Development of the affinity materials for phosphorylated proteins/peptides enrichment in phosphoproteomics analysis

Immobilized metal ion affinity chromatography: waltz of metal ions and biomacromolecules

INTRODUCTION

Immobilized metal ion affinity chromatography (IMAC) is an effective method developed in the 1980s for the separation and purification of proteins. The system consists of a solid-phase matrix, a linking ligand, and a metal ion. The method is based on the ability of metal ions to bind specifically to certain specific amino acid residues of proteins, thereby selectively enriching and purifying proteins.

AREAS COVERED

This review aims to describe current knowledge of fundamental principle of IMAC and summarize the supports, chelating ligands, and metal ions of IMAC. In addition, how IMAC technology is used in proteomics and nucleic acids research are highlighted.

EXPERT OPINION

Over the past decades, IMAC has been extensively utilized as a predominant technique for protein enrichment in a variety of biological and medical research, such as disease diagnosis, tumor biomarker identification, protein purification, and nucleic acids research. In the future, IMAC should be integrated with other emerging proteomics technologies to promote the applications of metalloproteomes in disease diagnosis, metallodrug development, and clinical translation.

Superhydrophilic Nanostructured Microparticles for Enhanced Phosphoprotein Enrichment from Alzheimer's Disease Brain

Alzheimer's disease (AD) is an incurable neurodegenerative disorder and closely related to abnormal phosphoproteoforms. The analysis of low-abundance phosphoproteoforms relies heavily on the enrichment of phosphoproteins. However, existing phosphoprotein enrichment materials suffer from either low selectivity or low coverage due to the unavoidable unspecific adsorption of background proteins. Here, we propose a strategy of nanostructure-enabled superhydrophilic surfaces and synthesize Ti4+-functionalized superhydrophilic nanostructured microparticles (SNMs-Ti4+) via an emulsion interfacial polymerization process. In this process, hydrophilic and hydrophobic monomers assemble into a stable oil-in-water emulsion, producing microparticles with abundant hydrophilic phosphate nanoprotrusions on the surface. The microparticles are subsequently functionalized with Ti4+. SNMs-Ti4+ exhibit enormous nanoprotrusions and abundant Ti4+ modifications, which allow SNMs-Ti4+ to effectively adsorb the phosphoproteins and suppress the unspecific adsorption of background proteins. Using these SNMs-Ti4+, we identified 2256 phosphoproteins from HeLa cells, twice the number of those enriched with commercial kits. From AD mouse brains, 2603 phosphoproteins were successfully enriched, and 10 times of AD-related differentially regulated phosphoproteins were discovered than those without enrichment. These microparticles show great prospects for biomarker detection, disease diagnosis, and downstream biological process disclosure.

In Situ MXene-Controlled Synthesis of Polycrystalline TiO2 for Highly Efficient Enrichment of Phosphopeptides

Phosphopeptide enrichment methods based on commercial TiO2 suffer from difficulties in regulating intermolecular interactions, resulting in low coverage rate and the loss of information on multiphosphorylation sites, thereby limiting comprehensive phosphoproteomic analysis. In this work, MXene Ti3C2Tx was incorporated into the design of enrichment materials, with its surface structure functionalized and regulated to address the low elution efficiency of TiO2 for multiphosphorylated peptides. Upon oxidation treatment, the Ti3C2Tx material formed numerous uniformly distributed TiO2 nanoparticles on the surface of Ti3C2Tx-O, providing abundant affinity sites (Ti-O) for selective phosphopeptide enrichment. The polycrystalline structure and rich oxygen vacancies of the material effectively regulated its binding affinity with phosphate groups, achieving simultaneous high-efficiency enrichment of both monophosphorylated and multiphosphorylated peptides. Its performance was significantly superior to that of commercial TiO2 and IMAC materials. This study presents great promise for the practical application of comprehensive phosphoproteomic analysis in the future and broadens the application of MXene in the biological field.

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.

