) method that utilized a magnetic adsorbent (Fe3O4@COF-LZU1) with in-situ growth for the efficient extraction of estrone (E1), 17β-estradiol (E2), and estriol (E3). When combined with HPLC-FLD, this method allows for the efficient detection of estrogens in dairy products. The stability of the MP-MSPE was improved by the presence of a dialysis membrane, which remained a high extraction efficiency (90 %) even after ten reuse cycles. The hydrogen bonding, π-π interactions and pore size effect contribute to the excellent adsorption of three estrogens onto Fe3O4@COF-LZU1. Under optimal conditions, the method exhibits a low detection limit (0.01-0.15 μg L-1), wide linear range (0.1-800 μg L-1), and favorable recoveries (77.3 %-109.4 %) at three concentration levels (10, 50 and 100 μg L-1). This proposed method is characterized by its simplicity, high efficiency and eco-friendliness, making it a promising approach for extracting estrogens from dairy products.

Fiber optic cadmium ion sensors based on functionalization of a magnetic ion-imprinted polymer

Cadmium poisoning is a chronic accumulation process, and long-term drinking of even low cadmium content water will cause kidney damage, so an ultra-low detection limit is particularly important. However, at the present stage, the traditional detection method cannot reach a sufficiently low detection limit, the response time is too long, and the cost of detection is very high, so that real-time measurement cannot be realized. Therefore, the traditional cadmium ion detection method has a slow response and an insufficient detection limit. This paper presents a fiber optic cadmium ion sensor functionalized based on an Fe3O4@SiO2@CS magnetic ion imprinting polymer (M-IIP). The sensor is based on the coupling characteristics of the optical microfiber coupler (OMC) cone region to achieve a highly sensitive response to the change in the cadmium ion concentration. M-IIP materials were prepared by surface imprinting polymerization to achieve low cross-sensitivity and thus improve the detection limit of the sensor. The results show that the developed fiber sensor has high specificity and a rapid response to cadmium ions. The experimental limit of detection (LOD) reached 0.051 nM within 0-1 μM with a response time of less than 50 s. Moreover, the proposed fiber cadmium ion sensor exhibits excellent performance in terms of sensitivity, stability, repeatability and biocompatibility.

Preparation of high-efficiency titanium ion immobilized magnetic graphite nitride nanocomposite for phosphopeptide enrichment

BACKGROUND

Protein phosphorylation has been implicated in life processes including molecular interaction, protein structure transformation, and malignant disease. An in-depth study of protein phosphorylation may provide vital information for the discovery of early biomarkers. Mass spectrometry (MS)-based techniques have become an important method for phosphopeptide identification. Nevertheless, direct detection remains challenging because of the low ionization efficiency of phosphopeptides and serious interference from non-phosphopeptides. There is a great need for an efficient enrichment strategy to analyze protein phosphorylation prior to MS analysis.

RESULTS

In this study, a novel nanocomposite was prepared by introducing titanium ions into two-dimensional magnetic graphite nitride. The nanocomposite was combined with immobilized metal ion affinity chromatography (IMAC) and anion-exchange chromatography mechanisms for phosphoproteome research. The nanocomposite had the advantages of a large specific surface (412.9 m2 g-1), positive electricity (175.44 mV), and excellent magnetic property (35.7 emu g-1). Moreover, it presented satisfactory selectivity (α-casein:β-casein:bovine serum albumin = 1:1:5000), a low detection limit (0.02 fmol), great recyclability (10 cycles), and high recovery (92.8%). The nanocomposite demonstrated great practicability for phosphopeptides from non-fat milk, human serum, and saliva. Further, the nanocomposite was applied to enrich phosphopeptides from a more complicated specimen, A549 cell lysate. A total of 890 phosphopeptides mapping to 564 phosphoproteins were successfully detected with nano LC-MS.

SIGNIFICANCE

We successfully designed and developed an efficient analysis platform for phosphopeptides, which includes protein digestion, phosphopeptide enrichment, and MS detection. The MS-based enrichment platform was further used to analyze phosphopeptides from complicated bio-samples. This work paves the way for the design and preparation of graphite nitride-based IMAC materials for phosphoproteome 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.

