Development of Gd3+-immobilized glutathione-coated magnetic nanoparticles for highly selective enrichment of phosphopeptides

Enrichment of phosphopeptides by arginine-functionalized magnetic chitosan nanoparticles

One of the most crucial and prevalent post-translational modifications is the phosphorylation of proteins. The study and examination of protein phosphorylation hold immense importance in comprehending disease mechanisms and discovering novel biomarkers. However, the inherent low abundance, low ionization efficiency, and coexistence with non phosphopeptides seriously affect the direct analysis of phosphopeptides by mass spectrometry. In order to tackle these problems, it is necessary to carry out selective enrichment of phosphopeptides prior to conducting mass spectrometry analysis. Herein, magnetic chitosan nanoparticles were developed by incorporating arginine, and were then utilized for phosphopeptide enrichment. A tryptic digest of β-casein was chosen as the standard substance. After enrichment, combined with matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS), the detection limit of the method was 0.4 fmol. The synthesized magnetic material demonstrated great potential in the detection of phosphopeptides in complex samples, as proven by its successful application in detecting phosphopeptides in skim milk and human saliva samples.

Facile fabrication of Ti4+-immobilized magnetic nanoparticles by phase-transitioned lysozyme nanofilms for enrichment of phosphopeptides

In this study, titanium (IV)-immobilized magnetic nanoparticles (Ti4+-PTL-MNPs) were firstly synthesized via a one-step aqueous self-assembly of lysozyme nanofilms for efficient phosphopeptide enrichment. Under physiological conditions, lysozymes readily self-organized into phase-transitioned lysozyme (PTL) nanofilms on Fe3O4@SiO2 and Fe3O4@C MNP surfaces with abundant functional groups, including -NH2, -COOH, -OH, and -SH, which can be used as multiple linkers to efficiently chelate Ti4+. The obtained Ti4+-PTL-MNPs possessed high sensitivity of 0.01 fmol μL-1 and remarkable selectivity even at a mass ratio of β-casein to BSA as low as 1:400 for phosphopeptide enrichment. Furthermore, the synthesized Ti4+-PTL-MNPs can also selectively identify low-abundance phosphopeptides from extremely complicated human serum samples and their rapid separation, good reproducibility, and excellent recovery were also proven. This one-step self-assembly of PTL nanofilms facilitated the facile and efficient surface functionalization of various nanoparticles for proteomes/peptidomes.

State of the art on the separation and purification of proteins by magnetic nanoparticles

The need for excellent, affordable, rapid, reusable and biocompatible protein purification techniques is justified based on the roles of proteins as key biomacromolecules. Magnetic nanomaterials nowadays have become the subject of discussion in proteomics, drug delivery, and gene sensing due to their various abilities including rapid separation, superparamagnetism, and biocompatibility. These nanomaterials also referred to as magnetic nanoparticles (MNPs) serve as excellent options for traditional protein separation and analytical methods because they have a larger surface area per volume. From ionic metals to carbon-based materials, MNPs are easily functionalized by modifying their surface to precisely recognize and bind proteins. This review excavates state-of-the-art MNPs and their functionalizing agents, as efficient protein separation and purification techniques, including ionic metals, polymers, biomolecules, antibodies, and graphene. The MNPs could be reused and efficaciously manipulated with these nanomaterials leading to highly improved efficiency, adsorption, desorption, and purity rate. We also discuss the binding and selectivity parameters of the MNPs, as well as their future outlook. It is concluded that parameters like charge, size, core-shell, lipophilicity, lipophobicity, and surface energy of the MNPs are crucial when considering protein selectivity, chelation, separation, and purity.

Advances in phosphoproteomics and its application to COPD

INTRODUCTION

Chronic obstructive pulmonary disease (COPD) was the third leading cause of global death in 2019, causing a huge economic burden to society. Therefore, it is urgent to identify specific phenotypes of COPD patients through early detection, and to promptly treat exacerbations. The field of phosphoproteomics has been a massive advancement, compelled by the developments in mass spectrometry, enrichment strategies, algorithms, and tools. Modern mass spectrometry-based phosphoproteomics allows understanding of disease pathobiology, biomarker discovery, and predicting new therapeutic modalities.

AREAS COVERED

In this article, we present an overview of phosphoproteomic research and strategies for enrichment and fractionation of phosphopeptides, identification of phosphorylation sites, chromatographic separation and mass spectrometry detection strategies, and the potential application of phosphorylated proteomic analysis in the diagnosis, treatment, and prognosis of COPD disease.

EXPERT OPINION

The role of phosphoproteomics in COPD is critical for understanding disease pathobiology, identifying potential biomarkers, and predicting new therapeutic approaches. However, the complexity of COPD requires the more comprehensive understanding that can be achieved through integrated multi-omics studies. Phosphoproteomics, as a part of these multi-omics approaches, can provide valuable insights into the underlying mechanisms of COPD.