Metal-chelated polydopamine nanomaterials: Nanoarchitectonics and applications in biomedicine, catalysis, and energy storage

Polydopamine (PDA)-based materials inspired by the adhesive proteins of mussels have attracted increasing attention owing to the universal adhesiveness, antioxidant activity, fluorescence quenching ability, excellent biocompatibility, and especially photothermal conversion capability. The high binding ability of PDA to a variety of metal ions offers a paradigm for the exploration of metal-chelated polydopamine nanomaterials with fantastic properties and functions. This review systematically summarizes the latest progress of metal-chelated polydopamine nanomaterials for the applications in biomedicine, catalysis, and energy storage. Different fabrication strategies for metal-chelated polydopamine nanomaterials with various composition, structure, size, and surface chemistry, such as the pre-functionalization method, the one-pot co-assembly method, and the post-modification method, are summarized. Furthermore, emerging applications of metal-chelated polydopamine nanomaterials in the fields ranging from cancer therapy, theranostics, antibacterial, catalysis to energy storage are highlighted. Additionally, the critical remaining challenges and future directions of this area are discussed to promote the further development and practical applications of PDA-based materials.

Unraveling Clinical Glycoproteome by Integrating Affinity Enrichment with Nanopore Sequencing

This prospect explores the integration of enrichment strategies with nanopore detection to advance clinical glycoproteomics. Glycoproteins, crucial for understanding biological processes, pose challenges due to their low abundance and structural diversity. Enrichment techniques using lectin affinity, boronate affinity, and hydrazide chemistry and especially molecular imprinted polymers may selectively and specifically isolate glycoproteins from complex samples, while nanopore technology enables label-free, real-time, and single-molecule analysis. This approach holds promise for disease-related glycosylation studies, biomarker discovery, personalized medicine, and streamlined clinical analysis. Standardization, optimization, and data analysis remain challenges, requiring interdisciplinary collaborations and technological advancements. Overall, this integration may offer transformative potential for clinical glycoproteomics and innovative diagnostic and therapeutic strategies.

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.

A nitrogen-doped graphene tube composite based on immobilized metal affinity chromatography for the capture of phosphopeptides

A novel immobilized metal affinity chromatography (IMAC) functional composite, mNi@N-GrT@PDA@Ti⁴⁺, was fabricated based on ultrathin magnetic nitrogen-doped graphene tube (mNi@N-GrT) after chelated Ti⁴⁺ with polydopamine, following as a magnetic solid-phase extraction sorbent for rapidly selective enrichment and mass spectrometry identification of phosphorylated peptides. After optimized, the composite exhibited high specificity in the enrichment of phosphopeptides from the digest mixture of β-casein and bovine serum albumin (BSA). The robust method presented the low detection limits (1 fmol, 200 μL) and excellent selectivity (1:100) in the molar ration mixture of β-casein and BSA digests. Furthermore, the selective enrichment of phosphopeptides in the complex bio-samples, was successfully carried out. The results showed that 28 phosphopeptides were finally detected in mouse brain, and 2087 phosphorylated peptides were identified in the HeLa cells extracts with specific selectivity of 95.6%. The enrichment performance of mNi@N-GrT@PDA@Ti⁴⁺ was satisfactory, suggesting that the functional composite provided a potential application in the enrichment of trace phosphorylated peptides from the complex biological matrix.

Magnetic anaerobic granular sludge for sequestration and immobilization of Pb

The development of magnetic adsorbents with high capacity to capture heavy metals has been the subject of intense research, but the process usually involves costive synthesis steps. Here, we propose a green approach to obtaining a magnetic biohybrid through in situ grown anaerobic granular sludge (AGS) with the help of magnetite, constituting a promising adsorbent for sequestration and immobilization of Pb in aqueous solutions and soils. The resultant magnetite-embedded AGS (M-AGS) was not only capable of promoting methane production but also conducive to Pb adsorption because of the large surface area and abundant function groups. The uptake of Pb on M-AGS followed the pseudo-second order, having a maximum adsorption capacity of 197.8 mg gDS^-1 at pH 5.0, larger than 159.7, 170.3, and 178.1 mg gDS^-1 in relation to AGS, F-AGS (ferrihydrite-mediated), and H-AGS (hematite-mediated), respectively. Mechanistic investigations showed that Pb binding to M-AGS proceeds via surface complexation, mineral precipitation, and lattice replacement, which promotes heavy metal capture and stabilization. This was evident from the increased proportion of structural Pb sequestrated from the aqueous solution and the enhanced percentage of the residual fraction of Pb extracted from the contaminated soils.

