Highly selective enrichment of phosphopeptides with high-index facets exposed octahedral tin dioxide nanoparticles for mass spectrometric analysis

Toward the Specificity of Bare Nanomaterial Surfaces for Protein Corona Formation

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

WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT

Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.

[Preparation of luminescent silica nanoparticles with immobilized metal ion affinity for labeling phosphorylated proteins in Western Blot]

Protein phosphorylation is an important type of post-translational protein modification. In Western Blot experiment, the assay of phosphoproteins need special phospho antibodies, which are expensive, difficult to preserve, poorly reproducible. To this end, the immobilized metal ion affinity luminescent silica nanoparticles for instead of phospho antibodies were prepared. A layer of polymer was created on the surface of the silica nanoparticles via co-polymerization to protect the nanoparticles and to functionalize them with the immobilized metal ion affinity property to specifically label the phosphorylated proteins in Western Blot assays. The affinity luminescent silica nanoparticles were prepared with the following procedure. First, the sol-gel precursor fluorescein isothiocyanate-3-aminopropyltriethoxysilane (FITC-APTES) with the fluorescent moiety was prepared by modifying APTES with FITC. The luminescent silica nanoparticles (FITC@SiO₂) were synthesized using the Stöber synthesis method in a reversed microemulsion. Briefly, 123.2 mL of cyclohexane, 25.6 mL of n-hexanol, and 5.44 mL of deionized water were ultrasonically mixed, and then 28.3 g of Triton X-100 were added and the mixture was magnetically stirred for 15 min to form a clear and transparent microemulsion system. Within 10 min, 0.8 mL of FITC-APTES precursor, 1.6 mL of tetraethoxysilane (TEOS), and 0.96 mL of concentrated ammonia (25%-27%, mass fraction) were added to the microemulsion, and the mixture was stirred at 24 ℃ for 24 h. After the reaction, the microemulsion system was destroyed by adding 200 mL of ethanol. The resulting FITC@SiO₂ luminescent silica nanoparticles were centrifuged, and washed three times with ethanol. After dryness, the FITC@SiO₂ nanoparticles were modified with methacryloxy-propyltrimethoxysilane (MPS) to introduce the double bonds for further modification. The functional monomer nitrilotriacetic acid (NTA) and glycidyl methacrylate (GMA) were copolymerized on the surface of the nanoparticles to convert FITC@SiO₂-MPS to FITC@SiO₂-MPS-GMA-NTA. The polymer coating of the silica nanoparticles was not only able to protect the silica from hydrolysis, but also to introduce the functional groups of nitrilotriacetic acid, which can chelate with metal ions. Elemental analysis demonstrated that the NTA groups had been bonded to the surface of the nanoparticles via copolymerization. The polymerization did not affect the morphology and fluorescence properties of the nanoparticles. The FITC@SiO₂-MPS-GMA-NTA nanoparticles were activated with three different metal ions Zr⁴⁺, Fe³⁺, and Ti⁴⁺, for the enrichment of phosphorylated peptides derived form α-casein tryptic digestion. HPLC-MS analysis indicated that the FITC@SiO₂-MPS-GMA-NTA-Ti ⁴⁺ nanoparticles are the best for the enrichment of phosphorylated peptides. The FITC@SiO₂-MPS-GMA-NTA-Ti⁴⁺ nanoparticles were used for labelling the phosphorylated proteins in Western Blot experiment. The electrophoretic band of α-casein could be clearly labeled with the FITC@SiO₂-MPS-GMA-NTA-Ti ⁴⁺ nanoparticles, while the bovine albumin band could not be labelled. This indicates that the luminescent FITC@SiO₂-MPS-GMA-NTA-Ti⁴⁺nanoparticles can be used to label the phosphorylated proteins in Western Blot experiments.

Current Applications of Gas Sensor Based on 2-D Nanomaterial: A Mini Review

Gas sensor, as one of the most important devices to detect noxious gases, provides a vital way to monitor the concentration and environmental information of gas in order to guarantee the safety of production. Therefore, researches on high sensitivity, high selectivity, and high stability have become hot issues. Since the discovery of the nanomaterial, it has been increasingly applied to the gas sensor for its distinguishing surface performances. However, 0-D and 1-D nanomaterials, with limited electronic confinement effect and surface effect, cannot reach the requirement for the production of gas sensors. This paper gives an introduction about the current researching progress and development trend of 2-D nanomaterials, analyzes the common forms of 2-D nanoscale structure, and summarizes the mechanism of gas sensing. Then, widely concerned factors including morphological properties and crystalline structure of 2-D nanomaterial, impact of doped metal on the sensibility of gas sensors, impact of symmetry, and working temperature on the selectivity of gas sensors have been demonstrated in detail. In all, the detailed analysis above has pointed out a way for the development of new 2-D nanomaterial and enhancing the sensibility of gas sensors.

