Mass spectrometric analysis of mono- and multi-phosphopeptides by selective binding with NiZnFe2O4 magnetic nanoparticles

A magnetic calcium phosphate for selective capture of multi-phosphopeptides

The specific enrichment of multi-phosphopeptides in the presence of non-phosphopeptides and mono-phosphopeptides was still a challenge for phosphoproteomics research. Most of these enrichment materials relied on Zn, Ti, Sn, and other rare precious metals as the bonding center to enrich multi-phosphopeptides while ignoring the use of common metal elements. The addition of rare metals increased the cost of the experiment, which was not conducive to their large-scale application in biomedical proteomics laboratories. In addition, multiple high-speed centrifugation steps also resulted in the loss of low-abundance multi-phosphopeptides in the treatment procedure of biological samples. This study proposed the use of calcium, a common element, as the central bonding agent for synthesizing magnetic calcium phosphate materials (designated as CaP-Fe3O4). These materials aim to capture multi-phosphopeptides and identifying phosphorylation sites. The current results demonstrate that CaP-Fe3O4 exhibited excellent selection specificity, high sensitivity, and stability in the enrichment of multi-phosphopeptides and the identification of phosphorylation sites. Additionally, the introduction of magnetic separation not only reduced the time required for multi-phosphopeptides enrichment but also prevented the loss of these peptides during high-speed centrifugation. These findings contribute to the widespread application and advancement of phosphoproteomics research.

Bifunctional MNPs@UIO-66-Arg core-shell-satellite nanocomposites for enrichment of phosphopeptides

A facile and mild method based on self-assembled lysozyme (LYZ) to fabricate bifunctional MNPs@UIO-66-Arg core-shell-satellite nanocomposites (CSSNCs) is reported for the high-efficiency enrichment of phosphopeptides. Under physiological conditions, LYZ rapidly self-assembled into a robust coating on Fe3O4@SiO2 magnetic nanoparticles (MNPs) with abundant surface functional groups, which effectively mediate heterogeneous nucleation and growth of UIO-66 nanocrystals. Well-defined MNPs@UIO-66 CSSNCs with stacked pores, showing high specific surface area (333.65 m2 g- 1) and low mass transfer resistance, were successfully fabricated by fine-tuning of the reaction conditions including reaction time and acetic acid content. Furthermore, the UIO-66 shells were further modified with arginine to obtain bifunctional MNPs@UIO-66-Arg CSSNCs. Thanks to the unique morphology and synergistic effect of Zr-O clusters and guanidine groups, the bifunctional MNPs@UIO-66-Arg CSSNCs exhibited outstanding enrichment performance for phosphopeptides, delivering a low limit of detection (0.1 fmol), high selectivity (β-casein/BSA, mass ratio 1:2000), and good capture capacity (120 mg g- 1). The mechanism for phosphopeptides capture may attribute to the hydrogen bonds, electrostatic interactions, and Zr-O-P bonds between phosphate groups in peptides and guanidyl/Zr-O clusters on bifunctional MNPs@UIO-66-Arg CSSNCs. In addition, the small stacking pores on the core-shell-satellite architecture may selectively capture phosphopeptides with low molecular weight, eliminating interference of other large molecular proteins in complex biological samples.

Heterogeneous MXene Hybrid-Oriented Exosome Isolation and Metabolic Profiling for Early Screening, Subtyping and Follow-up Evaluation of Bladder Cancer

Exosome metabolite-based noninvasive liquid biopsy is an emerging research hotspot that tends to substitute current means in clinics. Nanostructure-based mass spectrometry enables continuous exosome isolation and metabolic profiling with superior analysis speed and high efficiency. Herein, we construct a heterogeneous MXene hybrid that possesses ternary binding sites for exosome capture and outstanding matrix performance for metabolite analysis. Upon optimizing experimental conditions, the average extraction of exosomes and their metabolic patterns from a 60 mL urine sample is completed within 45 s (40 samples per batch for 30 min). According to the exosomal metabolic patterns and the subsequently established biomarker panel, we distinguish early bladder cancer (BCa) from healthy controls with an area under the curve (AUC) value greater than 0.995 in model training and validation sets. As well, we realize subtype classification of BCa in the blind test on metabolic patterns, with an AUC value of 0.867. We also explore the significant biomarkers that are sensitive to follow-up patients, which indeed present reverse change levels compared with pathological progression. This study has the potential to guide the development of the liquid biopsy approach.

