Immobilized metal ion affinity chromatography ZipTip pipette tip with polydopamine modification and Ti 4+ immobilization for selective enrichment and isolation of phosphopeptides

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

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

Design of Gd3+-immobilized two-dimensional magnetic magadiite nanosheets for highly selective enrichment of phosphopeptides

Exfoliated magadiite nanosheets embedded with Fe₃O₄ were constructed. Advantage was taken of the strong coordination between the silanol groups in magadiite nanosheets and the Gd³⁺ ion to prepare the final adsorbent, Gd³⁺-immobilized magnetic magadiite nanosheets. The adsorbent with two-dimensional (2D) morphology offered high surface area and abundant Gd³⁺ contents for phosphopeptides enrichment, on which Fe₃O₄ with positive electricity incorporated the magnetic properties. Combining with matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI TOF-MS), the method showed low detection limit (0.05 fmol). The feasibility of using the 2D nanocomposite for phosphopeptides enrichment was demonstrated using mixtures of β-casein and bovine serum albumin (1:5000). The standard deviation of captured phosphopeptides in three repeated experiments were in the range 0.15-0.42 (< 0.5% RSD). Further evaluation revealed that the nanocomposite was capable of enriching phosphopeptides from non-fat milk, human saliva, and serum. A novel Gd³⁺-immobilized two-dimensional magnetic magadiite nanosheets-based enrichment platform was designed. The developed material was employed as the adsorbent for the selective enrichment of phosphopeptides by coupling with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The material was successfully applied to enrich phosphopetides from standard peptide mixtures, nonfat milk, human saliva, and serum.

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

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

Reshaping of pipette tip: A facile and practical strategy for sorbent packing-free solid phase extraction

Pipette tip-based solid phase extraction (PT-SPE) has been proved to be an effective and user-friendly separation technique due to its miniaturized procedure and practical convenience. However, the vast majority of existing PT-SPE devices consist of a filter-sorbents-filter sandwich structure, which may suffer the unforeseen risk of sorbents leakage caused by the looseness of filters. More importantly, many high-capacity nanosorbents with particle size smaller than pore size of filters are unavailable. Thus, sorbent packing-free and sample low-consumption PT-SPE could be a more robust strategy for separation and detection, but such a possibility has not been explored yet. Herein we report a tubing reshaping strategy for facile fabrication of sorbent packing-free PT-SPE devices. Three types of reshaped PTs, namely stretched tube-like, self-crimping and filter in-built PTs, were fabricated via simple heating and stretching operations. The reshaped PTs exhibited flexible surface chemical post-modification. The SPE process was directly performed in reshaped PTs with an obviously enhanced extraction efficiency compared to once-shaping PTs while no need of packing sorbents. Extraction of nucleosides from human urine by boronic acid-functionalized reshaped PTs was demonstrated. Our findings technically renovate the structural composition of PT-SPE devices. As PTs are inexpensive and high-plasticity, the sorbent packing-free SPE scheme presented herein could find more promising applications and provides a new perspective for design and fabrication of novel sorbent packing-free SPE devices.

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

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

Fabrication and evaluation of molecularly imprinted magnetic nanoparticles for selective recognition and magnetic separation of lysozyme in human urine

The Lyz-MMIPs displayed a uniform core–shell structure, favorable magnetic properties, good accessibility, and good stability and had a good affinity and excellent binding selectivity to Lyz.

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

Metal ions differed greatly in affinity towards phosphopeptides, and thus it is essential to systematically compare the phosphopeptides enrichment ability of different metal ions usually used in the IMAC techniques. In this work, for the first time, eight metal ions, including Nb⁵⁺, Ti⁴⁺, Zr⁴⁺, Ga³⁺, Y³⁺, In³⁺, Ce⁴⁺, Fe³⁺, were immobilized on the polydopamine (PDA)-coated Fe₃O₄ (denoted as Fe₃O₄@PDA-Mⁿ⁺), and systematically compared by the real biosamples, in addition to standard phosphopeptides. Fe₃O₄ microspheres were synthesized via the solvothermal reaction, followed by self-polymerization of dopamine on the surface. Then through taking advantage of the hydroxyl and amino group of PDA, the eight metal ions were easily adhered to the surface of Fe₃O₄@PDA. After characterization, the resultant Fe₃O₄@PDA-Mⁿ⁺ microspheres were applied to phosphopeptides enrichment based on the binding affinity between metal ions and phosphopeptides. According to the results, different metal ions presented diverse phosphopeptides enrichment efficiency in terms of selectivity, sensitivity and the enrichment ability from real complex samples, and Fe₃O₄@PDA-Nb⁵⁺ and Fe₃O₄@PDA-Ti⁴⁺ showed obvious advantages of the phosphopeptides enrichment effect after the comparison. This systematic comparison may provide certain reference for the use and development of IMAC materials in the future.

Large-pore, silica particles with antibody-like, biorecognition sites for efficient protein separation

The MI-LPSPs, with antibody-like, bio-recognition sites, displayed good affinity and excellent binding selectivity to BSA.

Preparation of Polypropylene Spin Tips Filled with Immobilized Titanium(IV) Ion Monolithic Adsorbent for Robust Phosphoproteome Analysis

In this study, we developed a Ti(IV) monolithic spin tip for phosphoproteome analysis of a minute amount of biological sample for the first time. The surface of polypropylene pipet tip was activated by the photoinitiator benzophenone under UV light radiation followed by polymerization of ethylene glycol methacrylate phosphate and bis-acrylamide in the tip to form a porous monolith with reactive phosphate groups. The as-prepared tips grafted with monolithic adsorbent were then chelated with titanium(IV) ion for phosphopeptide enrichment. It was found that the tips enabled fast and efficient capture of phosphopeptides from microscale complex samples. The monolithic tip was demonstrated to have a detection limit as low as 5 fmol β-casein tryptic digest, along with an exceptionally high specificity to capture phosphopeptides from complex tryptic digest mixed with an unphosphorylated protein and a phosphorylated protein at a molar ratio up to 1000:1. When the tip was applied to enrich phosphopeptides from 5 μg of tryptic digest of complex HeLa cell proteins, 1185 high confidence of phosphorylated sites were successfully identified with the specificity as high as 92.5%. So far, this is the most sensitive phosphoproteomics analysis using a standard liquid chromatography-tandem mass spectrometry (LC-MS/MS) system for proteome-wide phosphorylation analysis in mammalian cells.

Bio-inspired magnetic molecularly imprinted polymers based on Pickering emulsions for selective protein recognition

Hydrophobic halloysite nanotube stabilized Pickering emulsions and their application in protein separation.