Highly Efficient Separation of Methylated Peptides Utilizing Selective Complexation between Lysine and 18-Crown-6.

Protein methylation is one of the most common and important post-translational modifications, and it plays vital roles in epigenetic regulation, signal transduction, and chromatin metabolism. However, due to the diversity of methylation forms, slight difference between methylated sites and nonmodified ones, and ultralow abundance, it is extraordinarily challenging to capture and separate methylated peptides from biological samples. Here, we introduce a simple and highly efficient method to separate methylated and nonmethylated peptides using 18-crown-6 as a mobile phase additive in high-performance liquid chromatography. Selective complexation between lysine and 18-crown-6 remarkably increases the retention of the peptides on a C18 stationary phase, leading to an excellent baseline separation between the lysine methylated and nonmethylated peptides. A possible binding mechanism is verified by nuclear magnetic resonance titration, biolayer interferometry technology, and quantum chemistry calculation. Through establishment of a simple enrichment methodology, a good selectivity is achieved and four methylated peptides with greatly improved signal-to-noise (S/N) ratios are successfully separated from a complex peptide sample containing 10-fold bovine serum albumin tryptic digests. By selecting rLys N as an enzyme to digest histone, methylation information in the histone could be well identified based on our enrichment method. This study will open an avenue and provide a novel insight for selective enrichment of lysine methylated peptides in post-translational modification proteomics.

Hydrophilic Nanocomposite Functionalized by Carrageenan for the Specific Enrichment of Glycopeptides.

A hydrophilic nanocomposite was synthesized by an easy route to improve glycopeptides enrichment efficiency. This new composite, prepared with a method based on electrostatic interaction, was demonstrated to be efficient for immobilization of carrageenan on graphene oxide/poly(ethylenimine) support (denoted as GO-PEI-Carr). Carrageenan, which has a large number of hydroxyl groups and is fully negatively charged, is a new modified phase of hydrophilic materials in glycoproteomics. The introduction of carrageenan provided the composite not only a perfect surface charge but also a greater ability to enrich glycosylated peptides. Thirty-four glycopeptides from human serum immunoglobulin G (IgG) tryptic digests were obviously observed with greatly improved signal-to-noise (S/N) ratio. A good selectivity was still kept even when the molar ratio of IgG and bovine serum albumin (BSA) tryptic digest mixtures reached to 1:500. Meanwhile, 76 glycopeptides derived from 56 glycoproteins with 83 N-glycosylation sites were identified from human serum and 149 glycopeptides derived from 129 glycoproteins with 157 N-glycosylation sites were identified from mouse liver tissues, which showed the ability to enrich glycopeptides from complex biological samples. In addition, GO-PEI-Carr exhibited a unique repeatability and stability even after enrichment of glycopeptides for 20 times. It also performed a higher sensitivity (1 fmol/µL IgG), a better enrichment capacity (up to ∼300 mg/g), and an ideal enrichment recovery (90.8% and 109.5%) for glycopeptides enrichment, indicating a great potential for the application of glycoproteomic research.

Hydrophilic Phytic Acid-Coated Magnetic Graphene for Titanium(IV) Immobilization as a Novel Hydrophilic Interaction Liquid Chromatography-Immobilized Metal Affinity Chromatography Platform for Glyco- and Phosphopeptide Enrichment with Controllable Selectivity.

In this work, multifunctional Ti4+-immobilized phytic acid-modified magnetic graphene (denoted as MagG@PEI@PA-Ti4+) nanocomposites were fabricated through a facile route for simultaneous/respective enrichment of N-glyco- and phosphopeptides. Phytic acid (PA), with six phosphate groups, possesses excellent hydrophilicity and metal ion coordination ability, which endowed the MagG@PEI@PA-Ti4+ with combined properties of immobilized metal ion affinity chromatography (IMAC)- and hydrophilic interaction liquid chromatography (HILIC)-based materials. On the basis of the different binding ability of N-glyco- and phosphopeptides on MagG@PEI@PA-Ti4+, the MagG@PEI@PA-Ti4+ nanocomposites could enrich N-glyco- and phosphopeptides simultaneously or respectively by using different enrichment conditions, achieving controllable selective enrichment of N-glyco- and phosphopeptides. The proposed nanocomposites demonstrated an outstanding performance for selective enrichment of N-glycopeptides (selectivity, 1:1000 molar ratios of IgG/BSA; sensitivity, 0.5 fmol/µL IgG; loading capacity, 300 mg g-1; recovery, >90%) and phosphopeptides (selectivity, 1:5000 molar ratios of α-casein/BSA; sensitivity, 0.1 fmol/µL α-casein; loading capacity, 100 mg g-1; recovery, >90%). Taking advantage of these merits, a total of 393 N-glycopeptides derived from 259 glycoproteins and 574 phosphopeptides derived from 341 phosphoproteins were identified from 200 µg of HeLa cell extracts through a single-step enrichment using MagG@PEI@PA-Ti4+.

