Facile synthesis of Fe3O4@PDA core-shell microspheres functionalized with various metal ions: A systematic comparison of commonly-used metal ions for IMAC enrichment

Preparation and characterization of a biomimetic honeycomb cross-linked chitosan membrane and its application in the serum of gastric cancer patients

Chitosan, as a biological macromolecule with excellent biocompatibility, has great potential for application in immobilized metal affinity chromatography (IMAC) strategies. In-depth analysis of low-abundance phosphopeptides in organisms can help reveal the pathological mechanisms of diseases. Here, we developed an IMAC material based on a biomimetic honeycomb chitosan membrane. The material demonstrates excellent biocompatibility, good hydrophilicity, and strong metal chelating capacity, which collectively confer outstanding enrichment properties. The material has high sensitivity (0.05 fmol), great selectivity (1:2000), excellent cycling stability (at least 10 cycles) and acid-base stability. In addition, the material was employed in human serum, successfully enriching 129 phosphopeptides from the serum of gastric cancer patients and 146 phosphopeptides from healthy controls. Sequence logo suggests a potential association between gastric cancer and glutamine. Ultimately, an in-depth gene ontology analysis was carried out on the phosphopeptides that were enriched in the serum samples. Compared to normal controls, our results demonstrated dysregulated expression of biological process, cellular component, and molecular function in gastric cancer patients. This suggests that the disease involves, such as blood coagulation pathways, cholesterol metabolism, and heparin binding. All experimental outcomes converge to demonstrate the substantial promise of the material for applications within proteomics research.

Advanced functional materials as reliable tools for capturing food-derived peptides to optimize the peptidomics pre-treatment enrichment workflow

Peptidomics strategies with high throughput, sensitivity, and reproducibility are key tools for comprehensively analyzing peptide composition and potential functional activities in foods. Nevertheless, complex signal interference, limited ionization efficiency, and low abundance have impeded food-derived peptides' progress in food detection and analysis. As a result, novel functional materials have been born at the right moment that could eliminate interference and perform efficient enrichment. Of note, few studies have focused on developing peptide enrichment materials for food sample analysis. This work summarizes the development of endogenous peptide, phosphopeptide, and glycopeptide enrichment utilizing materials that have been employed extensively recently: organic framework materials, carbon-based nanomaterials, bio-based materials, magnetic materials, and molecularly imprinted polymers. It focuses on the limitations, potential solutions, and future prospects for application in food peptidomics of various advanced functional materials. The size-exclusion effect of adjustable aperture and the modification of magnetic material enhanced the sensitivity and selectivity of endogenous peptide enrichment and aided in streamlining the enrichment process and cutting down on enrichment time. Not only that, the immobilization of metal ions such as Ti4+ and Nb5+ enhanced the capture of phosphopeptides, and the introduction of hydrophilic groups such as arginine, L-cysteine, and glutathione into bio-based materials effectively optimized the hydrophilic enrichment of glycopeptides. Although a portion of the carefully constructed functional materials currently only exhibit promising applications in the field of peptide enrichment for analytical chemistry, there is reason to believe that they will further advance the field of food peptidomics through improved pre-treatment steps.

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.

Designed Directional Growth of Ti-Metal-Organic Frameworks for Decoding Alzheimer's Disease-Specific Exosome Metabolites

Exosomes, a growing focus for liquid biopsies, contain diverse molecular cargos. In particular, exosome metabolites with valuable information have exhibited great potential for improving the efficiency of liquid biopsies for addressing complex medical conditions. In this work, we design the directional growth of Ti-metal-organic frameworks on polar-functionalized magnetic particles. This design facilitates the rapid synergistic capture of exosomes with the assistance of an external magnetic field and additionally synergistically enhances the ionization of their metabolites during mass spectrometry detection. Benefiting from this dual synergistic effect, we identified three high-performance exosome metabolites through the differential comparison of a large number of serum samples from individuals with Alzheimer's disease (AD) and normal cognition. Notably, the accuracy of AD identification ranges from 93.18 to 100% using a single exosome metabolite and reaches a flawless 100% with three metabolites. These findings emphasize the transformative potential of this work to enhance the precision and reliability of AD diagnosis, ushering in a new era of improved diagnostic accuracy.

