Resol/triblock copolymer composite-guided smart fabrication of carbonized mesopores for efficiently decoding exosomal glycans.

Soft-template carbonized mesopores were developed for the purpose of enriching urinary exosomal glycans through organic-organic self-assembly using block copolymers and resol precursors. With a high surface area of 229 m2 g-1, a small pore size of 3.1 nm, and a significant amount of carbon that specifically interacts with oligosaccharides in glycans, this carbonized mesopore material exhibits high selectivity and low limits of detection (5 ng µL-1) towards glycans. Our analysis of complex urine samples from healthy volunteers and bladder carcinoma patients successfully profiled 48 and 56 exosomal glycans, respectively, and 16 of them were significantly changed. Moreover, one upregulated bisecting N-acetylglucosamine (GlcNAc)-type glycan with core fucose, two upregulated and two downregulated terminal-sialylated glycans were revealed to be linked to bladder carcinoma. This approach is of significant importance for understanding diseases that arise from protein glycosylation mutations, and it may contribute to the development of novel diagnostic and therapeutic strategies for bladder carcinoma.

Dual metal cations coated magnetic mesoporous silica probe for highly selective capture of endogenous phosphopeptides in biological samples.

For the first time, dual metal ions (Ti4+-Zr4+) were successfully modified into the channel of magnetic mesoporous silica to obtain an affinity probe for highly selective capture of endogenous phosphopeptides in biological samples. The newly prepared Fe3O4@mSiO2@Ti4+-Zr4+ composites possessed the advantages of ordered mesoporous channels, superparamagnetism, and enhanced affinity properties of dual metal ions of Ti4+ and Zr4+. The phosphopeptide enrichment efficiency of the Fe3O4@mSiO2@Ti4+-Zr4+ composite was investigated, and the result indicated an ultrahigh size exclusive ability (weight ratio of ß-casein tryptic digests, BSA, and α-casein protein reached up to 1:1000:1000). Compared to magnetic affinity probes with single metal ions (Fe3O4@mSiO2@Ti4+, Fe3O4@mSiO2@Zr4+), the composite possessed stronger specificity, higher sensitivity, and better efficiency; and more importantly, it showed much enhanced enrichment ability towards both mono- and multi-phosphorylated peptides. Additionally, by utilizing the Fe3O4@mSiO2@Ti4+-Zr4+ affinity probe, a total number of 104 endogenous phosphopeptides including 95 mono-phosphopeptides and 9 multi-phosphopeptides were captured and identified from human saliva, indicating the great potential for the application of the novel probe for the peptidome analysis in the future. Graphic abstract.

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

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

Magnetite nanoparticles coated with mercaptosuccinic acid-modified mesoporous titania as a hydrophilic sorbent for glycopeptides and phosphopeptides prior to their quantitation by LC-MS/MS.

A hydrophilic material consisting of a magnetite core coated with mercaptosuccinic acid modified mesoporous titania (denoted as Fe3O4@mTiO2-MSA) has been fabricated. It is shown to be a viable sorbent for capturing glycopeptides and phosphopeptides. The sorbent combines the features of metal oxide-based affinity chromatography and of hydrophilic interaction liquid chromatography (HILIC) with the advantages of using mesoporous titania. The use of magnetic microspheres provides magnetic response and simplifies separation. Following elution with 10% ammonia, the peptides were submitted to LC-MS/MS analysis. The method enabled 327 phosphopeptides and 65 glycopeptides to be identified in three isolated replicates of merely 5 µL samples of human saliva. Among them, the phosphorylation sites and glycosylation sites were detected in 20 peptide segments. Graphical abstract Schematic presentation of preparation of novel hydrophilic magnetic mesoporous titania nanomaterials (Fe3O4@mTiO2-MSA). This specific sorbent exhibits highly selective and efficient simultaneous adsorption ability for both glycopeptides and phosphopeptides from biosamples by mass spectrometric analysis.

A capillary column packed with a zirconium(IV)-based organic framework for enrichment of endogenous phosphopeptides.