An easy and straightforward synthesized nano calcium phosphate for highly capture of multiply phosphorylated peptides

Multisite phosphorylation of proteins regulates various cellular life activities, however, the capture of low abundance multi-phosphopeptides from biosamples and identification of phosphorylation sites are largely limited due to the limited enrichment materials and their unclear interactions with multi-phosphopeptides. Here we propose using two cheap raw materials (CaCl₂·2H₂O and Na₂HPO₄·12H₂O) in 10 min at room temperature to synthesize the structurally simple Nanometric Calcium Phosphate (CaP) to resolve this challenge. The current results showed that the "simple" CaP has good selection specificity, high sensitivity and stability for multi-phosphopeptides enrichment and the identification of phosphorylation sites, which facilitate the popularization and application of phosphoproteomics research. Further, the interaction of CaP and multi-phosphopeptides were qualitatively characterized at the molecular/atomic level and the high affinity between them was quantified by the isothermal titration microcalorimeter based on the laws of thermodynamics. The results indicated that the interaction was a spontaneous (ΔG < 0) exothermic reaction with enthalpy reduction (ΔH < 0) and driven mainly by hydrogen bond and electrostatic interaction process.

Monodisperse Ti4+-immobilized macroporous adsorbent resins with polymer brush for improved multi-phosphopeptides enrichment in milk

Enrichment of phosphopeptides before mass spectrometry (MS) analysis is essential due to the limitations of low abundance and poor ionization efficiency in complex biological samples. Immobilized metal affinity chromatography (IMAC), especially titanium ion (Ti⁴⁺)-IMAC, has become a popular strategy for enrichment of phosphopeptides due to high selectivity and sensitivity. Conventional Ti⁴⁺-immobilized macroporous adsorption resin (MAR) fabricated by monolayer modification can preferentially capture mono-phosphopeptide over multi-phosphopeptides, which takes on more functions in the regulation of cell behaviors of organism. In this paper, a kind of monodisperse MAR microsphere with functional polymer brush (Ti⁴⁺-Brush@MAR) was prepared and modified via surface-initiated atom transfer radical polymerization (SI-ATRP). Compared with common Ti⁴⁺-MAR without polymer brush, Ti⁴⁺-Brush@MAR exhibited high enrichment specificity not only for mono-phosphopeptides but also for multi-phosphopeptides in β-casein or milk digest samples. As a result, a total of 93 unique phosphopeptides mapped to 18 phosphoproteins were identified from 5 μL milk, and the limit of detection is 10 fmol. It is expected that Ti⁴⁺-Brush@MAR would be utilized to enrich both multi-phosphopeptides and mono-phosphopeptides in additional biological or food samples.

Electrophoresis of Phosphoproteins on a Tandem Polymerized Gel

A substrate with n phosphorylated sites may have 2ⁿ phosphor-forms for temporal-spatial regulation of biological events. Because phosphates do not significantly change molecular masses but net charges of proteins, those isoforms cannot be separated by regular mass-based sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE). A tandem polymerized gel was developed to resolve phosphor-isoforms with different masses, charges, and posttranslational modifications. Without the usage of SDS, the electrophoresis was primarily performed on three adjacent acidic polyacrylamide gels. After being concentrated on a stacking gel, protonated proteins were then separated on the Zr⁴⁺ immobilized gel through the coordination of metal ions with phosphates followed by further charge and mass (z/m)-based electrophoretic separation on a TiO₂ containing gel. The presence of TiO₂ nanoparticles in the third gel is aimed for the initiation of the polymerization of acrylamide in acidic conditions upon ultraviolet irradiation. Distinct isoforms of α-S1-casein, α-S2-casein, β-casein, and κ casein model proteins located on 11, 8, 8, and 7 different bands of the tandem gel were unambiguously identified, respectively. With the tandem polymerized gel electrophoresis, new phosphorylation events that may occur simultaneously or sequentially were discovered in not only model proteins but also complex biological samples including human saliva, chicken egg, and sprouting maize. This provides a new tool to dissect complex biological processes that are triggered by dynamic phosphorylation events.

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.

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.

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.