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.

Selective enrichment of N-linked glycopeptides and glycans by using a dextran-modified hydrophilic material.

Glycosylation analysis of proteins from biological sources utilizing mass spectrometry based approaches is challenging due to the relatively low abundance of glycopeptides, the structural diversity of glycans, and the coexisting matrices. In this study, a customized dextran-bonded silica-based stationary phase was introduced for selective enrichment of glycopeptides and glycans from complex biological samples. This material has exhibited superior selectivity and broader glycosylation site coverage over commercial Sepharose in glycoproteomic evaluation. Additionally, the glycomic analysis of fetuin, α1 -acid glycoprotein, and human serum N-glycome also indicated the relatively higher sensitivity, selectivity, and glycoform coverage of dextran-bonded silica than that of Sepharose and porous graphitized carbon. Therefore, the dextran-bonded silica is expected to make contributions in the fields of glycoproteomics and glycomics.

Synthesis and evaluation of a maltose-bonded silica gel stationary phase for hydrophilic interaction chromatography and its application in Ginkgo Biloba extract separation in two-dimensional systems.

Maltose covalently bonded to silica was prepared by using carbonyl diimidazole as a cross-linker and employed as a stationary phase for hydrophilic interaction liquid chromatography. The column efficiency and the effect of water content, buffer concentration, and pH value influenced on retention were investigated. The separation or enrichment selectivity was also studied with nucleosides, saccharides, amino acids, peptides, and glycopeptides. The results indicated that the stationary phase processed good separation efficiency and separation selectivity in hydrophilic interaction liquid chromatography mode. Moreover, a two-dimensional hydrophilic interaction liquid chromatography× reversed-phase liquid chromatography method with high orthogonality was developed to analyze the Ginkgo Biloba extract fractions. The development of this two-dimensional chromatographic system would be an effective tool for the separation of complex samples of different polarities and contents.

Evaluation of a silicon oxynitride hydrophilic interaction liquid chromatography column in saccharide and glycoside separations.

The retention characteristics of a silicon oxynitride stationary phase for carbohydrate separation were studied in hydrophilic interaction chromatography mode. Four saccharides including mono-, di-, and trisaccharides were employed to investigate the effects of water content and buffer concentration in the mobile phase on hydrophilic interaction liquid chromatography retention. For the tested saccharides, the silicon oxynitride column demonstrated excellent performance in terms of separation efficiency, hydrophilicity, and interesting separation selectivity for carbohydrates compared to the bare silica stationary phase. Finally, the silicon oxynitride hydrophilic interaction liquid chromatography column was employed in the separation of complex samples of fructooligosaccharides, saponins, and steviol glycoside from natural products. The resulting chromatograms demonstrated good separation efficiency and longer retention compared with silica, which further confirmed the advantages and potential application of silicon oxynitride stationary phase for hydrophilic interaction liquid chromatography separation.

Sequential elution of multiply and singly phosphorylated peptides with polar-copolymerized mixed-mode RP18/SCX material.

Novel polar-copolymerized mixed-mode RP18/SCX material was developed for feasible phosphopeptide enrichment, in which multiply and singly phosphorylated peptides could be sequentially eluted and separated with high selectivity.

High-efficiency two-dimensional separation of natural products based on ß-cyclodextrin stationary phase working in both hydrophilic and reversed hydrophobic modes.