Post-synthesis of a titanium-rich magnetic COF nanocomposite with flexible branched polymers for efficient enrichment of phosphopeptides from human saliva and serum

A Ti4+-functionalized magnetic covalent organic framework material with flexible branched polymers (mCOF@ε-PL@THBA-Ti4+) built via an immobilized metal ion affinity chromatography (IMAC) enrichment strategy was proposed through post-synthesis modification. Hydrophilic ε-poly-L-lysine (ε-PL) rich in amino active groups was first introduced in the fabrication of the phosphopeptide enrichment material to increase the hydrophilicity while providing more functional modification pathways of the material. 2,3,4-Trihydroxy-benzaldehyde (THBA) provides abundant binding sites for the immobilization of numerous Ti4+, which is advantageous for the subsequent efficient phosphopeptide enrichment. The magnetic nanocomposite exhibited outstanding performance of phosphopeptide enrichment with good selectivity (1 : 5000), a low detection limit (2 fmol), and relatively high loading capacity (66.7 mg g-1). What's more, after treatment with mCOF@ε-PL@THBA-Ti4+, 16 endogenous phosphopeptides from fresh saliva of healthy people were recognized by MALDI-TOF MS, and 50 phosphopeptides belonging to 35 phosphoproteins from the serum of uremia patients were detected by nano-LC-MS/MS. Proteomics data analysis for the differential protein selection between uremia and normal controls was conducted using R software, and four down-regulated and three up-regulated proteins were obtained. The results suggested that the prepared material has potential applications in biomarker discovery.

Effective extraction of the metabolites of toluene and xylene based on a postsynthetic-modified magnetic covalent organic polymer

Toluene and xylene are volatile organic compounds, and long-term exposure to toluene and xylene may cause brain structure and nervous system damage. To evaluate exposure to toluene and xylene in the environment, it is usually possible to monitor their metabolites in organisms, hippuric acid (HA) and methylhippuric acid (MHA). In this work, we designed a new magnetic solid phase extraction (MSPE) sorbent, zirconium postsynthetic-modified magnetic covalent organic polymer (Fe₃O₄@COP-COOZr), for purifying and enriching HA and 4-MHA. Zirconium ions were immobilized on the magnetic COP surface by postsynthetic modification without the use of additional coating layers or chelating ligands. The developed Fe₃O₄@COP-COOZr interacted with HA and 4-MHA through the π-π stacking effect and electrostatic interactions, as well as strong chelation with coordinatively unsaturated zirconium sites. The promising affinity material of Fe₃O₄@COP-COOZr in MSPE had high stability and recyclability. The established MSPE-HPLC-UV method showed low sorbent consumption (10 mg) and high sensitivity (LODs less than 0.1 μg L^-1), and can be used for the analysis of HA and 4-MHA in real samples. The recoveries of the proposed method in real urine samples for the simultaneous determination of HA and 4-MHA were in the range of 83.5-103.2 %, and the RSDs were 0.9-7.1 %.

Rational design, structure properties, and synthesis strategies of dual-pore covalent organic frameworks (COFs) for potent applications: A review

Dual-pore covalent organic frameworks (COFs) offer a molecular scaffold for introducing building blocks into periodically organized polygonal skeletons to produce fascinating structural features. The rapid development of this material has attracted intensive interest from researchers with diverse expertise. This review selects the leading scientific findings about dual-pore COFs and highlights their functions and perspectives on design, structure properties, and synthesis strategies. Dual-pore COFs, as newly hetero-pore COFs by integrating particular pores into one polygonal skeleton, have been compared to conventional COFs. Dual-pore COFs display hierarchical/heterogeneous porosities and homogeneous porosity, which endow them with exceptional features involving mass diffusion, charge transfer, and large surface area with abundant active sites. Additionally, the strategic dual-pore design by opting for different approaches, such as integration of [D_2h + C₂] symmetries, kagome-type lattices, and other symmetric arrangements of monomers, are inclusively discussed. Identification and construction of dual-pores in COFs via optimal synthetic methods, such as desymmetrization, multiple linking sites, and orthogonal reactions, are highlighted as the primary pore engineering routes to simultaneously regulate the growth and alter the characteristics of COFs for promising applications. Lastly, a focused discussion on various challenges and critical fundamentals of dual-pore engineering is successfully outlined, with potential prospects of introducing dual-pore in COFs.