A zirconium(IV)-based metal organic framework (Zr-MOF) was deposited on polydopamine-coated silica microspheres to form microspheres of type SiO2@PDA@Zr-MOF. These were packed into capillary columns for enrichment of phosphopeptides. The column was off-line coupled to both matrix-assisted laser desorption/ionization time of flight mass spectrometry and LC-ESI-MS/MS. The method has a detection limit as low as 4 fmol of ß-casein digest and a selectivity as high as 1:1000 (molar ratio of ß-casein and BSA digest). It was applied to the analysis of human saliva. In total, 240 endogenous phosphopeptides were identified in only 25 µL human saliva. Graphical abstract A zirconium-based metal organic framework (Zr-MOF) was modified outside of polydopamine-coated silica microspheres to form microspheres named SiO2@PDA@Zr-MOF. Then they were packed in capillary columns for selective enrichment of phosphopeptides via interaction between Zr-O clusters and phosphate groups. The pre-concentration resulted in a better detection of phosphopeptides by mass spectrometry. Tris: Tris(hydroxymethyl)aminomethane; DMF: Dimethyl Formamide; Zr-MOF: Zirconium(IV)-organic framework; MOAC: Metal oxide affinity chromatography.

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

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

Rapid synthesis of titanium(IV)-immobilized magnetic mesoporous silica nanoparticles for endogenous phosphopeptides enrichment.

The MALDI-TOF MS has already been a main platform for phosphoproteome analysis. However, there are some weaknesses in direct analysis of endogenous phosphopeptides by MALDI-TOF MS because of the serious suppression effect and poor ionization efficiency, which is brought by the excess of nonphosphopeptides and protein. It is essential to enrich endogenous phosphopeptides from complex biosamples efficiently prior to MALDI-TOF MS analysis. Herein, we present a time-saving and detailed protocol for the synthesis of titanium(iv)-immobilized magnetic mesoporous silica nanoparticles (denoted as Fe3 O4 @mSiO2 -Ti4+ ), the subsequent enrichment process, and MALDI-TOF MS analysis. We tested the LOD, size-exclusive effect, reproducibility, and stability of Fe3 O4 @mSiO2 -Ti4+ nanoparticles. Furthermore, the ability of this protocol for identifying endogenous phosphopeptides in healthy human serum and saliva was investigated.

Development of immobilized Sn4+ affinity chromatography material for highly selective enrichment of phosphopeptides.

In this work, we first immobilized tin(IV) ion on polydopamine-coated magnetic graphene (magG@PDA) to synthesize Sn4+ -immobilized magG@PDA (magG@PDA-Sn4+ ) and successfully applied the material to highly selective enrichment of phosphopeptides. The material gathered the advantages of large surface area of graphene, superparamagnetism of Fe3 O4 , good hydrophilicity and biocompatibility of polydopamine, and strong interaction between Sn4+ and phosphopeptides. The enrichment performance of magG@PDA-Sn4+ toward phosphopeptides from digested ß-casein at different concentrations, with and without added digested BSA was investigated and compared with magG@PDA-Ti4+ . The results showed high selectivity and sensitivity of the Sn4+ -IMAC material toward phosphopeptides, as good as the Ti4+ -IMAC material. Finally, magG@PDA-Sn4+ was applied to the analysis of endogenous phosphopeptides from a real sample, human saliva, with both MALDI-TOF MS and nano-LC-ESI-MS/MS. The results indicated that the as-synthesized Sn4+ -IMAC material not only has good enrichment performance, but also could serve as a supplement to the Ti4+ -IMAC material and expand the phosphopeptide coverage enriched by the single Ti4+ -IMAC material, demonstrating the broad application prospects of magG@PDA-Sn4+ in phosphoproteome research.

Highly efficient and selective enrichment of glycopeptides using easily synthesized magG/PDA/Au/l-Cys composites.

Highly selective and efficient enrichment of glycopeptides from complex biological samples is necessary. In this study, novel zwitterionic hydrophilic polydopamine-coated magnetic graphene composites (magG/PDA/Au/l-Cys) were synthesized and applied to the enrichment of glycopeptides. The size, morphology, and composition of magG/PDA/Au/l-Cys composites were investigated by transmission electron microscopy, scanning electron microscopy, FT-infrared spectroscopy, and X-ray diffraction. The composites possessed a number of desirable characteristics, including good biocompatibility easy separation property and excellent hydrophilicity. By virtue of the features contributed by different ingredients, the prepared composites demonstrated superior performance for glycopeptide enrichment with high sensitivity (0.1 fmol), efficiency, selectivity (1:100), and repeatability (at least ten times). In addition, the composites were successfully applied to the enrichment of glycopeptides from human serum and 40 unique N-glycosylation peptides from 31 different N-linked glycoproteins were identified. The superior hydrophilic material is of great potential for the analysis of glycoproteins.