Facile preparation of porphyrin-based porous organic polymers for specific enrichment and isolation of phosphopeptides and phosphorylated exosomes

Exosomes, which can be used to investigate various disease processes, are novel disease markers that have been extensively studied in recent years. In this work, zirconium-rich porphyrin-based porous organic polymers (Imi-Pops-Zr) were synthesized by a facile and low-cost strategy for specific enrichment and isolation of phosphorylated peptides and exosomes. The proposed material demonstrates a low detection limit (0.5 fmol), a high selectivity (bovine serum albumin (BSA): β-casein = 1000:1), and a loading capability of 100 mg/g for phosphopeptides. For complex practical samples, after enrichment with Imi-Pops-Zr, 4 characteristic phosphopeptides from human serum, 20 and 12 phosphopeptides from human saliva and defatted milk were detected, respectively. Besides, 74 phosphorylated peptides with 67 phosphorylation sites belonging to 61 phosphoproteins and 67 phosphorylated peptides with 63 phosphorylation sites belonging to 65 phosphoproteins were detected from the serum of normal controls and uremic patients, respectively. Biological processes, cellular components and molecular functions revealed that interleukin-6, tumor necrosis factor, high density lipoprotein and proteases binding may be associated with uremia. Furthermore, Imi-Pops-Zr was successfully used to enrich and isolate exosomes from human serum. The experimental results show that Imi-Pops-Zr has promising application in the specific enrichment of phosphorylated peptides and exosomes in complex bio-samples.

Recent advances in development of functional magnetic adsorbents for selective separation of proteins/peptides

Nowadays, proteins separation has attracted great attention in proteomics research. Because the proteins separation is helpful for making an early diagnosis of many diseases. Magnetic nanoparticles are an interesting and useful functional material, and have attracted extensive research interest during the past decades. Because of the excellent properties such as easy surface functionalization, tunable biocompatibility, high saturation magnetization etc, magnetic microspheres have been widely used in isolation of proteins/peptides. Notably, with the rapid development of surface decoration strategies, more and more functional magnetic adsorbents have been designed and fabricated to meet the growing demands of biological separation. In this review, we have collected recent information about magnetic adsorbents applications in selective separation of proteins/peptides. Furthermore, we present a comprehensive prospects and challenges in the field of protein separation relying on magnetic nanoparticles.

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.

Magnetic mesoporous silica nanoparticles modified by phosphonate functionalized ionic liquid for selective enrichment of phosphopeptides

In this study, new magnetic nanoparticles (denotated as Fe3O4@mSiO2-PFIL-Ti4+) have been prepared by immobilizing titanium ions with phosphonate functionalized ionic liquid (PFIL) on the wall of core-shell structured mesoporous nanomaterials. The resulting nanoparticles possess large specific surface area, strong hydrophilicity and fast magnetic response. The composites can capture traces of phosphopeptides from the tryptic β-casein digest (0.08 fmol), a digest mixture of β-casein and BSA (1 : 10 000, molar ratio) as well as a blend of β-casein digest and a great quantity of phosphorylated protein (β-casein) and non-phosphorylated protein (BSA) (1 : 2000 : 2000, mass ratio), respectively, showing excellent sensitivity, selectivity and size exclusion ability. Additionally, Fe3O4@mSiO2-PFIL-Ti4+ shows excellent steadiness and can be reused at least 12 times. Moreover, this material was successfully applied to enrich endogenous phosphopeptides from complex bio-samples, including human saliva and serum.

Tractable Method for Rapid Quality Assessment of Therapeutic Antibodies in Harvested Cell Culture Fluid based on FcγRIIIa-Immobilized Magnetic Microspheres

FcγRIIIa-binding affinity is one of the key factors to ensure the efficacy of many antitumor therapeutic antibodies, which should be monitored along with the titer, protein aggregation, and other critical quality attributes. The conventional workflow for the quality assessment of therapeutic antibodies in harvested cell culture fluid (HCCF) is time-consuming and costly nevertheless. In this study, a tractable method was established for rapid quality assessment of a HCCF sample through differentially extracting IgG with different FcγRIIIa affinity levels using FcγRIIIa-immobilized magnetic microspheres, followed by size exclusion chromatography (SEC) to determine the amount and monomer percentage of IgGs in the preceding eluate. FcγRIIIa-immobilized magnetic microspheres with polydopamine (PDA) and hydrophilic dendrimer (PAMAM) coating (denoted as Fe₃O₄@PDA@PAMAM-FcγRIIIa) were synthesized for the first time as magnetic adsorbents. The PDA cladding endowed the composites with good chemical stability in acidic elution buffer, and the PAMAM dendrimer empowered the composites of high ligand immobilization capacity and hydrophilic surface. The labile FcγRIIIa was immobilized under mild conditions. By directly applying a simple magnetic solid phase extraction procedure to treat HCCF, favored IgG species with high FcγRIIIa affinity would be selectively captured by Fe₃O₄@PDA@PAMAM-FcγRIIIa composites for subsequent SEC analysis. The monomer peak area value in SEC, which was set as the read-out of the proposed method, correlated directly with the theoretical overall quality of standard-spiked HCCF samples.

