Controllable Preparation of CuFeMnO4 Nanospheres as a Novel Multifunctional Affinity Probe for Efficient Adsorption and Selective Enrichment of Low-Abundance Peptides and Phosphopeptides

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.

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.

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.

Light, pH, and Temperature Triple-Responsive Magnetic Composites for Highly Efficient Phosphopeptide Enrichment

Smart materials can dynamically and reversibly change their structures and functions in response to external stimuli. In this study, we designed a smart magnetic composite (MNP-pSPA-b-pNIPAm) with a triple response to ultraviolet (UV) light, pH, and temperature. Relying on the response of spiropyranyl acrylate (SPA) and N-isopropylacrylamide (NIPAm) to external stimuli (light, pH, and temperature), MNP-pSPA-b-pNIPAm was used for the controlled capture and release of phosphopeptides. The established phosphopeptide enrichment platform exhibits high sensitivity (detection limit of 0.04 fmol), high selectivity (BSA/β-casein, 1000:1), and good reusability (6 cycles). In addition, the method was also applied to the enrichment of phosphopeptides in real samples (skim milk, human saliva, and serum), demonstrating the feasibility of this method for phosphoproteomic analysis. After enriching from human nonsmall cell lung cancer cell (A549) lysates with MNP-pSPA-b-pNIPAm, 2595 phosphopeptides corresponding to 2281 phosphoproteins were identified. The novel responsive enrichment probe is highly specific for phosphoproteomic analysis and provides an effective method for studying the significance of protein phosphorylation in complex biological samples.

Label-free designed nanomaterials enrichment and separation techniques for phosphoproteomics based on mass spectrometry

The surface chemical characteristics of nanomaterials have a substantial impact on the affinity probe used to enrich proteins and peptides for MALDI-MS analysis of a real human sample. Detecting phosphoproteins involved in signalling is always difficult, even with recent developments in mass spectrometry, because protein phosphorylation is often temporary from complicated mixtures. This review summarizes current research on the successful enrichment of various intriguing glycoproteins and glycol peptides using surface affinity materials with distinctive qualities such as low cost, excellent structural stability, diversity, and multifunction. As a consequence, this review will provide a quick overview of the scholars from various backgrounds who are working in this intriguing interdisciplinary field. Label-free cancer biomarkers and other diseases will benefit from future challenges.

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.

Dendrimer-Modified Silica Nanoparticles for Efficient Enrichment of Low-Concentration Peptides

Peptide profiling based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is of particular interest as it can provide physiologically and pathologically related information of the bio-samples. Due to the complexity of real biological samples, MALDI-TOF MS-based peptide mapping methods rely strongly on particular enrichment methods to improve the signal intensity. This paper introduces third-generation dendrimer-modified SBA-15 with the surface functionalization of amino and carboxyl group, respectively (denoted as SBA-15/G3-NH₂ and SBA-15/G3-COOH), for the efficient capture of low-abundance peptides. The enrichment ability of the nanocomposites was evaluated by standard peptides digests and real biological samples. The synthesized nanocomposites incorporated the benefit of dendrimers and mesoporous silica nanomaterial SBA-15, showing enhanced peptide enrichment ability. Therefore, this work may provide a new class of nanomaterials for peptide mapping from biological samples.

A Comprehensive Updated Review on Magnetic Nanoparticles in Diagnostics

Magnetic nanoparticles (MNPs) have been studied for diagnostic purposes for decades. Their high surface-to-volume ratio, dispersibility, ability to interact with various molecules and superparamagnetic properties are at the core of what makes MNPs so promising. They have been applied in a multitude of areas in medicine, particularly Magnetic Resonance Imaging (MRI). Iron oxide nanoparticles (IONPs) are the most well-accepted based on their excellent superparamagnetic properties and low toxicity. Nevertheless, IONPs are facing many challenges that make their entry into the market difficult. To overcome these challenges, research has focused on developing MNPs with better safety profiles and enhanced magnetic properties. One particularly important strategy includes doping MNPs (particularly IONPs) with other metallic elements, such as cobalt (Co) and manganese (Mn), to reduce the iron (Fe) content released into the body resulting in the creation of multimodal nanoparticles with unique properties. Another approach includes the development of MNPs using other metals besides Fe, that possess great magnetic or other imaging properties. The future of this field seems to be the production of MNPs which can be used as multipurpose platforms that can combine different uses of MRI or different imaging techniques to design more effective and complete diagnostic tests.

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.

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.