Dual-Functional Ti(IV)-IMAC Material Enables Simultaneous Enrichment and Separation of Diverse Glycopeptides and Phosphopeptides

Simultaneous enrichment and fractionation of diverse proteins/peptides possessing different post-translational modifications (PTMs) from the same biological samples is highly desirable to reduce sample consumption, avoid complicated sample processing, and enable studies of potential crosstalks between different PTMs. In this work, we report a new approach to enable simultaneous enrichment and separation of glycopeptides, phosphopeptides, and mannose-6-phosphate (M6P) glycopeptides by using a dual-functional Ti(IV)-IMAC material. Moreover, we also made the separation of neutral and sialyl glycopeptides and mono- and multi-phosphopeptides possible by performing different elution processes according to the differences in their electrostatic or hydrophilic properties. These separations are effective and efficient to eliminate the signal suppression from neutral glycopeptides for sialyl glycopeptide detection, allowing separation of mono-phosphopeptides from multi-phosphopeptides, as well as detection of M6P glycopeptides that are free from the abovementioned modifications. This new strategy significantly improves the coverage and identification numbers of glycopeptides, phosphopeptides, and M6P glycopeptides by 1.9, 2.3, and 4.3-fold compared with the conventional method, respectively. This is the first report on simultaneous enrichment and separation of neutral and sialyl glycopeptides, mono- and multi-phosphopeptides, and M6P glycopeptides via dual-functional Ti(IV)- IMAC, revealing novel insights into potential crosstalk among these important PTMs.

Optical chemosensors for the detection of proximally phosphorylated peptides and proteins

Proximal multi-site phosphorylation is a critical post-translational modification in protein biology. The additive effects of multiple phosphosite clusters in close spatial proximity triggers integrative and cooperative effects on protein conformation and activity. Proximal phosphorylation has been shown to modulate signal transduction pathways and gene expression, and as a result, is implicated in a broad range of disease states through altered protein function and/or localization including enzyme overactivation or protein aggregation. The role of proximal multi-phosphorylation events is becoming increasingly recognized as mechanistically important, although breakthroughs are limited due to a lack of detection technologies. To date, there is a limited selection of facile and robust sensing tools for proximal phosphorylation. Nonetheless, there have been considerable efforts in developing optical chemosensors for the detection of proximal phosphorylation motifs on peptides and proteins in recent years. This review provides a comprehensive overview of optical chemosensors for proximal phosphorylation, with the majority of work being reported in the past two decades. Optical sensors, in the form of fluorescent and luminescent chemosensors, hybrid biosensors, and inorganic nanoparticles, are described. Emphasis is placed on the rationale behind sensor scaffolds, relevant protein motifs, and applications in protein biology.

Ti4+-immobilized hierarchically porous zirconium-organic frameworks for highly efficient enrichment of phosphopeptides

Ti⁴⁺-immobilized hierarchically porous zirconium-organic frameworks (denoted as THZr-MOFs) was prepared for phosphopeptide enrichment. The THZr-MOFs showed high specific surface area of 185.28 m² g^-1, wide pore-size distribution of 3 ~ 20 nm, good chemical stability and excellent hydrophilicity. Introduction of hierarchical pores in MOFs not only facilitated the accessibility of phosphopeptides to the internal metal affinity sites and reduce their mass transfer resistance, but also increased the exposure sites of metal affinity interaction and binding energies of Zr and Ti elements. Benefited from these advantages, the THZr-MOFs showed high adsorption capacity (79.8 μg mg^-1) towards standard phosphopeptide. A low detection limit (0.05 fmol μL^-1) and high enrichment selectivity (β-casein/BSA with a molar ratio of 1:5000) were also obtained by MALDI-TOF MS. The THZr-MOFs were applied to analyze complex samples including nonfat milk, human serum, and HeLa cell lysate. In total, 1432 phosphopeptides derived from 762 phosphoproteins were identified from human HeLa cell lysate. Schematic representation of the application of Ti⁴⁺-immobilized hierarchically porous zirconium-organic frameworks (denoted as THZr-MOFs) in high-efficiency and selective enrichment of low-abundance phosphopeptides from the tryptic digest of human HeLa cell lysate.

Sn-based metal-organic framework for highly selective capture of monophosphopeptides

Sn-based metal-organic framework (MOF) was utilized to effectively capture monophosphopeptides due to the unique affinity. The Sn-based MOF demonstrated the good sensitivity and selectivity in the model phosphoproteins enrichment and was successfully applied in the biological fluids.