Fe3O4@PDA@PEI Core-Shell Microspheres as a Novel Magnetic Sorbent for the Rapid and Broad-Spectrum Separation of Bacteria in Liquid Phase

Bacterial infection is a significant cause of morbidity and mortality to humans worldwide. Thus, a method for nonspecific, sensitive, and rapid enrichment of such bacteria is essential for bacteria detection and treatment. This study demonstrates a self-made core-shell Fe3O4@Polydopamine@Polyethyleneimine magnetic beads (Fe3O4@PDA@PEI MBs) with a high density positive charge-based magnetic separation scheme for the broad-spectrum rapid enrichment of microorganisms in the liquid phase. MBs with a high-density positive charge have a strong electrostatic attraction to most microorganisms in nature. Our scheme is as follows: (1) wrapping dopamine (DA) on the iron oxide through self-polymerization and wrapping PEI on the outermost shell layer in a mode of crosslinking with the PDA; (2) subsequently, the Fe3O4@PDA@PEI MBs were used to concentrate microorganisms from the sample solution; (3) performing magnetic separation and calculating the adsorption efficiency. The as-prepared Fe3O4@PDA@PEI MBs composite was carefully characterized by zeta potential analysis, Value stream-mapping (VSM), transmission electron microscopy (TEM), and Fourier transforms infrared spectrometry (FT-IR). In this study, both gram-positive and gram-negative bacteria could be captured in three minutes through electrostatic interaction. Furthermore, the adsorption efficiency on gram-negative (>98%) is higher than that on gram-positive (>95%), allowing for a simple, rapid assay to enrich organisms in resource-limited settings.

An eco-friendly, low-cost, and automated strategy for phosphoproteome profiling

An automated, online analysis platform using a reusable phos-trap column helps reduce organic solvent, plastic consumables, waste, and labor costs in phosphoproteomic studies.

TiO2-modified fibrous core-shell mesoporous material to selectively enrich endogenous phosphopeptides with proteins exclusion prior to CE-MS analysis

As an important post-translational modification of proteins, phosphorylation plays a key role in regulating a variety of complicated biological reactions. Owing to the fact that phosphopeptides are low abundant and the ionization efficiency could be suppressed in mass spectroscopic detection, highly efficient and selective enrichment methods are essential to identify protein phosphorylation by mass spectrometry. Here, we develop novel titanium oxide coated core shell mesoporous silica (CSMS@TiO₂) nanocomposites for enrichment of phosphopeptides with simultaneous exclusion of massive proteins. The CSMS@TiO₂ nanocomposites have essential features, including uniform 1.0 μm diameter, 120 nm thick shell, 7.0 nm mesopores perpendicular to the surface, large surface area of 77 m²/g and pore volume of 0.15 cm³/g, therefore can greatly improve the sensitivity for identifying phosphopeptides by capillary electrophoresis-mass spectrometry. The proposed CSMS@TiO₂ nanocomposites are applied for analysis of β-casein tryptic digest and bovine serum albumin (BSA) protein mixture, respectively. The results show that the number of phosphopeptides detected is tremendously increased by using CSMS@TiO₂ nanocomposite, proving selectively enriching phosphopeptides due to the size-exclusive and specific interaction of the TiO₂-modified mesopores. The enrichment of the phosphopeptides is achieved even for the digests at very low concentration of β-casein (1 fmol/μL). This research would open up a promising idea to utilize mesoporous materials in peptidomics analysis.

Titanium dioxide-functionalized dendritic mesoporous silica nanoparticles for highly selective isolation of phosphoproteins

Selective isolation of phosphoproteins is of great significance in biological applications. Herein, titanium dioxide-functionalized dendritic mesoporous silica nanoparticles are prepared via a post-grafting method for selective capture of phosphoproteins. The fabricated nanoparticles possess a unique central-radial pore structure with a surface area of 666.66 m² /g and a pore size of 22.2 nm. The high-binding affinity of TiO₂ with the phosphate groups facilitates the selective adsorption of phosphoproteins. Moreover, the open central-radial pore structure endows the dendritic mesoporous nanoparticles with better adsorption performance toward phosphoproteins with respect to the commercial titanium dioxide nanoparticles and titanium dioxide-functionalized conventional mesoporous silica nanoparticles by providing more accessible affinity sites. At pH 2, an adsorption capacity of 157.2 mg/g is derived for β-casein. The feasibility of the as-prepared dendritic material in real biological sample assay is demonstrated by the selective isolation of phosphoproteins from defatted milk, as illustrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis assay.