Design and synthesis of magnetic binary metal oxides nanocomposites through dopamine chemistry for highly selective enrichment of phosphopeptides.

In this work, for the first time, magnetic binary metal oxides nanocomposites which integrated Zr and Ti into one entity on an atomic scale on polydopamine coated magnetic graphene (magG/PD/(Zr-Ti)O4 ) was designed and synthesized, and applied to the enrichment of phosphopeptides. The newly prepared magG/PD/(Zr-Ti)O4 composites gathered the advantages of large surface area, superparamagnetism, biocompatibility and the enhanced affinity properties to phosphopeptides. MagG/PD/ZrO2 , magG/PD/TiO2 , as well as the simple physical mixture of them were introduced to compare with magG/PD/(Zr-Ti)O4 composites. High sensitivity (1 pg/µL or 4.0 × 10(-11) M) and selectivity (weight ratio of ß-casein and BSA reached up to 1:8000) toward phosphopeptides were also presented for magG/PD/(Zr-Ti)O4 composites. Additionally, mouse brain tissue was chose as the real samples to further investigate the phosphopeptides enrichment ability of this new material.

Synthesis of bifunctional TiO2@SiO2-B(OH)2@Fe3O4@TiO2 sandwich-like nanosheets for sequential selective enrichment of phosphopeptides and glycopeptides for mass spectrometric analysis.

In this work, the bifunctional TiO2@SiO2-B(OH)2@Fe3O4@TiO2 sandwich-like nanosheets were designed and synthesized for the sequential selective enrichment of phosphopeptides and glycopeptides. Due to the bifunctional property of the titanium dioxide and the boronic acid group, the nanosheets were successfully applied to the enrichment of phosphopeptides and glycopeptides sequentially, evaluated by capturing phosphopeptides from tryptic digestion of model phosphoprotein bovine ß-casein diluted to 0.02 ng/µL (8 × 10(-16) mol/µL) and glycopeptides from tryptic digestion of model glycoprotein horseradish peroxidase (HRP) diluted to 0.1 ng/µL (2.5 × 10(-15) mol/µL). The enrichment selectivity of the bifunctional nanosheets was evaluated by capturing phosphopeptides from a peptide mixture of ß-casein and bovine serum albumin (BSA) with the molar ratio of 1:1000 (8.3 × 10(-12) mol of ß-casein and 8.3 × 10(-9) mol of BSA in 100 µL) and glycopeptides from a peptide mixture of HRP and BSA up to the ratio of 1:50 (5.0 × 10(-11) mol of HRP and 2.5 × 10(-9) mol of BSA in 100 µL). Graphical Abstract A workflow of the sequential enrichment strategy for phosphopeptides and glycopeptides by the bifunctional TiO2@SiO2-B(OH)2@Fe3O4@TiO2 sandwich-like nanosheets.

Facile synthesis of magnetic poly(styrene-co-4-vinylbenzene-boronic acid) microspheres for selective enrichment of glycopeptides.

In this work, the composites of magnetic Fe3 O4 @SiO2 @poly (styrene-co-4-vinylbenzene-boronic acid) microspheres with well-defined core-shell-shell structure were facilely synthesized and applied to selectively enrich glycopeptides. Due to the relatively large amount of vinyl groups introduced by 3-methacryloxy-propyl-trimethoxysilane on the core-shell surface, the poly(styrene-co-4-vinylbenzeneboronic acid) (PSV) was coated with high efficiency, resulting in a large amount of boronic acid on the outermost polymer shell of the Fe3 O4 @SiO2 @PSV microspheres, which is of great importance to improve the enrichment efficiency for glycopeptides. The obtained Fe3 O4 @SiO2 @PSV microspheres were successfully applied to the enrichment of glycopeptides with strong specificity and high selectivity, evaluated by capturing glycopeptides from tryptic digestion of model glycoprotein HRP diluted to 0.05 ng/µL (1.25 × 10(-13) mol, 100 µL), tryptic digest of HRP and nonglycosylated BSA up to the ratio of 1:120 w/w and the real complex sample human serum with 103 unique N-glycosylation peptides of 46 different glycoproteins enriched.