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

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

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 %.

Mass tag-encoded nanointerfaces for multiplexed mass spectrometric analysis and imaging of biomolecules

Revealing multiple biomolecules in the physiopathological environment simultaneously is crucial in biological and biomedical research. Mass spectrometry (MS) features unique technical advantages in multiplexed and label-free analyses. However, owing to comparably low abundance and poor ionization efficiency of target biomolecules, direct MS profiling of these biological species in vitro or in situ remains a challenge. An emerging route to solve this issue is to devise mass tag (MT)-encoded nanointerfaces which specifically convert the abundance or activity of biomolecules into amplified ion signals of mass tags, offering an ideal strategy for synchronous MS assaying and mapping of multiple targets in biofluids, cells and tissues. This review provides a thorough and organized overview of recent advances in MT-encoded nanointerfaces elaborately tailored for several practical applications in multiplexed MS bioanalysis and biomedical research. First, we start with elucidation of the structural characteristics and working principle of MT-encoded nanointerfaces in specific labeling and sensing of multiple biological targets. In addition, we further discuss the application scenarios of MT-encoded nanointerfaces particularly in multiplexed biomarker assays, cell analysis, and tissue imaging. Finally, the current challenges are pointed out and future prospects of these nanointerfaces in MS analysis are forecast.

A novel magnetic fluid for ultra-fast and highly efficient extraction of N1-methylnicotinamide in urine samples

Among the three pre-treatment materials, Fe3O4@HPMC@DMSA NPs were selected to be the best material and were used to perform MSPE-HPLC-UV.

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.

Two-dimensional magnetic bimetallic organic framework nanosheets for highly efficient enrichment of phosphopeptides

Highly selective enrichment and sensitive detection of phosphopeptides is pivotal for comprehensive phosphoproteomics analysis; however, it also poses a long-standing challenge. Here, a novel two-dimensional (2D) magnetic bimetallic organic framework (MOF) nanosheet with Zr-O clusters and Ti-O clusters (denoted as the Fe₃O₄@Zr-Ti BPDC nanosheet) is prepared via a solvothermal method and in situ deposition of Fe₃O₄ nanoparticles for the first time. Taking advantage of the abundant dual affinities of Zr-O and Ti-O clusters for phosphopeptides, large surface area and high chemical stability, the Fe₃O₄@Zr-Ti BPDC nanosheets exhibit excellent enrichment performance for phosphopeptides. Within the framework of density functional theory, the interaction between Zr-O clusters, Ti-O clusters and phosphorylated molecules was studied to find the possible reason behind the superior adsorption performance of the bimetallic MOF nanosheets. We found that electrons would migrate from Ti to Zr spontaneously after doping Ti element and enhance the electrostatic traction between Zr species and phosphorylated molecules, demonstrating that the synergistic effect of Zr-Ti was helpful to improve the enrichment efficiency for phosphopeptides. Furthermore, the Fe₃O₄@Zr-Ti BPDC nanosheets showed good enrichment performance in complex bio-samples, including nonfat milk, human saliva, and a breast cancer cell lysate, indicating their tremendous potential in the analysis of trace phosphorylated biomolecules in complex bio-samples.

Highly selective titanium (IV)-immobilized O-Phospho-L-tyrosine modified magnetic nanoparticles for the enrichment of intact phosphoproteins

Phosphorylation is one of the most important protein post-translational modifications, which possesses dramatic regulatory effects on the function of proteins. In consideration of the low abundance and low stoichiometry of phosphorylation and non-specific signal suppression, efficient capture of the phosphoproteins from complex biological samples is critical to meet the need of protein profiling. In this work, a facile preparation of titanium (IV)-immobilized O-Phospho-L-tyrosine modified magnetic nanoparticles were developed for the enrichment of intact phosphoproteins. The prepared magnetic nanoparticles were characterized by various instruments and had a spherical shape with an average diameter of 300 nm. The adsorption isotherms were investigated and the maximum capacity for β-casein was calculated to be 961.5 mg/g. Standard protein mixtures and biological samples (non-fat milk and human serum) were selected to test the enrichment performance. Sodium dodecyl sulfate-poly acrylamide gel electrophoresis analysis demonstrated the excellent enrichment performance with high selectivity. With the superparamagnetic property, titanium (IV)-immobilized O-Phospho-L-tyrosine modified magnetic nanoparticles were convenient for the practical application and clinical promotion, thus having a promising prospect in the field of phosphoprotein research. This article is protected by copyright. All rights reserved.