Engineering Magnetic Guanidyl-Functionalized Supramolecular Organic Framework for Efficient Enrichment of Global Phosphopeptides

Comprehensive mass spectrometry-based proteomics analysis is currently available but remains challenging, especially for post-translational modifications of phosphorylated proteins. Herein, multifunctional magnetic pillar[5]arene supramolecular organic frameworks were fabricated and immobilized with arginine (mP5SOF-Arg) for highly effective enrichment of global phosphopeptides. The specific phosphate-P5/phosphate-guanidine affinities and large surface area with regular porosity contribute to the high enrichment capacity. By coupling with mass spectrometry, high detection sensitivity (0.1 fmol), excellent selectivity (1:5000 molar ratios of β-casein/cytochrome c), and high recyclability (seven cycles) were achieved for phosphopeptide analysis. mP5SOF-Arg can efficiently enrich phosphopeptides from practical samples, including defatted milk, egg yolk, and human saliva. Notably, a total of 450 phosphopeptides were explored for highly selective identification from A594 cells and 1445 phosphopeptides were identified from mouse liver tissue samples. mP5SOF-Arg exhibited great potential to serve as the basis for peptidomic research to identify phosphopeptides and provided insight for biomarker discovery.

Biomedical applications of dendritic fibrous nanosilica (DFNS): recent progress and challenges

Dendritic fibrous nanosilica (DFNS), with multi-component and hierarchically complex structures, has recently been receiving significant attention in various fields of nano-biomedicine. DFNS is an emerging class of mesoporous nanoparticles that has attracted great interest due to unique structures such as open three-dimensional dendritic superstructures with large pore channels and highly accessible internal surface areas. This overview aims to study the application of DFNS towards biomedical investigations. This review is divided into four main sections. Sections 1–3 are related to the synthesis and characterization of DFNS. The biomedical potential of DFNS, such as cell therapy, gene therapy, immune therapy, drug delivery, imaging, photothermal therapy, bioanalysis, biocatalysis, and tissue engineering, is discussed based on advantages and limitations. Finally, the perspectives and challenges in terms of controlled synthesis and potential nano-biomedical applications towards future studies are discussed.

Dendritic fibrous nanosilica (DFNS) , with multi-component and hierarchically complex structures, has recently been receiving significant attention in various fields of nano-biomedicine.

PAMAM–PMAA brush-functionalized magnetic composite nanospheres: a smart nanoprobe with tunable selectivity for effective enrichment of mono-, multi-, or global phosphopeptides

A novel PAMAM–PMAA brush functionalized magnetic composite nanosphere was successfully prepared for selective enrichment of mono-, multi-, or global phosphopeptides by modulating buffer polarity and acidity.

Multiphosphorylated peptides: importance, synthetic strategies, and applications for studying biological mechanisms

Advances in the synthesis of multiphosphorylated peptides and peptide libraries: tools for studying the effects of phosphorylation patterns on protein function and regulation.

A polymer monolith composed of a perovskite and cucurbit[6]uril hybrid for highly selective enrichment of phosphopeptides prior to mass spectrometric analysis

A hybrid monolith was prepared from perovskite and cucurbit[6]uril [poly(hydroxyethyl methacrylate-pentaerythritol triacrylate) monolith] for the enrichment of phosphopeptides. By coupling with mass spectrometry, three goals were simultaneously realized, viz. (a) selective enrichment of phosphopeptides from non-phosphopeptides, (b) identification of mono- and multi-phosphopeptides, and (c) recognition of tyrosine phosphopeptides. The perovskite introduced into the monolith warrants high selectivity for phosphopeptides even at a high (10,000:1) ratio of non-phosphopeptides to phosphopeptides, and and enables identification of eight mono- and multi-phosphopeptides from standard β-casein tryptic digests. Tyrosine phosphopeptides were specifically detected via the recognition capability of cucurbit[6]uril integrated into the monolith. The method has remarkably specific enrichment capacity for phosphopeptides from samples including human serum, nonfat milk, and human acute myelocytic leukemia cell lysate. Graphical abstractSchematic representation of a monolith integrated with perovskite and cucurbit[6]uril. The monolithic column was coupled with mass spectrometry and applied to the enrichment of phosphopeptides. The method has remarkably specific enrichment capacity for phosphopeptides from complex biological samples.