Natural products are rather complex samples containing a large number of compounds ranging from polar to nonpolar, small molecules to macromolecules, as well as numerous homologs/analogs with quite similar structures, which create great opportunities and treasures for discovery of bioactive drugs. For the purpose of better understanding the complex natural products and controlling their qualities, powerful analytical techniques for adequately separating chemical constituents and tracking potentially bioactive components are quite essential. Here, a design concept of bidirectional ß-cyclodextrin (ß-CD)-modified chromatographic stationary phase toward separation of bufadienolides extracted from toad is proposed. Bufadienolides could be divided into two classes: toad venom ligand (AAUBs) and toad toxin (AACBs) with remarkable differences in structures and polarity. The hydrophobic cavity of ß-CD can encapsulate the steroid part of AACBs while the hydroxyls exposed on the ß-CD surface have strong hydrophilic interactions with the arginine part of AACBs. Isothermal titration calorimetry and hydrogen nuclear magnetic resonance titration experiment further validate the rationality of this design. Furthermore, the ß-CD-based stationary phase can be used as a hydrophilic material to construct a HILIC × RPLC 2D separation mode for the separation of AACBs, also works as a reverse phase material to construct a RPLC × RPLC 2D separation mode for the separation of AAUBs with good orthogonality. This study will open an avenue and provide a novel insight for high-efficiency two-dimensional separation of natural products.

Zirconia layer coated mesoporous silica microspheres as HILIC SPE materials for selective glycopeptide enrichment.

Characterization of protein glycosylation requires highly specific methods for the enrichment of glycopeptides because of their sub-stoichiometric glycosylation-site occupancy. The hydrophilic affinity based strategy has attracted more attention, owing to its broad glycan specificity, good reproducibility, and compatibility with mass spectrometric (MS) analysis. Several polar matrices have emerged for hydrophilic interaction chromatography (HILIC) approaches, including sepharose, cellulose, ZIC-HILIC and titania. Here, we present the solid-phase extraction (SPE) utility of zirconia coated mesoporous silica (ZrO(2)/MPS) microspheres for glycopeptide isolation prior to MS analysis. The high specificity of this SPE approach was demonstrated by the enrichment of glycopeptides from the digests of model glycoproteins in HILIC mode. ZrO(2)/MPS microspheres show superior selectivity and glycosylation heterogeneity coverage for glycopeptide enrichment to conventional sepharose. Furthermore, digested mixtures of the phosphoprotein α-casein and IgG were also treated with ZrO(2)/MPS HILIC SPE materials, which exhibited that glycopeptides could be effectively enriched with interference from phosphorylated peptides.

Selective enrichment of glycopeptides for mass spectrometry analysis using C18 fractionation and titanium dioxide chromatography.

Comprehensive glycoprotein characterization based on mass spectrometry (MS) is challenging because of low concentration of glycopeptides and suppression effect of abundant non-glycosylated peptides in MS. Therefore, it is vital to enrich glycopeptides before MS analysis. A new method was developed to selectively enrich glycopeptides from complex sample by coupling C18 fractionation with titanium dioxide (TiO(2)) enrichment. The new method allows to selectively enrich N-linked glycopeptides with various glycan forms and different sequence lengths. Compared with single TiO(2) method, the established method demonstrated higher glycopeptide selectivity and higher glycosylation heterogeneity coverage. Further application of this method to mixture of non-glycosylated protein and glycoprotein digests at different levels reveals the feasibility of enrichment of tryptic glycopeptides from simple proteomics samples.

Hydrophilic graphene oxide-dopamine-cationic cellulose composites and their applications in N-Glycopeptides enrichment.

Glycosylation is one of the most important post-translational modifications of proteins, and plays an important role in the structure and function of proteins. However, due to the diversity of glycopeptide forms and their low abundance, it is extraordinarily challenging to capture and separate glycopeptides with high selectivity from complex biological samples with mass spectrometric analysis. Here, we synthesized a new type of hydrophilic composite based on electrostatic interactions, which has been proven to be effective in immobilizing cationic cellulose on graphene oxide-dopamine carriers (expressed as GO-DA-JR), for highly specific enrichment of N-glycopeptides. The introduction of cationic cellulose provides not only a perfect surface charge for the composite but also a greater ability to enrich glycosylated peptides. Thirty-two glycopeptides from human serum immunoglobulin G (IgG) tryptic digests were observed with a greatly improved signal-to-noise ratio (S/N) and also presented high performance in anti-interfering enrichment of glycopeptides from complex samples containing 100-fold bovine serum albumin tryptic digests. In addition, GO-DA-JR has higher sensitivity (1 fmol/µL IgG) and better enrichment capacity (up to 150 mg/g). Moreover, the results of glycopeptide enrichment and glycosylation analysis from human serum also show egood enrichment selectivity from real biological samples. This work exhibits high selectivity, high sensitivity, good stability and operability, indicating its potential for applications of glycopeptides enrichment in post-translational modification proteomics.