Nanoarchitectonics of a MOF-in-Nanochannel (HKUST-1/TiO2) Membrane for Multitarget Selective Enrichment and Staged Recovery

Enrichment and separation of specific endogenous molecules are essential for disease diagnosis and the pharmaceutical industry. Although many solid sorbents have been developed for target molecule enrichment, simultaneous separation of multitargets is still a challenge for adsorbents. In this study, we develop a multitarget selective sorbent based on a nanochannel membrane prepared by the anodization of a Ti-Cu alloy. The in situ growth of a metal-organic framework (MOF, herein using Cu-based HKUST-1) in the nanochannels enables the resulting MOF-in-nanochannel membrane to act as a nanofilter. Benefitting from the size-exclusion effect of MOFs and the distinct surface characteristics of each component in the HKUST-1/TiO₂ nanochannels, the as-proposed membranes can be simply operated as a filter and exhibit satisfactory selectivities and enrichment capacities in the separation of aromatic amino acids, histidine-rich proteins, and phosphoproteins. More importantly, the adsorbed multitargets can be further controllably released from the membrane in a sequence via a staged recovery process. The use of this system is envisioned to provide an innovative and potential design for efficient sorption media for the selective enrichment and staged separation of specific biomolecules.

TiO2 with Confined Water Boosts Ultrahigh Selective Enrichment of Phosphorylated Proteins

In the selective enrichment of phosphorylated proteins (PPs) from biological samples, the non-phosphorylated proteins (NPPs) adhered onto enrichment adsorbents due to the hydrophobic interaction, resulting in poor selectivity and low recovery of target PPs. Herein, superhydrophilic TiO₂-coated porous SiO₂ microspheres are prepared and boost remarkable selectivity toward standard PP spiked with 2000 mass-fold NPP interference. The outstanding performance of the superhydrophilic microspheres is attributed to the coordination interaction between TiO₂ and PPs, and the confined water layer generated from superhydrophilicity avoids the irreversible adsorption of NPPs by keeping NPP inner hydrophobic regions in a compact structure, which is verified by single molecule force spectroscopy, circular dichroism, and quartz crystal microbalance. This strategy for enrichment is expected to solve the challenge in proteomics and sheds light on the interactions between biomolecules and superwettability.

Development of New Lanthanide(III) Ion-Based Magnetic Affinity Material for Phosphopeptide Enrichment

Lanthanide (III) ion-based magnetic IMAC materials consisting of core-shell-like silica-coated magnetic nanoparticles as supporting material, chelidamic acid as chelating agent, and Ln3+ ions were developed in this study. Magnetic nanoparticles...

Bimetallic Ordered Large-Pore MesoMOFs for Simultaneous Enrichment and Dephosphorylation of Phosphopeptides

Despite the fact that bimetallic metal-organic frameworks (MOFs) could afford multiple functionalities by a synergistic effect of individual metallic centers, their intrinsic microporous structure frequently restricts their wide applications with bulky molecules involved. An urgent need is consequently triggered to design bimetallic hierarchical mesoporous MOFs (mesoMOFs). Herein, Zr/Ce mesoMOFs with a uniform pore size of up to 8 nm was successfully synthesized by a copolymer template strategy with the aid of a Hoffmeister ion. The obtained Zr/Ce mesoMOFs feature high porosity, good chemical and thermal stabilities, and tunable element components, and up to 70% Zr could be incorporated into the mesoporous Ce-based framework without deteriorating its crystallinity. Thanks to the synergistic effect of inherent Ce and Zr as well as the large and open pore channels, a broad range of phosphopeptides with different molecule sizes could be effectively checked out, thanks to their simultaneous enrichment and dephosphorylation capabilities. Such an ability to efficiently concentrate phosphopeptides remained intact even in the presence of abundant non-phosphorylated species. The practical detection of phosphopeptides from human serum was also verified, prefiguring the great potentials of bimetallic large-pore mesoMOFs for the proteome applications.