Membrane protein isolation and identification by covalent binding for proteome research.

A novel method to achieve highly efficient identification of membrane proteins (MPs) has been developed based on a covalent binding (CB) strategy. For this purpose, magnetic nanoparticles coated with a PEG layer were synthesized. The PEG chain end was functionalized to form the PEG-tresyl group, which is an octopus-like long arm to capture the free amino groups of MPs. The long arm could be used to bind proteins in a high concentration of the SDS medium. Then, the SDS and interfering substances were completely depleted by washing. The CB proteins could form a molecular monolayer on the surface of the nanoparticles in the denatured state, which was significantly favorable for the proteolysis of MPs. Therefore, isolation with CB and highly efficient digestion resulted in a larger scale of MPs. The method has been verified by a proteome identification of mouse liver samples. A total of 2946 MPs were identified in an MP fraction. A total of 1505 proteins were characterized as integral MPs, and 735 MPs were identified beyond the largest database summarized by PeptideAtlas. This approach has great potential for membrane proteome research.

Hydrophilic polydopamine-coated magnetic graphene nanocomposites for highly efficient tryptic immobilization.

In this work, polydopamine-coated magnetic graphene (MG@PDA) nanocomposites were synthesized by a facile method. Trypsin was then directly immobilized on the surface of the nanocomposites through simple PDA chemistry with no need for introducing any other coupling groups. The as-made MG@PDA nanocomposites inherit not only the large surface area of graphene which makes them capable of immobilizing high amount of trypsin (up to 0.175 mg/mg), but also the good hydrophilicity of PDA which greatly improves their biocompatibility. Moreover, the strong magnetic responsibility makes them easy to be separated from the digested peptide solution when applying a magnetic field. The feasibility of the trypsin-immobilized MG@PDA (MG@PDA-trypsin) nanocomposites for protein digestion was investigated and the results indicated their high digestion efficiency in a short digestion time (10 min). In addition, the reusability and stability of the MG@PDA-trypsin nanocomposites were also tested in our work. To further confirm the efficiency of MG@PDA-trypsin nanocomposites for proteome analysis, they were applied to digest proteins extracted from skimmed milk, followed by nano RPLC-ESI-MS/MS analysis, and a total of 321 proteins were identified, much more than those obtained by 16-h in-solution digestion (264 proteins), indicating the great potential of MG@PDA-trypsin nanocomposites as the supports for high-throughput proteome study.

Metal oxide affinity chromatography platform-polydopamine coupled functional two-dimensional titania graphene nanohybrid for phosphoproteome research.

In this work, a facile route was initially developed for preparation of a novel metal oxide affinity chromatography (MOAC) material by grafting titania nanoparticles on polydopamine (PD)-coated graphene (denoted as G@PD@TiO2). In the first step, self-assemble polymerization of dopamine on graphene was performed in basic solution at room temperature, which not only offered the coupling linker between titania and graphene but also improved the hydrophilicity and biological compatibility of the nanohybrids. Thereafter, the titania nanoparticles were grafted on the surface of the PD-coated graphene via a simple hydrothermal treatment. The as-prepared G@PD@TiO2 nanohybrids exhibited high sensitivity (detection limit of 5 fmol) and high selectivity for phosphopeptides at a low molar ratio of phosphopeptides/nonphosphopeptides (1:1000). Moreover, the as-prepared nanohybrids were also investigated for enrichment of phosphopeptides from real biological samples (human serum and mouse brain). A total number of 556 phosphorylation sites were identified from the digest of mouse brain proteins, showing great potential in the practical application.

Magnetic quaternary ammonium polymer bearing porous agarose for selective extraction of Aristolochic acids in the plasma.