A targeted approach for the synthesis of multi-phosphorylated peptides: a tool for studying the role of phosphorylation patterns in proteins

Protein phosphorylation barcodes, clusters of several phosphorylation sites within a short unfolded region, control many cellular processes. Existing biochemical methods used to study the roles of these barcodes suffer from low selectivity and provide only qualitative data. Chemically synthesized multiphosphopeptide libraries are selective and specific, but their synthesis is extremely difficult using the current peptide synthesis methods. Here we describe a new microwave assisted approach for synthesizing a library of multiphosphopeptides, using the C-terminus of rhodopsin as a proof of concept. Our approach utilizes multiple protocols for synthesizing libraries of multiphosphopeptides instead of the inefficient single protocol methods currently used. Using our approach we demonstrated the synthesis with up to seven phosphorylated amino acids, sometimes next to each other, an accomplishment that was impractical before. Synthesizing the Rhodopsin derived multiphosphopeptide library enabled dissecting the precise phosphorylation barcode required for the recruitment, activation and modulation of the conformation of Arrestin. Since phosphorylation barcodes modulate the activity of hundreds of GPCRs, synthesizing libraries of multiphosphopeptides is the method of choice for studying their molecular mechanisms of action. Our approach provides an invaluable tool for evaluating how protein phosphorylation barcodes regulate their activity.

Organic molecule-assisted synthesis of Fe3O4/graphene oxide nanocomposites for selective capture of low-abundance peptides and phosphopeptides

The iron oxide nanoparticles (Fe₃O₄) were prepared by organic molecule-assisted method in aqueous solution. The facile synthetic process of Fe₃O₄ nanoparticles was conducted only by mixing FeCl₂ and 2-methylimidazole (2-MIM) without any additives. A possible growth mechanism of the Fe₃O₄ nanocrystals was proposed for this mild reaction. Then, the Fe₃O₄ nanoparticles were anchored onto graphene oxide (GO) sheets in water by ultrasound-assisted method, forming an affinity probe with strong biocompatibility. Due to the hydroxy and carboxylic groups of GO sheets, Fe₃O₄/GO probe exhibits excellent performance for enriching low-abundance hydrophilic peptides, while the Fe₃O₄ nanoparticles endure the probe with specific affinity to phosphopeptides. The analytical protocol was developed for sequential enrichment of low-abundance peptides and phosphopeptides by the affinity probe. It exhibited the sequence coverage of 26% for capture of 17 low-abundance peptides from bovine serum albumin (BSA), as well as the selectivity of 1:1:100 for phosphopeptides from α-/β-casein/BSA, and low detectable concentration of 2.5 fmol and probe reusability of 5 times for capture of phosphopeptides from α-/β-casein. Consequently, the prepared Fe₃O₄/GO material possesses excellent feature as multifunctional affinity probe for low-abundance peptides including phosphopeptides from complex biological matrices detected by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Novel Ti4+-Chelated Polyoxometalate/Polydopamine Composite Microspheres for Highly Selective Isolation and Enrichment of Phosphoproteins

Selective isolation and enrichment of phosphoproteins play critical roles for identification of biomarkers in biological applications. Herein, a kind of polyoxometalate (P₅W₃₀)/polydopamine (PDA) composite microspheres is readily synthesized via an in situ polymerization way, followed by immobilization of Ti⁴⁺ on the surface of the microspheres to obtain P₅W₃₀/PDA-Ti⁴⁺. Due to metal affinity and π stacking interaction, this novel material exhibits high selectivity to β-casein (β-ca), and the theoretical maximum adsorption capacity is as high as 1250 mg g^-1, fitting well with the Langmuir model. The captured β-ca can be collected by using Britton-Robinson (B-R) buffer at pH 7.0, and a recovery of 81.5% is acquired. The enrichment factor is over 150 at a mass ratio of BSA/β-ca = 100:1, indicating that phosphoproteins can be purified by P₅W₃₀/PDA-Ti⁴⁺. Moreover, the application of P₅W₃₀/PDA-Ti⁴⁺ as sorbent in real biological samples has been investigated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis, and the consequences show that this kind of material is able to selectively isolate phosphoproteins from complex samples such as drinking milk and chicken egg white.

Postsynthetic Functionalization of Zr4+-Immobilized Core-Shell Structured Magnetic Covalent Organic Frameworks for Selective Enrichment of Phosphopeptides