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.

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.

In Situ Controllable Fabrication of Two-Dimensional Magnetic Fe3O4/TiO2@Ti3C2Tx Composites for Highly Efficient Phosphopeptides Enrichment

Highly efficient enrichment of phosphopeptides is of great significance for phosphoproteomics-related biological and pathological processes research, but it remains challenging due to the lack of affinity materials which hold high enrichment efficiency and capacity. Ti₃C₂T_x MXene, a novel two-dimensional material with outstanding physicochemical properties, has attracted wide research interests for application in various fields. However, there are few reports on the use of MXene-derived materials for phosphopeptides separation in the biomedical field. In this work, we proposed a facile one-pot method that in situ oxidation and modification of Ti₃C₂T_x MXene, to prepare two-dimensional (2D) magnetic Fe₃O₄/TiO₂@Ti₃C₂T_x composites for potential application in phosphopeptides enrichment. Benefiting from the outstanding magnetic responsiveness and multiaffinity sites (Ti-O, Fe-O, and NH₂ groups), the Fe₃O₄/TiO₂@Ti₃C₂T_x composites possessed excellent enrichment performance with high sensitivity (0.1 fmol μL^-1), excellent selectivity (β-casein: bovine serum albumin = 1:5000, molar ratio), good repeatability (5 times), and high enrichment capacity (200 mg g^-1). Moreover, the results of selective enrichment of phosphopeptides from nonfat milk, human saliva, human serum, and rat brain lysates indicated the great potential of Fe₃O₄/TiO₂@Ti₃C₂T_x composites in low-abundance phosphopeptides enrichment from complex biological samples. This work has put forward a versatile method to prepare magnetic MXene composites and promoted the use of MXene composites in phosphoproteome in biomedicine.

Two-dimensional guanidinium-based covalent organic nanosheets for controllable recognition and specific enrichment of global/multi-phosphopeptides

Highly specific capture of phosphopeptides, especially multi-phosphopeptides, from complex biological samples is critical for comprehensive phosphoproteomic analysis, but it still poses great challenges due to the lack of affinity material with ideal enrichment efficiency. Here, two-dimensional (2D) covalent organic framework (COFs) nanosheets was applied for selective separation of phosphopeptides for the first time. Particularly, by incorporating guanidinium units, the 2D guanidinium-based COF nanosheets (denoted as TpTG_Cl CONs) exhibited controllable and specific enrichment performance towards global/multi-phosphopeptides. TpTG_Cl CONs was easy to prepare and showed large surface area, low steric hindrance, abundant accessible interaction sites and high chemical stability. Taking these merits together, TpTG_Cl CONs exhibited excellent efficiency for phosphopeptide enrichment, such as low detection limits (0.05 fmol μL^-1 for global phosphopeptides and 0.1 fmol μL^-1 for multi-phosphopeptides), high selectivity (1:5000 of molar ratios of β-casein/BSA for both global and multi-phosphopeptides), high adsorption capacity (100 mg g^-1 for global phosphopeptides and 50 mg g^-1 for multi-phosphopeptides). Furthermore, TpTG_Cl CONs could be reused due to the high chemical stability. In addition, TpTG_Cl CONs were successfully applied to controllable and specific capture of endogenous global/multi-phosphopeptides from human serum and human saliva, indicating its good potential in rapid and sensitive detection of biomarkers from biological fluid. Finally, rat liver protein digest was used to confirm the high specificity of TpTG_Cl CONs towards multi-phosphopeptides and demonstrated its potential as an ideal enrichment probe for comprehensive phosphoproteomic analysis.

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.

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.

Toward the Specificity of Bare Nanomaterial Surfaces for Protein Corona Formation

Aiming at creating smart nanomaterials for biomedical applications, nanotechnology aspires to develop a new generation of nanomaterials with the ability to recognize different biological components in a complex environment. It is common opinion that nanomaterials must be coated with organic or inorganic layers as a mandatory prerequisite for applications in biological systems. Thus, it is the nanomaterial surface coating that predominantly controls the nanomaterial fate in the biological environment. In the last decades, interdisciplinary studies involving not only life sciences, but all branches of scientific research, provided hints for obtaining uncoated inorganic materials able to interact with biological systems with high complexity and selectivity. Herein, the fragmentary literature on the interactions between bare abiotic materials and biological components is reviewed. Moreover, the most relevant examples of selective binding and the conceptualization of the general principles behind recognition mechanisms were provided. Nanoparticle features, such as crystalline facets, density and distribution of surface chemical groups, and surface roughness and topography were encompassed for deepening the comprehension of the general concept of recognition patterns.