A regenerative and selective electrochemical aptasensor based on copper oxide nanoflowers-single walled carbon nanotubes nanocomposite for chlorpyrifos detection

Chlorpyrifos is a commonly used organophosphorus pesticide in agriculture. However, its neurotoxicity poses a huge threat to human health. To detect trace amounts of chlorpyrifos, we herein developed a regenerative electrochemical aptasensor for the sensitive detection of chlorpyrifos. The nanocomposite consisting of copper oxide nanoflowers (CuO NFs) and carboxyl-functionalized single walled carbon nanotubes (c-SWCNTs) was prepared to improve the sensing performance for chlorpyrifos detection. Various characterization methods such as scanning electron microscopy (SEM), fourier transform infrared spectroscopy (FT-IR) and cyclic voltammetry (CV) were used to demonstrate the successful fabrication of biosensor. Differential pulse voltammetry (DPV) was utilized to optimize test conditions and quantify chlorpyrifos. Under optimal conditions, the biosensor obtained a good linearity for chlorpyrifos ranging from 0.1 to 150ng/mL, with a lower detection limit of 70pg/mL. This aptasensor also exhibited high selectivity and outstanding repeatability, and was successfully applied to the determination of chlorpyrifos in spiked apple and celery cabbage with satisfactory recoveries. Furthermore, the sensor can be easily regenerated by urea for continuous application. With all the features, the proposed strategy provides an excellent platform for regenerative and selective detection of chlorpyrifos.

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.

Low-cost iron oxide magnetic nanoclusters affinity probe for the enrichment of endogenous phosphopeptides in human saliva

Simple and low cost iron oxide magnetic nanoclusters (Fe₃O₄ MNCs) affinity material has been directly applied for phosphorylated peptides/proteins enrichment.

Hydrophilic modification of titania nanomaterials as a biofunctional adsorbent for selective enrichment of phosphopeptides

TiO2-based metal oxide affinity chromatography (MOAC) nanomaterials show high potential in phosphoproteome mass-spectrometric (MS) analysis. However, a drawback of TiO2 nanomaterials is poor water solubility, which greatly reduces the enrichment efficiency of phosphopeptides and eventually limits their use in phosphoproteome MS analysis. In this work, a hydrophilic TiO2 hybrid material (denoted as NH2@TiO2) is successfully designed with 1,6-hexanediamine modified on the surface of TiO2 nanoparticles and applied as a biofunctional adsorbent for selective enrichment of phosphopeptides. The novel TiO2 hybrid material with high hydrophilicity and biocompatibility is characterized using scanning electron microscopy (SEM), energy dispersive X-ray (EDX) and infrared (IR) spectroscopy, and its performance in selective enrichment of phosphopeptides is evaluated with the standard protein digests, human serum and the tryptic digests of nonfat milk.

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

Reversible protein phosphorylation is a key event in numerous biological processes. Mass spectrometry (MS) is the most powerful analysis tool in modern phosphoproteomics. However, the direct MS analysis of phosphorylated proteins/peptides is still a big challenge because of the low abundance and insufficient ionization of phosphorylated proteins/peptides as well as the suppression effects of nontargets. Enrichment of phosphorylated proteins/peptides by affinity materials from complex biosamples is the most widely used strategy to enhance the MS detection. The demand of efficiently enriching phosphorylated proteins/peptides has spawned diverse affinity materials based on different enrichment principles (e.g., electronic attraction, chelating). In this review, we summarize the recent development of various affinity materials for phosphorylated proteins/peptides enrichment. We will highlight the design and fabrication of these affinity materials, discuss the enrichment mechanisms involved in different affinity materials, and suggest the future challenges and research directions in this field.

Template-free synthesis of uniform mesoporous SnO2 nanospheres for efficient phosphopeptide enrichment

Mesoporous SnO₂ nanospheres were prepared via a one-step and template-free method and excellent enrichment performance was achieved in their applications for phosphopeptide enrichment.