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.

[Covalent organic framework functional materials and their applications in glycopeptide enrichment].

Protein glycosylation is among the most important post-translational modifications in living organisms and the research in the field of protein glycosylation continues to garner attention. Currently, the efficient separation and enrichment of glycoproteins and glycopeptides is the primary challenge of glycoproteomics research. The number of glycoproteins is small in complex biological samples. Moreover, the presence of highly-abundant, non-glycosylated, and modified peptides makes the detection of low-abundance glycopeptides more difficult. Therefore, efficient glycopeptide enrichment methods are required to improve the detection of these compounds. The development of highly selective glycopeptide enrichment tools is important to efficiently capture glycoproteins or glycopeptides at the molecular level. Compared with traditional glycopeptide-enriched materials, covalent organic framework materials have the advantages of large specific surface area and rich modification sites, thereby exhibiting great application potential in the field of glycopeptide enrichment. In this study, a novel covalent organic framework material (O-T-D-COFs) was prepared and applied for selective glycopeptide enrichment. We applied the solvothermal method, using 2,5-dimethoxy benzene-1,4-2 formaldehyde and 1,3,5-Tris(4-aminophenyl) benzene, to synthesize imino-based COFs. The Schiff base generated via copolymerization condensation reaction constitutes the framework of the material. Next, the synthesized intermediate material was oxidized to improve the enrichment performance of the material. The functional, specific glycopeptide-binding groups were modified on the COF channels and the structure of the material was characterized using scanning and transmission electron microscope, as well as infrared spectrum and solid-state nuclear magnetic resonance. The enrichment conditions comprised the loading and elution steps, including the optimization of the elution conditions. We could observe the clear profile of 32 glycopeptides derived from human serum immunoglobulin G (IgG) tryptic digests with a significantly improved signal-to-noise (S/N) ratio. We applied a complex sample system to verify the enrichment selectivity of the material when the molar ratios of the IgG and bovine serum albumin (BSA) tryptic digest mixtures reached 1∶50. In addition, we investigated the enrichment performance of the detection limit, enrichment capacity, recovery rate of the material, and the application potential in glycopeptides enrichment using real samples. The material showed a good detection limit (2.5 fmol/µL), an ideal enrichment capacity (120 mg/g), and enrichment recovery (103.5%±6.6% and 101.5%±10.4%). We identified a total of 86 glycopeptides derived from 53 glycoproteins with 94 N-glycosylation sites from only 1 µL human serum. The O-T-D-COFs exhibited a good glycopeptide separation and enrichment potential, indicating that the COF material has promising application potential in glycoproteomics.

Highly efficient enrichment of phosphopeptides from HeLa cells using hollow magnetic macro/mesoporous TiO2 nanoparticles.

In this work, hollow magnetic macro/mesoporous TiO2 nanoparticles (denoted as Fe3O4@H-fTiO2) were synthesized by a facile "hydrothermal etching assisted crystallization" route to improve the phosphopeptide enrichment efficiency. The porous nanostructure of TiO2 shell and large hollow space endowed the Fe3O4@H-fTiO2 with a high surface area (144.71 m2 g-1) and a large pore volume (0.52 cm3 g-1), which could provide more affinity sites for phosphopeptide enrichment. Besides, the large pore size of TiO2 nanosheets and large hollow space could effectively prevent the "shadow effect", thereby facilitating the diffusion and release of phosphopeptides. Compared with the hollow magnetic mesoporous TiO2 with small and deep pores (denoted as Fe3O4@H-mTiO2) and solid magnetic macro/mesoporous TiO2, the Fe3O4@H-fTiO2 nanoparticles showed a better selectivity (molar ratio of α-casein/BSA up to 1:10000) and a higher sensitivity (0.2 fmol/µL α-casein) for phosphopeptide enrichment. Furthermore, 1485 unique phosphopeptides derived from 660 phosphoproteins were identified from HeLa cell extracts after enrichment with Fe3O4@H-fTiO2 nanoparticles, further demonstrating that the Fe3O4@H-fTiO2 nanoparticles had a high-efficiency performance for phosphopeptide enrichment. Taken together, the Fe3O4@H-fTiO2 nanoparticles will have unique advantages in phosphoproteomics analysis.

Yolk-shell magnetic mesoporous TiO2 microspheres with flowerlike NiO nanosheets for highly selective enrichment of phosphopeptides.