Magnetic-Propelled Janus Yeast Cell Robots Functionalized with Metal-Organic Frameworks for Mycotoxin Decontamination

Cell robots that transform natural cells into active platforms hold great potential to enrich the biomedical prospects of artificial microrobots. Here, we present Janus yeast cell microrobots (JYC-robots) prepared by asymmetrically coating Fe₃O₄ nanoparticles (NPs) and subsequent in situ growth of zeolitic imidazolate framework-67 (ZIF-67) on the surface of yeast cells. The magnetic actuation relies on the Fe₃O₄ NPs wrapping. As the compositions of cell robots, the cell wall with abundant polysaccharide coupling with porous and oxidative ZIF-67 can concurrently remove mycotoxin (e.g., zearalenone (ZEN)). The magnetic propulsion accelerates the decontamination efficiency of JYC-robots against ZEN. Although yeast cells with fully coating of Fe₃O₄ NPs and ZIF-67 (FC-yeasts) show faster movement than JYC-robots, higher toxin-removal efficacy is observed for JYC-robots compared with that of FC-yeasts, reflecting the vital factor of the yeast cell wall in removing mycotoxin. Such design with Janus modification of magnetic NPs (MNPs) and entire coating of ZIF-67 generates active cell robot platform capable of fuel-free propulsion and enhanced detoxification, offering a new formation to develop cell-based robotics system for environmental remediation.

MG@PD@TiO2 nanocomposite based magnetic solid phase extraction coupled with LC-MS/MS for determination of lysophosphatidylcholines biomarkers of plasma in psoriasis patients

Lysophosphatidylcholine (LPC) was commonly known as a class of significant differential metabolites of high relevance with many diseases including psoriasis, of which the accurate determination is of great importance to diagnosis or prediction to many diseases. However, it is challenging and complicated because of the enormous biological sample complexity and impurities interference. In this study, we synthesized a magnetic nanocomposite MG@PD@TiO₂ and took advantage of the interactions of Lewis acid-base between the phosphate groups in LPCs and Ti ions on MG@PD@TiO₂ nanomaterials for selective separation and enrichment of LPCs from complex biological matrix. The solid-phase extraction sample pretreatment process by means of MG@PD@TiO₂ nanomaterials coupled with LC-MS/MS method was then applied to actual determination of six typical LPCs (LPC 10:0, 14:0, 16:0, 18:0, 18:1, 22:0) in human plasma. The extraction conditions were scientifically optimized by single-factor test (adsorbent amount, adsorption and desorption time, elution solvent type, eluant volume). Under the optimal conditions, the detection limits (LOD, S/N = 3) and quantification limits (LOQ, S/N = 10) were 1 and 5 ng/mL for LPC 10:0 and LPC 14:0, 0.02 and 0.1 ng/mL for LPC 16:0 and LPC 18:1, 0.05 and 0.2 ng/mL LPC 18:0 and LPC 22:0, respectively. The intra- and inter-day precisions were 3.82-12.60 % (n = 6) and 3.29-13.50 % (n = 6) respectively, the recoveries were in the range of 91.92-113.69 % and the stability of the analytes in the matrix performed well with RSDs≤15.51 %. Finally, the developed method was successfully applied to the accurate determination of six LPCs biomarkers of plasma in patients with psoriasis (n = 10) and control groups (n = 10).

Recent trends in sorbents for bioaffinity chromatography

Isolation or enrichment of biological molecules from complex biological samples is mostly a prerequisite in proteomics, genomics, and glycomics. Different techniques have been used to advance the efficiency of the purification of biological molecules. Bioaffinity chromatography is one of the most powerful technique that plays an important role in the isolation of target biological molecules by the specific interactions with ligands that are immobilized on different support materials. This review examines the recent developments in bioaffinity chromatography particularly over the past 5 years in the literature. Also properties of supports, immobilization techniques, types of binding agents, and methods used in bioaffinity chromatography applications are summarized.

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.