Magnetic Nanoparticles for Protein Separation and Purification

Proteins are essential for various functions such as brain activity and muscle contraction in humans. Even though food is a source of proteins, the bioavailability of proteins in most foods is usually limited due to matrix interaction with other biomolecules. Thus, it is essential to extract these proteins and provide them as a nutraceutical supplement to maintain protein levels and avoid protein deficiency. Hence, protein purification and extraction from natural sources are highly significant in biomedical applications. Chromatography, crude mechanical disruption, use of extractive chemicals, and electrophoresis are some of the methods applied to isolate specific proteins. Even though these methods possess several advantages, they are unable to extract specific proteins with high purity. A suitable alternative is the use of nanoparticles, which can be beneficial in protein purification and extraction. Notably, magnetic iron and iron-based nanoparticles have been employed in protein extraction processes and can be reused via demagnetization due to their magnetic property, smaller size, morphology, high surface-to-volume ratio, and surface charge-mediated property. This chapter is a summary of various magnetic nanoparticles (MNPs) that can be used for the biomolecular separation of proteins.

Advances in proteomics sample preparation and enrichment for phosphorylation and glycosylation analysis

As the common and significant chemical modifications, post-translational modifications (PTMs) play a key role in the functional proteome. Affected by the signal interference, low concentration, and insufficient ionization efficiency of impurities, the direct detection of PTMs by mass spectrometry (MS) still faces many challenges. Therefore, sample preparation and enrichment are an indispensable link before MS analysis of PTMs in proteomics. The rapid development of functionalized materials with diverse morphologies and compositions provides an avenue for sample preparation and enrichment for PTMs analysis. In this review, we summarize recent advances in the application of novel functionalized materials in sample preparation for phosphoproteomes and glycoproteomes analysis. In addition, this review specifically discusses the design and preparation of functionalized materials based on different enrichment mechanisms, and proposes research directions and potential challenges for proteomic PTMs research.

Recent Advances in the Application of Covalent Organic Frameworks in Extraction: A Review

Covalent organic frameworks (COFs) are a class of emerging materials that are synthesized based on the covalent bonds between different building blocks. COFs possess unique attributes in terms of high porosity, tunable structure, ordered channels, easy modification, large surface area, and great physical and chemical stability. Due to these features, COFs have been extensively applied as adsorbents in various extraction modes. Enhanced extraction performance could be reached with modified COFs, where COFs are presented as composites with other materials including nanomaterials, carbon and its derivatives, silica, metal-organic frameworks, molecularly imprinted polymers, etc. This review article describes the recent advances, developments, and applications of COF-based materials being utilized as adsorbents in the extraction methods. The COFs, their properties, their synthesis approaches as well as their composite structures are reviewed. Most importantly, suggested mechanisms for the extraction of analyte(s) by COF-based materials are also discussed. Finally, the current challenges and future prospects of COF-based materials in extraction methods are summarized and considered in order to provide more insights into this field.

Facile synthesis of Ti4+-immobilized magnetic covalent organic frameworks for enhanced phosphopeptide enrichment

In this work, core-shell structured Ti⁴⁺-immobilized magnetic covalent organic frameworks (denoted as Fe₃O₄@TAPTDHTA-Ti⁴⁺ composites) were prepared for enhanced phosphopeptide enrichment by one-pot synthesis of COFs shell with inherent bifunctional groups on Fe₃O₄ NPs and further Ti⁴⁺ immobilization. The widely distributed bifunctional groups could provide abundant chelating sites for Ti⁴⁺ immobilizing. Combining with the high specific surface area and mesoporous structure, the Fe₃O₄@TAPTDHTA-Ti⁴⁺ composites exhibited excellent enrichment efficiency for phosphopeptides, such as low detection limit (0.05 fmol μL^-1), high selectivity (1:5000 of molar ratio of β-casein/bovine serum albumin (BSA) tryptic digests), high adsorption capacity (62.9 μg mg^-1) and strong size-exclusive effect (1:250:250 of molar ratio of β-casein tryptic digest/β-casein/BSA). In addition, this method was general for immobilizing other metal ions (Zr⁴⁺ and Fe³⁺). Notably, the Fe₃O₄@TAPTDHTA-Fe³⁺ composites exhibited controllable affinity towards mono-phosphopeptides and multi-phosphopeptides. Furthermore, the Fe₃O₄@TAPTDHTA-Ti⁴⁺ composites were successfully applied to selectively capture phosphopeptides from complex biological samples including the tryptic digest of nonfat milk, human serum and human saliva. More significantly, 3333 phosphopeptides derived from 1409 phosphoproteins with 3492 phosphorylation sites were clearly identified from the tryptic digest of HeLa cell lysate. In addition to providing a potential excellent enrichment probe for comprehensive phosphoproteomic analysis, this study also offers a new perspective for the functionalization of COFs.