In this work, we fabricated a yolk-shell magnetic composite that contains mesoporous TiO2 as the inner shell and flowerlike NiO as the outer shell (denoted as Fe3O4@H-TiO2@f-NiO) to reduce the limitations of single-component metal oxides in phosphopeptide enrichment. The NiO nanosheets play a synergistic role in phosphopeptide enrichment. And the unique flowerlike structure of NiO with sufficient space can facilitate the reversible insertion/extraction of peptides, which will have less impact on the enrichment process of the inner TiO2 shell. The yolk-shell structure and two types of porous nanostructures endowed this composite with a high surface area (156.58 m2 g-1) and a large pore volume (0.37 cm3 g-1). Owing to the high surface area and combined properties of TiO2 and NiO, the Fe3O4@H-TiO2@f-NiO microspheres showed a better performance for phosphopeptide enrichment than the same material without NiO nanosheets (Fe3O4@H-TiO2). According to the LC-MS/MS results, 972 unique phosphopeptides were identified from HeLa cell extracts with a high selectivity (91.9%) by Fe3O4@H-TiO2@f-NiO relative to 837 phosphopeptides (selectivity: 60.2%) by Fe3O4@H-TiO2. The results demonstrated that, compared with single-component metal oxides, composite metal oxides could enhance the selectivity and sensitivity for phosphopeptide enrichment.

Sequential enrichment of singly- and multiply-phosphorylated peptides with zwitterionic hydrophilic interaction chromatography material.

An interesting and novel method for the selective and sequential enrichment of singly- and multiply-phosphorylated peptides with a zwitterionic material "Click TE-Cys" is presented. Retention mechanisms between phosphopeptides and Click TE-Cys are systematically investigated by checking the influence of acetonitrile content, pH value, and buffer concentration on the retention of phosphopeptides. Both hydrophilic interaction and electrostatic interaction are involved in retention between phosphopeptides and Click TE-Cys. Based on these results, an optimized method is established for selective enrichment of phosphopeptides using Click TE-Cys. This method not only exhibits high selectivity for phosphopeptides, but also fractionates singly- and multiply-phosphorylated peptides into two fractions. This method was evaluated using relatively complex samples, including peptide mixtures of α-casein and bovine serum albumin (BSA) at a molar ratio of 1:10 and skim milk. This efficient and optimized protocol has great potential for enriching multiply-phosphorylated peptides and could be a valuable tool for specific enrichment of phosphopeptides in phosphoproteome analysis.

A dextran-bonded stationary phase for saccharide separation.

A-saccharide-based stationary phase for hydrophilic interaction liquid chromatography (HILIC) is presented. The method uses carbonyl di-imidazole (CDI) as a cross-linker for dextran in aqueous solution. Different from the traditional immobilized saccharide stationary phase, this method was using a simple way to bond the high molecular of polysaccharide immobilized on the silica gel. The new method avoided the time-consuming process but had a very considerable loading result. With silica-based surface bonded, it will be possible to develop well-defined surface modifications that promote the hydrophilic with dextran and high mechanical strength with silica. For all tested compounds, including polar compounds and carbohydrates, this dextran-bonded stationary phase performed well in terms of separation efficiency and column stability, and the retention mechanism matched that of typical HILIC retention. Moreover, good selectivity was achieved in the separation of oligosaccharides and glycopeptides.

A novel ionic-bonded cellulose stationary phase for saccharide separation.

A hydrophilic interaction liquid chromatography (HILIC) stationary phase of cellulose-coated silica was synthesized as a novel saccharide separation material. The material, prepared with a method based on ionic interaction, was demonstrated to be efficient for immobilization of saccharides on silica supports. The method is more efficient than traditional immobilized saccharide stationary phase synthesis methods. It was evolved from a method using anion exchanger microparticles agglomerated onto macroparticles of cation exchangers to produce anion exchangers. Cationic cellulose, which has a large number of hydroxyl groups, was immobilized on sulfonated silica. The cellulose-coated stationary phase we designed used strong hydrogen bonding between cellulose hydroxyl and carbohydrate compounds for HILIC retention and separation. The stationary phase was successfully used to separate the samples of polar compounds and the complex samples of oligosaccharides, and demonstrated good reproducibility and stability. The material exhibited good separation selectivity for carbohydrates and ability to enrich glycosylated peptides. The method described here is easy to achieve, environmentally safe and innovative than other methods. It also has extensive application possibilities to separate other categories polar compounds.