Chemical modification of covalent organic frameworks (COFs) is indispensable for integrating functionalities of greater complexity and accessing advanced COF materials suitable for more potential applications. Reported here is a novel strategy for fabricating controllable core-shell structured Zr⁴⁺-immobilized magnetic COFs (MCNC@COF@Zr⁴⁺) composed of a high-magnetic-response magnetic colloid nanocrystal cluster (MCNC) core, Zr⁴⁺ ion-functionalized two-dimensional COFs as the shell by sequential postsynthetic functionalization and, for the first time, the application of the MCNC@COF@Zr⁴⁺ composites for efficient and selective enrichment of phosphopeptides. The as-prepared MCNC@COF@Zr⁴⁺ composites possess regular porosity with large surface areas, high Zr⁴⁺ loading amount, strong magnetic responsiveness, and good thermal/chemical stability, which can serve as an ideal adsorbent for selective enrichment of phosphopeptides and simultaneous size exclusion of biomacromolecules, such as proteins. The high detection sensitivity (10 fmol) together with the excellent recovery of phosphopeptides is also obtained. These outstanding features suggest that the MCNC@COF@Zr⁴⁺ composites are of great benefit for pretreatment prior to mass spectrometry analysis of phosphopeptides. In addition, the performance of the developed approach in selective enrichment of phosphopeptides from the tryptic digests of defatted milk and directly specific capture of endogenous phosphopeptides from human serum gives powerful proof for its high selectivity and effectiveness in identifying the low-abundance phosphopeptides from complicated biological samples. This study not only provides a strategy for versatile functionalization of magnetic COFs but also opens a new avenue in their use in phosphoproteome analysis.

Highly Specific Enrichment of Multi-phosphopeptides by the Diphosphorylated Fructose-Modified Dual-Metal-Centered Zirconium-Organic Framework

Multisite phosphorylation of a protein, generally occurring in biological processes, plays important roles in the regulation of cellular functions. However, the identification of multi-phosphopeptides especially at low abundance is a big challenge as the extreme hydrophilicity and poor ionization efficiency of the multiphosphorylated peptides restrict the deep inspection of multisite phosphorylation processes. In this study, the highly specific enrichment of multiphosphorylated peptides was achieved via the modification of the dual-metal-centered zirconium-organic framework with the diphosphorylated fructose. The diphosphorylated fructose-modified dual-metal-centered zirconium-organic framework (DZMOF-FDP) demonstrated the highly specific affinity to the multiple phosphorylated peptides, with the density functional theory calculations explaining the plausible mechanism for multi-phosphopeptides on the DZMOF-FDP. The selective capture of multi-phosphopeptides from mimic samples confirmed the superior performance of the DZMOF-FDP, with comprehensive comparisons to other modification agents, such as orthophosphate and pyrophosphate. A number of 1871 multiphosphorylated peptides captured by DZMOF-FDP from tryptic digests of HeLa cell lysate could be identified, significantly higher than that by the pristine DZMOF. The deliberately designed modification with diphosphorylated fructose for the dual-zirconium-centered metal-organic framework materials suggests an efficient strategy to develop new enrichment methods in the selective capture of target analytes by judiciously optimizing specific modifiers for adsorbents.

Dendritic Mesoporous Silica Nanoparticles with Abundant Ti4+ for Phosphopeptide Enrichment from Cancer Cells with 96% Specificity

Selective enrichment and sensitive detection of phosphopeptides are of great significance in many bioapplications. In this work, dendritic mesoporous silica nanoparticles modified with polydopamine and chelated Ti⁴⁺ (denoted DMSNs@PDA-Ti⁴⁺) were developed to improve the enrichment selectivity of phosphopeptides. The unique central-radial pore structures endowed DMSNs@PDA-Ti⁴⁺ with a high surface area (362 m² g^-1), a large pore volume (1.37 cm³ g^-1), and a high amount of chelated Ti⁴⁺ (75 μg mg^-1). Compared with conventional mesoporous silica-based materials with the same functionalization (denoted mSiO₂@PDA-Ti⁴⁺) and commercial TiO₂, DMSNs@PDA-Ti⁴⁺ showed better selectivity and a lower detection limit (0.2 fmol/μL). Moreover, 2422 unique phosphopeptides were identified from HeLa cell extracts with a high specificity (>95%) enabled by DMSNs@PDA-Ti⁴⁺, better than those in previous reports.