Comparative evaluation of MAX-Ti3AlC2 and MXene-Ti3C2 as affinity chromatographic materials for highly selective enrichment of phosphopeptides

MAX and MXene have received considerable attention owing to their outstanding performance in fields like battery and catalysis. However, their possible biomedical applications have rarely been considered, especially the affinity chromatographic applications in proteomics. In this work, considering the large number of exposed metal sites, small binding potential resistance and fast mass transfer speed, layered ternary carbides MAX-Ti₃AlC₂ and MXene-Ti₃C₂ with a two-dimensional nanostructure were successfully explored for the first time as affinity chromatography stationary phases for the specific capture of phosphopeptides from complex biological samples. Helium ion microscopy, transmission electron microscopy, atomic force microscopy, X-ray diffraction spectra, X-ray photoelectron spectroscopy and zeta potential measurement results confirmed that the MXene-Ti₃C₂ was well exfoliated from the pristine MAX-Ti₃AlC₂. Ti₃AlC₂ showed better enrichment specificity than MXene-Ti₃C₂. The detection limit of Ti₃AlC₂ was as low as 5 fmol. Even when the molar ratio of BSA to β-casein tryptic digests increased to 1000 : 1, two characteristic phosphopeptides with a relatively clear background could be detected after enrichment. After five cycles of repeated use, the enrichment specificity of Ti₃AlC₂ still remains. Furthermore, 91 and 830 unique phosphopeptides from 23 and 525 phosphoproteins were identified from milk and BEL7402 cells, respectively. Among them, 27 and 170 phosphopeptides, 12 and 56 phosphoproteins identified from milk and BEL7402 cells were not detected with commercial TiO₂ after three independent replicates, which have great potential in providing complementary coverage of phosphoproteome. This work opens up new applications of Ti₃AlC₂ and MXene-Ti₃C₂, and will play more important role for phosphorylated proteomics in biomedicine.

C18-functionalized magnetic nanocomposites fabricated by one-step aqueous coating of tailored oligopeptides for enrichment of low-abundance peptides

Screening and monitoring endogenous peptides from complicated biosamples is still a major challenge in mass spectrometry-based proteomics research, mainly due to their low concentration and the interference of high-abundance proteins and other contaminants in biological samples. Herein, a facile and novel approach was described for rapid fabrication of C₁₈-functionalized magnetic nanocomposites (C₁₈-MNCs) based on one-step aqueous coating of C₁₈-Val-Lys-Val-Lys-Val-Lys (C₁₈-VK-VI) for the highly selective enrichment of low-abundance endogenous peptides from biological samples. C₁₈-VK-VI can readily self-assemble into complete monolayers mainly composed of β-sheets with C₁₈ hydrophobic chains erecting on the surface of GO@Fe₃O₄ MNCs under the physiological conditions. The resulting C₁₈VK-VI-GO@Fe₃O₄ MNCs exhibited good performance for peptides enrichment from digests of standard protein (myoglobin, MYO) and human serum, such as high sensitivity (0.05 fmol μL^-1) and selectivity (mass ratio of MYO digests and MYO = 1:500), rapid separation, and good reproducibility. Such a simple mild and rapid one-step aqueous coating method on the basis of oligopeptides self-assembly showed great potential in surface functionalization of various nanoadsorbents for proteome/peptidome researches.

Fabrication of magnetic trimetallic metal–organic frameworks for the rapid removal of tetracycline from water

The metal–organic framework (MOF-74) series has the most open metal sites.

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.

In-tube solid-phase microextraction capillary column packed with mesoporous TiO2 nanoparticles for phosphopeptide analysis

In this study, an in-tube solid-phase microextraction column packed with mesoporous TiO₂ nanoparticles, coupled with MALDI-TOF-MS, was applied to the selective enrichment and detection of phosphopeptides in complex biological samples. The mesoporous TiO₂ nanoparticles with high specific surface areas, prepared by a sol-gel and solvothermal method, were injected into the capillary using a slurry packing method with in situ polymerized monolithic segments as frits. Compared with the traditional solid-phase extraction method, the TiO₂ -packed column with an effective length of 1 cm exhibited excellent selectivity (α-casein/β-casein/BSA molar ratio of 1:1:100) and sensitivity (10 fmol of a β-casein enzymatic hydrolysis sample) for the enrichment of phosphopeptides. These performance characteristics make this system suitable for the detection of phosphorylated peptides in practical biosamples, such as nonfat milk.