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

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

Flexible and hierarchical metal-organic framework composite as solid-phase media for facile affinity-tip fabrication to selectively enrich glycopeptides and phosphopeptides

Micro-tip-based solid-phase microextraction is considered as one of the green and powerful analytical sample preparation techniques, but its efficiency is severely hampered by some basic issues such as tedious fabrication, instability of sorbent bed, and blocking of the tip, especially for biological samples due to low permeability. These issues are tackled by introducing a flexible and hierarchical substrate in the microtip, having good mechanical strength and specific functionality to capture the desired biomolecules. Considering the well-ordered and flexible structure of melamine foam, it was used as a substrate and for hydrophilic interaction chromatography (HILIC). Metal-organic framework, due to its excellent characteristics, was grafted on its surface anchored by self-assembling polydopamine. The resulting material was characterized and packed in the tip by just pressing the material in the conical structure of the tip. This affinity tip established good and tunable permeability and was used to selectively enrich glycopeptides as well as phosphopeptides. The affinity tip demonstrated excellent performance to enrich glycopeptides and phosphopeptides with a low limit of detection up to 0.5 fmol μL^-1 from tryptic digests of horseradish peroxidase and β-Casein, respectively, and was stable up to 5 rounds of enrichment. Moreover, this affinity-tip also exhibited high selectivity up to up to 1:1000 (HRP digest to BSA digest) for glycopeptides and 1:200 (β-Casein digest to BSA digest) for phosphopeptides and demonstrated several other fascinating characteristics such as; excellent size exclusion effect for the omission of large-sized proteins, modest backpressure, reproducibility, reusability, smooth enrichment, and successfully applied to a human saliva sample.

Development of zirconium modified adenosine triphosphate functionalized monolith for specific enrichment of N-glycans

In this study, to selectively enrich N-glycans from complex biological samples, a novel Zr(IV) modified adenosine triphosphate (Zr(IV)-ATP) functionalized monolith was prepared through a facile approach. Well-defined macroporous structure was observed in the ATP functionalized monolith, which allows rapid mass transfer under low backpressure and is beneficial for the enrichment of N-glycans. After being modified with Zr(IV), the resulting Zr(IV)-ATP functionalized monolith could selectively capture N-glycans through the specific interactions between the sulfonate groups of 1-aminopyrene-3,6,8-trisulfonic acid (APTS) labeled N-glycans and Zr(IV). An APTS labeled maltooligosaccharide ladder was used to optimize the enrichment conditions for APTS labeled N-glycans, and capillary electrophoresis (CE) coupled with laser-induced fluorescence (LIF) detector was employed to evaluate the enrichment efficiency. The results show that the APTS labeled maltooligosaccharides could be enriched under the selected conditions and the signal amplify factors of the maltooligosaccharides were between 7.4 and 19.5 with RSDs for reproducibility from 4.0% to 8.3% (n = 3). Finally, the proposed method was successfully used for the enrichment and detection of N-glycans released from Ribonuclease B.

Post-synthesis of biomimetic chitosan with honeycomb-like structure for sensitive recognition of phosphorylated peptides

Chemical modification of biological materials is indispensable for enrichment of phosphorylated peptides. In this work, we synthesized a biomimetic honeycombed affinity chromatography (IMAC) adsorbent by preparing Crosslinked Chitosan, chelating aminomethyl phosphate decorated with Ti (IV) cation. The as-prepared CTSM@AMPA-Ti⁴⁺ composites with stable structure, low steric hindrance, and high Ti⁴⁺ loading amount were used as a promising adsorbent for enrichment of phosphopeptides. CTSM@AMPA-Ti⁴⁺ showed extremely high sensitivity (0.4 fmol) and selectivity at a low composition molar ratio of β-casein/BSA (1:1000). What's more, it can keep its performance in the case that used to capture phosphorylated peptides from standard protein ten times or soaking in the acid/base solution for a long time. In addition, CTSM@AMPA-Ti⁴⁺ successfully captured 35 phosphorylated peptides from human saliva. This study offers a way about diversiform functionalization of CTSM in phosphoproteome analysis and disease research.