Detection of peptides with intact phosphate groups using MALDI TOF/TOF and comparison with the ESI-MS/MS

A wide variety of post-translational modifications such as oxidation, phosphorylation, glycosylation, methylation, and acetylation play critical roles in cellular functions. Detection of post-translational modifications in proteins is important to understand their crucial roles in cellular functions. Identifying each modification requires special attention in mass spectral acquisition and analysis. Here, we report a mass spectral method for the detection of multiple phosphorylations in peptides by analyzing their products after fragmentation. Synthetic peptides were used to identify these modifications by matrix-assisted laser desorption/ionization (MALDI) TOF/TOF. Peptides with serine, threonine, and tyrosine were used with mono- to tetra-phosphorylation sites in different combinations to get insights into their fragmentation and identify the location of these sites. The y-ion series were observed without the loss of phosphate groups and were thus very useful in determining the localization and sequence of the phosphate residues. Acetylation of the peptides was found to be useful in detecting the b1-ion and helped in identifying the N-terminus. When a mixture of the phosphorylated peptides (from mouse protein sequences) were analyzed by LC-MS/MS on a Velos Orbitrap Mass Spectrometer and the data subjected to analysis by Sequest using the mouse database, the peptides were identified along with the parent proteins. A comparison of MALDI TOF/TOF spectra with ESI MS/MS helped in eliminating falsely discovered peptides using the database search.

Hydrogen bond based smart polymer for highly selective and tunable capture of multiply phosphorylated peptides

Multisite phosphorylation is an important and common mechanism for finely regulating protein functions and subsequent cellular responses. However, this study is largely restricted by the difficulty to capture low-abundance multiply phosphorylated peptides (MPPs) from complex biosamples owing to the limitation of enrichment materials and their interactions with phosphates. Here we show that smart polymer can serve as an ideal platform to resolve this challenge. Driven by specific but tunable hydrogen bonding interactions, the smart polymer displays differential complexation with MPPs, singly phosphorylated and non-modified peptides. Importantly, MPP binding can be modulated conveniently and precisely by solution conditions, resulting in highly controllable MPP adsorption on material surface. This facilitates excellent performance in MPP enrichment and separation from model proteins and real biosamples. High enrichment selectivity and coverage, extraordinary adsorption capacities and recovery towards MPPs, as well as high discovery rates of unique phosphorylation sites, suggest its great potential in phosphoproteomics studies.

Capture of low-abundance multiply phosphorylated peptides (MPPs) is difficult due to limitation of enrichment materials and their interactions with phosphates. Here the authors show, a smart polymer driven by specific but tunable hydrogen bonding interactions can differentially complex with MPPs, singly phosphorylated and non-modified peptides.

Renal Clearable Peptide Functionalized NaGdF4 Nanodots for High-Efficiency Tracking Orthotopic Colorectal Tumor in Mouse

The effective delivery of bioimaging probes to a selected cancerous tissue has extensive significance for biological studies and clinical investigations. Herein, the peptide functionalized NaGdF₄ nanodots (termed as, pPeptide-NaGdF₄ nanodots) have been prepared for highly efficient magnetic resonance imaging (MRI) of tumor by formation of Gd-phosphonate coordinate bonds among hydrophobic NaGdF₄ nanodots (4.2 nm in diameter) with mixed phosphorylated peptide ligands including a tumor targeting phosphopeptide and a cell penetrating phosphopeptide. The tumor targeting pPeptide-NaGdF₄ nanodots have paramagnetic property with ultrasmall hydrodynamic diameter (HD, c.a., 7.3 nm) which greatly improves their MRI contrast ability of tumor and facilitates renal clearance. In detail, the capability of the pPeptide-NaGdF₄ nanodots as high efficient contrast agent for in vivo MRI is evaluated successfully through tracking small drug induced orthotopic colorectal tumor (c.a., 195 mm³ in volume) in mouse.

Simple preparation of magnetic metal-organic frameworks composite as a "bait" for phosphoproteome research

Phosphospecific enrichment techniques and mass spectrometry (MS) are primary tools for comprehending the cellular phosphoproteome. In this work, a rational and extremely facile route to synthesize the magnetic metal-organic frameworks (mMOFs) was employed and the prepared composite was first utilized as a "bait" for selective enrichment of phosphopeptides. Typically, the mMOFs was synthesized via electrostatic self-assembly between the negatively charged Fe₃O₄ magnetic nanoparticles (MNPs) and positively charged MIL-101(Fe). The obtained Fe₃O₄/MIL-101(Fe) composite possessed well-defined structures, rough surface, highly specific surface area and excellent magnetic property. To demonstrate their ability for enrichment of phosphopeptides, we applied Fe₃O₄/MIL-101(Fe) as a "bait" to capture the phosphopeptides from standard protein digestion and practical samples. The enriched phosphopeptides were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The MS results show that the Fe₃O₄/MIL-101(Fe) exhibits superior enrichment performance for phosphopeptides with low detectable concentration assessed to be 8 fmol, selectivity investigated to be 1:1000 using β-casein/bovine serum albumin mixture and enrichment recovery evaluated to be 89.8%. Based on these excellent properties, the prepared composite was used to enrich the phosphopeptides from tilapia eggs biological samples for the first time. A total number of 51 phosphorylation sites were identified from the digest of tilapia eggs proteins, suggesting the excellent potential of Fe₃O₄/MIL-101(Fe) composite in the practical application.