Aristolochic acids (AAs) naturally occurring in the herbal genus Aristolochia are associated with a high risk of kidney failure, multiple tumors and cancers. However, approaches with high selectivity and rapidity for measuring AAs in biological samples are still inadequate. Inspired by the mechanism of AAs-induced nephrotoxicity, we designed a hybrid magnetic polymer-porous agarose (denoted as MNs@SiO2M@DNV-A), mimicking the effect of basic and aromatic residues of organic anion transporter 1 (OAT1) for efficient enriching aristolochic acid I (AA I) and aristolochic acid II (AA II) in the plasma. The monomers of vinylbenzyl trimethylammonium chloride (VBTAC), N-vinyl-2-pyrrolidinone (NVP) and divinylbenzene (DVB) were employed to construct the polymer layer, which provided a selective adsorption for AAs by multiple interactions. The porous agarose shell contributed to remove interfering proteins in the plasma samples. A magnetic solid-phase extraction (MSPE) based on the proposed composite enhanced the selectivity toward AA I and AA II in the plasma samples. In combination of HPLC analysis, the proposed method was proved to be applicable to fast and specific quantification of AAs in blood samples, which was characterized by a good linearity, high sensitivity, acceptable recovery, excellent repeatability and satisfactory reusability.

Hydrophilic polydopamine-coated graphene for metal ion immobilization as a novel immobilized metal ion affinity chromatography platform for phosphoproteome analysis.

To discover trace phosphorylated proteins or peptides with great biological significance for in-depth phosphoproteome analysis, it is urgent to develop a novel technique for highly selective and effective enrichment of phosphopeptides. In this work, an IMAC (immobilized metal ion affinity chromatography) material with polydopamine coated on the surface of graphene and functionalized with titanium ions (denoted as Ti(4+)-G@PD) was initially designed and synthesized. The newly prepared Ti(4+)-G@PD with enhanced hydrophilicity and biological compatibility was characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and infrared (IR), and its performance for selective and effective enrichment of phosphopeptide was evaluated with both standard peptide mixtures and human serum.

Decyl-perfluorinated magnetic mesoporous microspheres for extraction and analysis perfluorinated compounds in water using ultrahigh-performance liquid chromatography-mass spectrometry.

In this work, the interior-walls decyl-perfluorinated functionalized magnetic mesoporous microspheres (F(17)-Fe(3)O(4)@mSiO(2)) were synthesized for the first time, and applied as adsorbents to extract and concentrate perfluorinated compounds (PFCs) from water samples. The fluorous functionalized interior pore-walls contributed to the high-selective preconcentration of PFCs due to fluorous affinity; and abundant silanol groups on the exterior surface of microspheres contributed to the good dispersibility in water sample. Four kinds of PFCs were selected as model analytes, including perfluorooctanoic acid, perfluorononanoic acid, perfluorododecanoic acid, and perfluorooctane sulphonate. In addition, UHPLC-ESI/MS/MS was introduced to the fast and sensitive detection of the analytes after sample pretreatment. Important parameters of the extraction procedure were optimized, including salinity, eluting solvent, the amount of F(17)-Fe(3)O(4)@mSiO(2) microspheres, and extraction time. The optimized procedure took only 10 min to extract analytes with high recoveries and merely 800-µL acetonitrile to elute analytes from the magnetic adsorbents. Validation experiments showed good linearity (0.994-0.998), precision (2.6-7.6%), high recovery (93.4-105.7%) of the proposed method, and the limits of detection were from 0.008 to 0.125 µg/L. The F(17)-Fe(3)O(4)@mSiO(2) magnetic microspheres have the advantages of great dispersibility in aqueous solution, high specificity of extraction, large surface area, and efficient separation ability. The results showed that the proposed method based on F(17)-Fe(3)O(4)@mSiO(2) microspheres is a simple, fast, and sensitive tool for the analysis of PFCs in water sample.

Enhanced specificity of bimetallic ions via mesoporous confinement for phosphopeptides in human saliva.

Phosphopeptides were of great significance in disease diagnosis and monitoring its dynamic changes. In this article, we proposed a more efficient method to synthesize a kind of bimetallic mesoporous silica nanomaterials (Fe3O4@mSiO2-PO3-Ti4+/Zr4+) and applied it to the analysis of phosphopeptides in human saliva samples based on IMAC technology. The chelation group was introduced into mesopores at the same time as the formation of mesoporous silica which significantly reduced the synthesis procedure and improved the synthesis efficiency. The as-prepared materials showed great sensitivity, selectivity and size-exclusion performance for phosphopeptides in standard ß-casein digests. More importantly, the materials identified 85 phosphopeptides in disease saliva samples which provided a candidate choice in future clinical examination.

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

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