Facile synthesis of titanium(IV) ion-immobilized arsenate-modified poly(glycidyl methacrylate) microparticles and the application to the specific enrichment of phosphoproteins

Selective separation and enrichment of phosphoproteins possess the distinct clinical and biological importance in the diagnosis, treatment, and management of several fatal human diseases. In this study, a facile synthesis of titanium(IV) ion-immobilized arsenate-modified poly(glycidyl methacrylate) microparticles (denoted as Ti⁴⁺-arsenate-PGMA-MPs) was developed for the efficient enrichment of intact phosphoproteins found in biologically complex protein samples. By virtue of the strong interaction between the titanium ions immobilized on the surface of Ti⁴⁺-arsenate-PGMA-MPs and phosphate groups of phosphoproteins, Ti⁴⁺-arsenate-PGMA-MPs had a high saturated adsorption capacity for phosphoproteins (901 mg/g for β-casein), which was much higher than that of non-phosphoproteins (73.5 mg/g for BSA). Ti⁴⁺-arsenate-PGMA-MPs were characterized by SEM, TEM, and FT-IR, and the average particle diameter was about 2.5 μm with good dispersibility. Besides, the application of Ti⁴⁺-arsenate-PGMA-MPs in real biological samples was investigated by SDS-PAGE analysis, and the results showed that Ti⁴⁺-arsenate-PGMA-MPs were able to enrich phosphoproteins efficiently.

Magnetic phosphorylated chitosan composite as a novel adsorbent for highly effective and selective capture of lead from aqueous solution

Separating and recovering lead from heavy metal contaminated wastewater is crucial for the environment remediation and reutilization of lead resources. Herein, a novel adsorbent, the phosphorylated chitosan-coated magnetic silica nanoparticles (Fe₃O₄@SiO₂@CS-P), was successfully fabricated and applied to highly selective adsorption of lead. Competitive experiments were conducted in a multi-ion solution (7 metal ions coexist) at pH 6.0, Fe₃O₄@SiO₂@CS-P exhibited an excellent selectively for capturing lead with the distribution coefficient (0.75 L g^-1) more ten times than other metal, while Fe₃O₄@SiO₂@CS demonstrated a highly selective adsorption of silver. These implied that phosphorylation of adsorbent not only improves the sorption performance of lead, but also changes the selective adsorption of metal types. Acidity experiments can draw conclusions that Fe₃O₄@SiO₂@CS-P exhibited better acid resistance (with barely any iron leaching) than silica-uncoated adsorbent (Fe₃O₄@CS-P) at pH 1.0. Furthermore, the FTIR and XPS spectra after adsorption suggested that the high adsorption performance and selective capture lead were predominantly controlled by the coordination of the phosphate groups on the surface of the adsorbent. This work shows a broad prospect of developing a series of novel, acid-resistant, good reusable and rapidly separable magnetic materials that can be used to efficiently and selectively capture lead from aqueous solutions.

Synthesis of Al3+-doping-TiO2 monodisperse microspheres and their application for phosphopeptides and glycopeptides enrichment

Glycosylation and phosphorylation are two of the most common and important post-translational modifications (PTMs) of proteins, which play critical roles in regulating a variety of complex biological processes and involvement in many diseases. Due to the low abundance of phosphopeptides and glycopeptides, highly selective enrichment methods are crucial to the identification of protein phosphorylation and glycosylation by mass spectrometry (MS). Here, monodisperse uniform Al³⁺-doping-TiO₂ mixed oxide microspheres were easily synthesized. The morphology was controlled by a sol-gel method, during the hydrothermal treatment. The obtained microspheres with uniform particle size distribution (about 1-2 μm)，high surface area and improved pore structures, were characterized by SEM, TEM, XRD and N₂ adsorption-desorption isotherms. Al³⁺-doping-TiO₂ was applied in enriching glycopeptides and phosphopeptides respectively or simultaneously by using different enrichment conditions, achieving selective enrichment of glycopeptides and phosphopeptides. 20 glycopeptides and 25 phosphopeptides enriched from the tryptic digest mixtures of human serum immunoglobulin G (IgG) and α-casein (molar ratio of 1:1) were obviously observed with greatly improved signal-to-noise (S/N) ratio. Meanwhile, the enrichment results of non-fat milk and human serum also show the enrichment selectivity from complex biological samples. This study will provide a novel insight for selective enrichment of glycopeptides and phosphopeptides in post-translational modification proteomics research.