Hydrophilic polydopamine-derived mesoporous channels for loading Ti(IV) ions for salivary phosphoproteome research

Salivary phosphoproteome holds great promise in clinic diagnosis. For profiling of salivary phosphoproteome, it is essential to develop efficient enrichment methods prior to mass spectrum (MS). Among developed enrichment strategies, immobilized metal ions affinity chromatography (IMAC) has exhibited outstanding performance. In this work, we report a coherent approach where polydopamine (PDA) is first utilized to form mesoporous structure through soft templating method, then chelated with Ti⁴⁺ to construct hydrophilic polydopamine-derived magnetic mesoporous nanocomposite (denoted Fe₃O₄@mPDA@Ti⁴⁺). In virtue of the merits including ordered mesoporous channels, appropriate superparamagnetism, and abundant Ti⁴⁺, the enrichment strategy based on Fe₃O₄@mPDA@Ti⁴⁺ combined with MS is employed for accurate identification of phosphopeptides in β-casein digest and human saliva. As expected, Fe₃O₄@mPDA@Ti⁴⁺ revealed a great selectivity (1:200) and a low detection limit (0.1 fmol μL^-1) toward phosphopeptides. More importantly, the further successful capture of phosphopeptides from human saliva indicated the prominent potential of this method for seeking phosphopeptide biomarkers in further analysis.

Size-Tunable Metal-Organic Framework-Coated Magnetic Nanoparticles for Enzyme Encapsulation and Large-Substrate Biocatalysis

Immobilizing enzymes on nanoparticles (NPs) enhances the cost-efficiency of biocatalysis; however, when the substrates are large, it becomes difficult to separate the enzyme@NP from the products while avoiding leaching or damage of enzymes in the reaction medium. Metal-organic framework (MOF)-coated magnetic NPs (MNPs) offer efficient magnetic separation and enhanced enzyme protection; however, the involved enzymes/substrates have to be smaller than the MOF apertures. A potential solution to these challenges is coprecipitating metal/ligand with enzymes on the MNP surface, which can partially bury (protect) the enzyme below the composite surface while exposing the rest of the enzyme to the reaction medium for catalysis of larger substrates. Here, to prove this concept, we show that using Ca²⁺ and terephthalic acid (BDC), large-substrate enzymes can be encapsulated in CaBDC-MOF layers coated on MNPs via an enzyme-friendly, aqueous-phase one-pot synthesis. Interestingly, we found that using MNPs as the nuclei of crystallization, the composite size can be tuned so that nanoscale composites were formed under low Ca²⁺/BDC concentrations, while microscale composites were formed under high Ca²⁺/BDC concentrations. While the microscale composites showed significantly enhanced reusability against a non-structured large substrate, the nanoscale composites displayed enhanced catalytic efficiency against a rigid, crystalline-like large substrate, starch, likely due to the improved diffusivity of the nanoscale composites. To our best knowledge, this is the first report on aqueous-phase one-pot synthesis of size-tunable enzyme@MOF/MNP composites for large-substrate biocatalysis. Our platform can be applied to immobilize other large-substrate enzymes with enhanced reusability and tunable sizes.

Iron-chelated thermoresponsive polymer brushes on bismuth titanate nanosheets for metal affinity separation of phosphoproteins

Separation of phosphoproteins plays an important role for identification of biomarkers in life science. In this work, bismuth titanate supported, iron-chelated thermoresponsive polymer brushes were prepared for selective separation of phosphoproteins. The iron-chelated thermoresponsive polymer brushes were synthesized by surface-initiated atom transfer radical polymerization of N-isopropylacrylamide and glycidyl methacrylate, followed by a ring opening reaction of epoxy group, and chelation of the obtained cis-diols with Fe³⁺ ions. The composite material was characterized to determine the size and thickness, the content of the organic polymer and the metal loading. The bismuth titanate supported, iron-chelated thermoresponsive polymer brushes showed selective binding for phosphoproteins in the presence of abundant interfering proteins, and a high binding capacity for phosphoproteins by virtue of the metal affinity between the metal ions on the polymer brushes and the phosphate groups in the phosphoproteins (664 mg β-Casein per g sorbent). The thermoresponsive property of the polymer brushes made it possible to adjust phosphoprotein binding by changing temperature. Finally, separation of phosphoproteins from a complex biological sample (i.e. milk) was demonstrated using the nanosheet-supported thermoresponsive polymer brushes.

Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials

Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.