A combination strategy using two novel cerium-based nanocomposite affinity probes for the selective enrichment of mono- and multi-phosphopeptides in mass spectrometric analysis

The sequential enrichment of mono- and multi-phosphopeptides was successfully achieved using two novel Ce-based nanocomposite affinity probes.

Dual-Metal Centered Zirconium-Organic Framework: A Metal-Affinity Probe for Highly Specific Interaction with Phosphopeptides

The highly specific affinity between probes and phosphopeptides is the fundamental interaction for selective identification of phosphoproteomes that uncover the mechanisms of signal transduction, cell cycle, enzymatic regulation, and gene expression in biological systems. In this study, a metal-affinity probe possessing both interactions of metal oxide affinity chromatography (MOAC) and immobilized metal ion affinity chromatography (IMAC) was facilely prepared by immobilizing zirconium(IV) on a zirconium-organic framework of UiO-66-NH₂, which holds dual-metal centers of not only the inherent Zr-O cluster but also the immobilized Zr(IV) center. This dual-metal centered zirconium-organic framework (DZMOF) demonstrates as a highly specific metal-affinity probe toward the extraction of phosphopeptides due to the metal-affinity interactions of MOAC and IMAC toward either mono-phosphorylated or multi-phosphorylated peptides. The binding energies of zirconium 3d_5/2 and 3d_3/2 in this DZMOF are 183.07 and 185.47 eV, respectively, which are higher than those of the intact UiO-66-NH₂ (182.84 and 185.17 eV, respectively), confirming the higher metal-affinity interaction between the DZMOF and phosphopeptides. This high metal-affinity probe presents an unprecedented strong performance in anti-nonspecific interference during the capturing of phosphopeptides of β-casein with the molar ratio of β-casein vs bovine serum albumin up to ca. 1:5000. The enrichment of phosphopeptides from a human saliva sample by DZMOF further confirms the great potential of DZMOF in the extraction of low-abundance phosphopeptides for real complex biological samples.

Magnetic Nanospheres Encapsulated by Mesoporous Copper Oxide Shell for Selective Isolation of Hemoglobin

A novel strategy for the preparation of magnetic nanospheres encapsulated by mesoporous copper oxide shell, shortly termed as Fe₃O₄@mCuO, is reported via the calcination of Cu(NH₃)₄(NO₃)₂ into continuous mesoporous CuO shell onto the surface of Fe₃O₄ nanoparticles. The magnetic nanospheres are characterized to possess stable core-shell structure with a crystalline mesoporous CuO layer, exhibiting a CuO loading content of 25.2 ± 1.1% along with a favorable magnetic susceptibility. Fe₃O₄@mCuO nanospheres exhibit favorable selectivity on the adsorption of hemoglobin with a high adsorption capacity of up to 1162.5 mg g^-1. After adsorption, the high magnetic susceptibility allows convenient separation of the nanospheres by an external magnet. The retained hemoglobin could be readily recovered by using 0.5% (m/v) sodium dodecyl sulfate (SDS) as stripping reagent, providing a recovery of 78%. Circular dichroism spectra illustrate virtually no change in the conformation of hemoglobin after the process of adsorption/desorption. Fe₃O₄@mCuO nanospheres are further applied for the selective isolation of hemoglobin from human whole blood, achieving high-purity hemoglobin as demonstrated by SDS-PAGE (polyacrylamide gel electrophoresis) assays.

NiCoMnO4: A Bifunctional Affinity Probe for His-Tagged Protein Purification and Phosphorylation Sites Recognition

A bifunctional affinity probe NiCoMnO4 was designed and prepared with controllable morphology and size using facile methods. It was observed that the probe could be applied in His-tagged proteins purification and phosphopeptides enrichment simply through the buffer modulation. NiCoMnO4 particles showed satisfactory cycling performance for His-tagged proteins purification and broad pH-tolerance of loading buffer for phosphopeptides affinity. Therefore, a high-throughput, cost-effective, and efficient protein/peptide purification method was developed within 10 min based on the novel bifunctional affinity probe.