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.

Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment

Phosphopeptide enrichment is an essential step in large-scale, quantitative phosphoproteomics by mass spectrometry. Several phosphopeptide affinity enrichment techniques exist, such as immobilized metal-ion affinity chromatography (IMAC) and metal oxide affinity chromatography (MOAC). We compared zirconium(IV) IMAC (Zr-IMAC) magnetic microparticles to more commonly used titanium(IV) IMAC (Ti-IMAC) and TiO₂ magnetic microparticles for phosphopeptide enrichment from simple and complex protein samples prior to phosphopeptide sequencing and characterization by mass spectrometry (liquid chromatography-tandem mass spectrometry, LC-MS/MS). We optimized sample-loading conditions to increase phosphopeptide recovery for Zr-IMAC-, Ti-IMAC-, and TiO₂-based workflows by 22, 24, and 35%, respectively. The optimized protocol resulted in improved performance of Zr-IMAC over Ti-IMAC and TiO₂ as well as high-performance liquid chromatography-based Fe(III)-IMAC with up to 23% more identified phosphopeptides. The different enrichment chemistries showed a high degree of overlap but also differences in phosphopeptide selectivity and complementarity. We conclude that Zr-IMAC improves phosphoproteome coverage and recommend that this complementary and scalable affinity enrichment method is more widely used in biological and biomedical studies of cell signaling and the search for biomarkers. Data are available via ProteomeXchange with identifier PXD018273.

Complementary multiple hydrogen-bond-based magnetic composite microspheres for high coverage and efficient phosphopeptide enrichment in bio-samples

Due to the number of phosphorylation sites, mono- and multiple-phosphopeptides exhibit significantly different biological effects. Therefore, comprehensive profiles of mono- and multiple-phosphopeptides are vital for the analysis of these biological and pathological processes. However, the most commonly used affinity materials based on metal oxide affinity chromatography (MOAC) show stronger selectivity toward mono-phosphopeptides, thus losing most information on multiple-phosphopeptides. Herein, we report polymer functionalized magnetic nanocomposite microspheres as an ideal platform to efficiently enrich both mono- and multiple-phosphopeptides from complex biological samples. Driven by complementary multiple hydrogen bonding interactions, the composite microspheres exhibited remarkable performance for phosphopeptide enrichment from model proteins and real bio-samples. Excellent selectivity (the molar ratio of nonphosphopeptides/phosphopeptides was 5000 : 1), high enrichment sensitivity (2 fmol) and coverage, as well as high capture rates of multiple-phosphopeptides revealed their great potential in comprehensive phosphoproteomics studies. More importantly, we successfully captured the cancer related phosphopeptides (from the phosphoprotein Stathmin-1) and identified their relevant phosphorylation sites from oral carcinoma patients' saliva and tissue lysate, demonstrating the potential of this material for phosphorylated disease marker detection and discovery.

Post translational modification-assisted cancer immunotherapy for effective breast cancer treatment

Post translational modifications (PTM) such as phosphorylation are often correlated with tumorigenesis and malignancy in breast cancer. Herein, we report a PTM-assisted strategy as a simplified version of a personalized cancer vaccine for enhanced cancer immunotherapy. Titanium modified dendritic mesoporous silica nanoparticles (TiDMSN) are applied to assist the specific enrichment of phosphorylated tumor antigens released upon immunogenic cell death. This strategy significantly improved the tumor inhibition efficacy in a bilateral breast cancer model and the expansion of both CD8+ and CD4+ T cells in the distant tumor site. The nanotechnology based PTM-assisted strategy provides a simple and generalizable methodology for effective personalized cancer immunotherapy.

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.