A new Ti-based IMAC nanohybrid with high hydrophilicity and enhanced absorption capacity for the selective enrichment of phosphopeptides

Ti-based immobilized metal affinity chromatography (IMAC) nanomaterial has shown high potential in phosphoproteome mass-spectrometric (MS) analysis. However, the limited surface area and poor solubility will greatly restrict its use in phosphoproteome research. To overcome these two key drawbacks, a novel Ti-based IMAC nanomaterial was prepared by Ti-bonded β-cyclodextrin (β-CD) anchored on the surface of carbon nanotubes (CNTs) (denoted as COOH-CNTs-CD-Ti) and successfully applied as a biofunctional adsorbent for selectively enriching trace phosphopeptides. In the selective enrichment process, CNTs provided greater surface area for the absorption of phosphopeptides, while β-CD also offered a greater opportunity for the interaction between phosphopeptides and Ti⁴⁺. COOH-CNTs-CD-Ti with the aforementioned properities exhibited higher selectivity for phosphopeptides from the standard protein digests, the tryptic digests of nonfat milk and human serum, showing a great selective enrichment capability towards complex biological samples.

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.

Facile fabrication of magnetic covalent organic frameworks for magnetic solid-phase extraction of diclofenac sodium in milk

A robust magnetic solid-phase extraction (MSPE) method based on magnetic covalent organic framework (MCOF) coupled with high-performance liquid chromatography (HPLC)-ultraviolet (UV)/mass spectrometry (MS) was proposed for the determination of trace diclofenac sodium (DS) in milk. The prepared MCOF exhibited high extraction efficiency, which can be attributed to its high specific surface area as well as strong π-π and hydrophobic interactions between MCOF and DS. In addition, the potential influencing factors, including sample volume, adsorbent dosage, extraction time, and elution parameters, were fully estimated. The experimental results demonstrated that the established method was sensitive for the quantification of DS with high accuracy. Remarkably, the detection limit of DS was found to be 10 ng/kg under the optimal conditions. More impressively, the developed method was successfully applied to monitor trace DS in milk, demonstrating its outstanding durability and practical potential as an appealing method to regular monitor trace pharmaceutical contaminants in real food samples.

Targeted immobilization of titanium (IV) on magnetic mesoporous nanomaterials derived from metal-organic frameworks for high-efficiency phosphopeptide enrichment in biological samples

A selectively modified porous metal/carbon nanocomposite was fabricated to enhance the enrichment of low-abundance phosphopeptides from biological samples. The carbon matrix derived from the metal-organic framework provides a suitable pore size to allow the diffusion of peptides, while the deliberately modified metal nanoparticles within the pores enhance their interaction with the phosphopeptides. This nanocomposite shows extremely high enrichment selectivity for phosphopeptides in the MALDI-TOF MS detection, even when the molar ratio of α-casein digests versus bovine serum albumin digests was up to about 1:20,000. By combining such nanocomposite with nano-LC-MS/MS, 4556 unique phosphopeptides were identified with high selectivity (95.2%) from HeLa cell extracts. Furthermore, phosphopeptides from prostate tissue digests were also determined. A total of 277 and 1242 phosphopeptides were identified from normal and tumor tissues of a patient with prostate cancer, respectively. This indicates that phosphorylation and prostate cancer can be related to each other.