Facile synthesis of polydivinylbenzene coated magnetic polydopamine coupled with pressurized liquid extraction for the extraction and cleanup of polycyclic aromatic hydrocarbons in soils

Due to the trace levels of polycyclic aromatic hydrocarbons (PAHs) in soil and the complexity of soil matrices, effective sample pretreatment methods are of great significance to obtain accurate analytical results. In this paper, polydopamine (PDA) encapsulated Fe₃O₄ particles were used as seeds for in situ polymerization of divinylbenzene (DVB) to derive magnetic hybrid material Fe₃O₄@PDA@PDVB. Coupled with pressurized liquid extraction, Fe₃O₄@PDA@PDVB was investigated as a selective adsorbent for the extraction and cleanup of PAHs in soil. The prepared magnetic material was characterized and demonstrated to possess strong hydrophobicity and superparamagnetism. Under optimal conditions, Fe₃O₄@PDA@PDVB can effectively extract 15 PAHs from a 30% methanol solution within 2 min, and it is more selective for PAHs than for n-alkane in soil extracts. The matrix effect significantly decreased after extraction by the prepared material, which showed superiority to a silica gel column method (EPA 3630C Method). The developed method was linear (5-1000 ng g^-1) with coefficient of determination (R²) ranging from 0.9986-0.9998, and the limits of detection were 0.13-0.54 ng g^-1. Additionally, repetitive experiments indicated that the prepared material was reproducible and reusable with relative standard deviations below 8.4% and 8.6%, respectively. Finally, the new method was successfully employed to determine the concentrations of PAHs in genuine soil and standard reference material, and the results were comparable to those of widely utilized EPA methodology.

Multifunctional Magnetic-Fluorescent Nanoparticle: Fabrication, Bioimaging, and Potential Antibacterial Applications

Magnetic-fluorescent nanoparticles integrating imaging and therapeutic capabilities have unparalleled advantages in the biomedical applications. Apart from the dual ability of unique biomolecular fluorescent recognition and magnetic modes, the nanoparticle also endows combined effective therapies with high physiological stability, long-term imaging, rapid response time, and excellent circulation ability. Herein, we developed a carboxyl-functionalized magnetic nanoparticle that was further functionalized by polydopamine (PDA) and Schiff base ligand (3-aminopyridine-2-carboxaldehyde N(4)-methylthiosemicarbazone, HL) to form multilayered coating single nanoparticles (Fe₃O₄@PDA@HL). Our work showed that the aggregation-induced emission (AIE) effect could be produced by embedding In³⁺ into the Fe₃O₄@PDA@HL nanostructure, which offered a new opportunity for utilization as a fluorescent detection and therapeutic platform. Cellular fluorescent imaging experiments provided bacterial cell biodistribution, demonstrating their excellent luminescent performance, magnetic aggregation, and separation capability. We simultaneously confirmed that the synergistic antibacterial effect was closely related to both Fe₃O₄@PDA@HL and In³⁺, leading to the disruption of membrane integrity and the leakage of intracellular components, thus inducing bacterial death. This approach presented in our work could promote the development of future bioimaging and clinical therapy applications.

Effect of shell structure of Ti-immobilized metal ion affinity chromatography core-shell magnetic particles for phosphopeptide enrichment

Magnetic materials in sample preparation for shotgun phosphoproteomics offer several advantages over conventional systems, as the enrichment can be achieved directly in solution, but they still suffer from some drawbacks, due to limited stability and selectivity, which is supposed to be affected by the hydrophilicity of the polymeric supports used for cation immobilization. The paper describes the development of an improved magnetic material with increased stability, thanks to a two-step covering of the magnetic core, for the enrichment of phosphopeptides in biological samples. Four materials were prepared featuring a polymeric shell with tunable hydrophilicity, obtained by "grafting from" polymerization of glycidyl methacrylate with 0-8.3% of polyethylene glycol methacrylate (PEGMA), the latter used to modulate the hydrophilicity of the material surface. Finally, the materials were functionalized with iminodiacetic acid for Ti4+ ion immobilization. The materials were analyzed for their composition by a combination of CHN elemental analysis and thermogravimetric analysis, also hyphenated to gas chromatography and mass spectrometric detection. Surface characteristics were evaluated by water contact angle measurements, scanning electron microscopy and energy dispersive X-ray spectrometry. These materials were applied to the enrichment of phosphopeptides from yeast protein digests. Peptides were identified by proteomics techniques using nano-high performance liquid chromatography coupled to mass spectrometry and bioinformatics. Qualitatively the peptides identified by the four systems were comparable, with 1606-1693 phosphopeptide identifications and a selectivity of 47-54% for all materials. The physico-chemical features of the identified peptides were also the same for the four materials. In particular, the grand average of hydropathy index values indicated that the enriched phosphopeptides were hydrophilic (ca. 90%), and only some co-enriched non-phosphorylated peptides were hydrophobic (21-28%), regardless of the material used for enrichment. Peptides had a pI ≤ 7, which indicated a well-known bias for acidic peptides binding, attributed to the interaction with the metal center itself. The results indicated that the enrichment of phosphopeptides and the co-enrichment of non-phosphorylated peptides is mainly driven by interactions with Ti4+ and does not depend on the amount of PEGMA chains in the polymer shell.