Immobilization of titanium dioxide/ions on magnetic microspheres for enhanced recognition and extraction of mono- and multi-phosphopeptides

The authors are presenting a novel strategy for global phosphoproteome recognition in practical samples. It integrates metal oxide affinity chromatography (MOAC) and immobilization metal ion affinity chromatography (IMAC). This resulted in a kind of titanium dioxide/ion-based multifunctional probe (dubbed T2M). The T2M combines the features of MOAC and IMAC including their recognition preferences towards mono- and multi-phosphorylated peptides. Hence, they exhibit an outstanding recognition capability towards global phosphoproteome, high sensitivity (the limit of detection of which is merely 10 fmol) and excellent specificity in MALDI-TOF MS detection. Their performance is further demonstrated by the identification of the phosphoproteome in non-fat milk and human saliva. By combining T2M with nano LC-MS/MS, remarkable results are obtained in the tryptic digestion of healthy eye lens and cataract lens phosphoproteomes. A total of 658 and 162 phosphopeptides, respectively, were identified. This indicates that phosphorylation and the appearance of cataract can be related to each other. Graphical abstract Schematic presentation of the preparation of titanium dioxide/ion-based multifunctional magnetic nanomaterials (T2M). The T2M based enrichment protocol exhibits outstanding recognition capability towards global phosphoproteome. This protocol shows great prospect for clarifying mechanism of phosphorylation-related diseases via further information acquisition.

Three-dimensional hierarchical frameworks based on molybdenum disulfide-graphene oxide-supported magnetic nanoparticles for enrichment fluoroquinolone antibiotics in water

Recently, water pollution caused by antibiotics is rapidly increasing. Thus, developing efficient, fast and sensitive detection methods for environmental antibiotics monitoring are still remaining elusive. Herein, a method for antibiotics analysis including lecofloxacin, pazcofloxacin and gatifloxacin in water by high performance liquid chromatography (HPLC) using molybdenum disulfide-graphene oxide-supported magnetic nanoparticles (Fe₃O₄/GO/MoS₂) as the adsorbent of magnetic solid-phase extraction was developed. The as-prepared magnetic Fe₃O₄/GO/MoS₂ nanocomposite exhibited good enrichment capability toward fluoroquinolone antibiotics and the analytes were absorbed within a short time ca. 2 min. The main drive forces of Fe₃O₄/GO/MoS₂ nanocomposite and antibiotics were most likely attributed to hydrogen bonding and electrostatic attraction. A sensitive and effective MSPE-HPLC method was developed with low detection limits (LODs) ranging from 0.25 to 0.50 ng mL^-1. The recoveries obtained from the analysis of water sample were between 85.6% and 106.1% with relative standard deviations (RSDs, n = 5) lower than 9.5%. The developed method has a good potential for the analysis of organic contaminants in water with low cost and high sensitivity. Therefore, this finding is a promising strategy for designing high efficiency and fast antibiotics detection system.

Point-of-Care Testing of Pathogenic Bacteria at the Single-Colony Level via Gas Pressure Readout Using Aptamer-Coated Magnetic CuFe2O4 and Vancomycin-Capped Platinum Nanoparticles

Pressure measurements are performed everyday with simple devices, and in the field of analytical chemistry the pressure-based signaling strategy offers two important advantages, signal amplification and particular applicability in point-of-care settings. Herein, by using vancomycin (Van)-functionalized platinum nanoparticles (PtNPs@Van) and aptamer-coated magnetic CuFe₂O₄ nanoprobes dual-recognition units integrated with a catalyzed breakdown of H₂O₂ for O₂ generation, we demonstrated that gas pressure can be used as a readout means for highly sensitive pathogenic bacteria identification and quantification. Using Staphylococcus aureus ( S. aureus) as a test case, integration of the molecular dual-recognition component with the catalyzed gas-generation reaction leads to a significant pressure change (Δ P), and the correlation between the concentration of S. aureus and the Δ P signal was found to be linear from 5.0 to 1.0 × 10⁴ cfu/mL with a detection limit of 1.0 cfu/mL. Other nontarget bacteria show negative results, verifying the high specificity of the present strategy. When employed to assay S. aureus in saliva and milk samples, the approach shows recoveries from 93.3% to 107.1% with relative standard derivation (RSD) less than 8.8%. By the integration of catalyzed gas-generation reaction with the designed molecular recognition event, obviously the pressure-based signaling strategy could facilitate pathogenic bacteria identification and quantification not only in the laboratory but also in point-of-care settings, which could have great potential in the application of food safety and infectious disease diagnosis.