Ni(II)-decorated porous titania microspheres as a stationary phase for column chromatography applications: Highly selective purification of hemoglobin from human blood

Titania (TiO₂)-based monodisperse-porous stationary phase/sorbent was synthesized by decoration of Ni(II) ions onto TiO₂ microspheres 4.2 µm in size, obtained by a staged-shape template hydrolysis and condensation protocol. Ni(II) ions were attached onto iminodiacetic acid-3-glycidoxypropyltrimethoxysilane (IDA-GPTMS) bound-titania microspheres by metal-chelate complex formation. The appropriate mean size, sufficiently high surface area and high porosity providing an appropriate column permeability make Ni(II)-decorated TiO₂ microspheres a good sorbent/stationary phase for batch/continuous-column chromatography applications. Ni(II)-decorated TiO₂ microspheres were investigated as a sorbent for purification of a typical histidine-rich protein, hemoglobin (Hb) via immobilized metal affinity chromatography (IMAC) in batch fashion, by including bovine serum albumin (BSA) as reference. The saturation capacities of batch adsorption runs performed with bovine Hb and BSA were determined as 137 ± 9 and 45 ± 3 mg/g, respectively. Human Hb with the purity of > 95% was recovered from whole blood by IMAC conducted in batch-fashion. Ni(II)-decorated microspheres were also evaluated as a stationary phase in a microfluidic-IMAC system, in which, human Hb was recovered from whole blood with a purity of 85%. The microfluidic-IMAC system constructed here, based on monodisperse-porous TiO₂ microspheres, is a promising tool for genomics/proteomics applications involving isolation of valuable biomolecules from low-volume samples.

Label-Free Potentiometric Ion Flux Immunosensor for Determination of Recombinant Human Myelin Basic Protein: Application to Downstream Purification from Transgenic Milk

Recombinant human myelin basic protein (rhMBP) produced in the milk of transgenic cows was found exclusively associated with milk caseins. This hindered its direct determination without extensive sample pretreatment. Here, a label-free potentiometric immunosensor was developed and validated for the determination of rhMBP. An ion flux was generated under zero-current based on surface blocking of the polymeric membrane ion-selective electrode by anti-hMBP antibody and tetrabutylammonium bromide as a marker ion. The immunosensor was successfully employed in the quantitative determination of hMBP in the range of 0.10-20.00 μg/mL with a limit of detection of 50.00 ng/mL. The applicability of the passive ion flux immunosensor for determination of target analyte in complex matrices was investigated. Downstream purification of rhMBP from the milk of transgenic cows was achieved using cation exchange chromatography, immobilized metal affinity chromatography, and immunoaffinity chromatography. The specificity of the immunosensor along with matrix effect of milk proteins were demonstrated. Results obtained using the rhMBP immunosensor were further cross-validated using an orthogonal testing protocol assembled of RP-HPLC and SE-HPLC. It should be noted that the proposed ion flux immunosensor provided a feasible and specific tool for monitoring rhMBP concentration/purity, immunogenic activity, and stability. Such approach provides an attractive economic alternative to sophisticated biosensors required for in-process quality control of biopharmaceutical products.

Fe3O4@C Core-Shell Carbon Hybrid Materials as Magnetically Separable Adsorbents for the Removal of Dibenzothiophene in Fuels

Herein, we demonstrate a new class of core-shell magnetic carbon hybrid materials (Fe₃O₄@C) for remarkable adsorptive desulfurization of dibenzothiophene (DBT), which have been successfully prepared through hydrocarbonization of glucose on the surface of Fe₃O₄ and the subsequent pyrolyzation process. The as-obtained Fe₃O₄@C retains amorphous nature of carbon shells with a large surface area and displays an increase of iron atoms as active sites under elevated pyrolyzation temperature which is favorable in the adsorption of sulfur-containing species through physical and chemical adsorption, respectively. We investigate the adsorption capacity and efficiency of Fe₃O₄@C as a magnetically adsorbent for the removal of DBT in model oils under various experimental conditions including the adsorbent obtained at different temperatures, the amount of adsorbents, the DBT initial concentration, the regeneration approach, as well as the interference species. Our results demonstrated that the as-obtained Fe₃O₄@C at 650 °C (Fe₃O₄@C-650) displays a remarkable estimated adsorption performance (57.5 mg DBT/g for 200 ppmw), extraordinary high desulfurization efficiency (99% for 200 ppmw), and a high selectivity for DBT compared with its derivatives. Moreover, Fe₃O₄@C can be recovered in a quite easy, economical, and eco-friendly manner by an external magnet after five cycles without significant weight loss, which significantly simplifies the operation procedure and favors the recycle of Fe₃O₄@C. Combined with the economic and eco-friendly merits, Fe₃O₄@C offers a new avenue to employ the magnetic carbon materials for industrial applications and provides a promising substitute for adsorptive desulfurization in view of academic, industrial, and environmental aspects.

A polyoxometalate-modified magnetic nanocomposite: a promising antibacterial material for water treatment

A polyoxometalate-modified magnetic nanocomposite integrates the double antibacterial effects of both Fe₃O₄ and polyoxometalate, rendering it a promising candidate as an antimicrobial material.

Magnetic metal-organic framework nanocomposites for enrichment and direct detection of environmental pollutants by negative-ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Nowadays, the detection and removal of environmental pollutants are particularly important, owing to their harmful influence on human beings' health. Specifically, metal-organic frameworks (MOFs) as the hot materials with great potential have been widely employed as adsorbents for pollutants removal, as well as matrixes for mass spectrometry detection. In this work, magnetic Zr-based MOF (denoted as Fe₃O₄@PDA@ZrMOF) with outstanding properties, such as low background interference, high desorption/ionization efficiency, excellent signal reproducibility, ultrahigh surface area and strong magnetic responsiveness, was synthesized by a modified thermal annealing method. The Fe₃O₄@PDA@ZrMOF not only can be utilized as adsorbent towards small molecules by π-π stacking interaction between nitrophenols and ZrMOF, but also can serve as a matrix for detection of small molecules under the negative ion mode of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). As a result, with the use of Fe₃O₄@PDA@ZrMOF, the detection limits of 4-nitrocatechol and 4-nitroguaiacol were estimated to be about 68 μg/ml and 25 μg/ml, respectively. In addition, enrichment of nitrophenols from PM_2.5 was investigated. The detected mass concentrations of 4-nitrocatechol and 4-nitroguaiacol in collected PM_2.5 samples were 0.11 ng/m³ and 0.15 ng/m³, respectively, indicating the highly efficient enrichment performance of Fe₃O₄@PDA@ZrMOF for low-abundance nitrophenol compounds in the environment.

Magnetic microspheres modified with Ti(IV) and Nb(V) for enrichment of phosphopeptides

Magnetic microspheres (Fe₃O₄) were coated with polydopamine (PDA) and loaded with the metal ions Ti(IV) and Nb(V) to give a material of type Fe₃O₄@PDA-Ti/Nb. It is shown to be useful for affinity chromatography and for enrichment of phosphopeptides from both standard protein solutions and real samples. For comparison, such microspheres loaded with single metal ions only (Fe₃O₄@PDA-Ti and Fe₃O₄@PDA-Nb) and their physical mixtures were also investigated under identical conditions. The binary metal ion-loaded magnetic microspheres display better enrichment efficiency than the single metal ion-loaded microspheres and their physical mixture. Both multiphosphopeptides and monophosphopeptides can be extracted. The Fe₃O₄@PDA-Ti/Nb microspheres exhibit ultra-high sensitivity (the lowest detection amount being 2 fmol) and selectivity at a low mass ratio such as in case of β-casein/BSA (1:1000). Graphical abstract Magnetic microspheres (Fe₃O₄) were coated with polydopamine (PDA) and loaded with the metal ions Ti(IV) and Nb(V) to give a material of type Fe₃O₄@PDA-Ti/Nb. Results showed its great potential as an affinity probe in phosphoproteome research due to rapid magnetic separation of phosphopeptides, ultrahigh sensitivity and selectivity, and remarkable reusability.