Creatine@SiO2 @Fe3 O4 nanocomposite as an efficient sorbent for magnetic solid-phase extraction of escitalopram and chlordiazepoxide from urine samples through quantitation via HPLC-UV

An efficient, cost-effective, and fast-synthesis method is presented in the current study to prepare magnetic nanoparticles covered by cheap and nitrogen-rich creatine. The hydrothermal method was used for the synthesis of the magnetic core. The prepared magnetic core was then covered by SiO₂ and subsequently functionalized using creatine. The prepared creatine@SiO₂ @Fe₃ O₄ was utilized as a sorbent in the magnetic solid-phase extraction of the selected antidepressants including escitalopram and chlordiazepoxide as the model drugs. The extracted drugs were desorbed by a suitable organic solvent and analyzed by high-performance liquid chromatography equipped with an ultraviolet detection system. The influence of different variables on the magnetic solid-phase extraction method was examined by the Plackett-Burman and Box-Behnken designs for screening and optimization, respectively. Under the obtained optimum conditions, the linear ranges of the method were found to be in the range of 1-500 µg L^-1 . The limits of detection and limits of quantification were in the range of 0.27-0.63 µg L^-1 and 0.89-1.93 µg L^-1 for the selected analytes, respectively. Furthermore, the enrichment factors were found to be 79.8 and 92.7 for chlordiazepoxide and escitalopram, respectively. The method was successfully employed for the analysis of selected drugs in urine samples.

One-pot synthesis of a peroxidase-like nanozyme and its application in visual assay for tyrosinase activity

Both single-atom nanozymes (SAzymes) and protein-template metal nanoparticles have attracted comprehensive attention in several respects owing to their excellent catalytic performance, green facile synthesis process, and robustness. Herein, the peroxidase-like activity of single-atom copper anchored on bovine hemoglobin-template gadolinium nanoparticles (Cu,Gd@BHb^FITC NPs) were successfully synthesized and two sensitive turn-on fluorescence strategies for tyrosinase (TYR) activity sensing were proposed for the first time. For strategy Ⅰ, TYR sensing was carried out from 1.00 to 7.80 U/mL with the detection limit (LOD) of 0.20 U/mL based on the fluorescence resonance energy transfer (FRET) between the fluorescein isothiocyanate (FITC) and the in situ generated polydopamine dots (PDA-dots). For strategy Ⅱ, The LOD of TYR was 0.05 U/mL with the linear range of 0.40-19.70 U/mL based on the elimination of inner-filter effect (IEF) between FITC and the reaction product (RC) of phenol and 4-Aminoantipyrine (AAP). The smartphone-assisted sensing platform was applied to construct the on-site detection of TYR with both strategies. The developed probe possessed good selectivity and was successfully utilized to TYR detection in serum 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.

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.

Recent trends in sorbents for bioaffinity chromatography

Isolation or enrichment of biological molecules from complex biological samples is mostly a prerequisite in proteomics, genomics, and glycomics. Different techniques have been used to advance the efficiency of the purification of biological molecules. Bioaffinity chromatography is one of the most powerful technique that plays an important role in the isolation of target biological molecules by the specific interactions with ligands that are immobilized on different support materials. This review examines the recent developments in bioaffinity chromatography particularly over the past 5 years in the literature. Also properties of supports, immobilization techniques, types of binding agents, and methods used in bioaffinity chromatography applications are summarized.

Glutathione-stabilized Fe3 O4 nanoparticles as the sorbent for magnetic solid-phase extraction of diazepam and sertraline from urine samples through quantitation via high-performance liquid chromatography

The synthesis and application of glutathione-coated magnetic nanocomposite were introduced with the purpose of developing a stable, cheap, operationally convenient, simple, fast, sensitive, and selective device for the microextraction of diazepam and sertraline for the first time. The prepared glutathione@Fe₃ O₄ nanocomposite was used as the sorbent in the form of magnetic solid-phase extraction. Afterward, the extracted analytes were desorbed by organic solvent and analyzed by high-performance liquid chromatography-ultraviolet detection. Several influential variables such as desorption time, desorption volume, sample pH, extraction time, and sorbent amount were screened through Plackett-Burman design and then optimized via Box-Behnken design. The obtained results showed that the above-mentioned method enjoys a good linear range (0.2-500 μg/L) with the coefficient of determination higher than 0.9927, low limits of determination (0.07-0.24 μg/L), acceptable limits of quantification (0.22-0.93 μg/L), good enrichment factors (128 and 153), and good spiking recoveries (95-105%) for diazepam and sertraline under the obtained optimized condition. Analyzing the real samples results in the confirmation of the presented method and it can be applied for the analysis of various organic compounds in biological samples.

In situ synthesis of a novel metal oxide affinity chromatography affinity probe for the selective enrichment of low-abundance phosphopeptides

RATIONALE

Due to the dynamic nature of phosphorylation states and the low stoichiometry of phosphopeptides, it is still a challenge to efficiently capture phosphopeptides from complex biological samples before mass spectrometry analysis. Among the enrichment strategies, metal oxide affinity chromatography (MOAC) is one of the most widely used and the one with the most potential. It is based on reversible Lewis acid-base interactions between the metal oxides and the negatively charged phosphate groups to achieve the specific selection of phosphopeptides.

METHODS

A novel MOAC affinity probe, denoted as G@PDA@ZrO₂ , was successfully synthesized by in situ grafting ZrO₂ onto the surface of graphene (G) modified with polydopamine (PDA). The novel MOAC probe thus obtained was used for phosphopeptide enrichment.

RESULTS

This novel MOAC affinity probe when used to selectively enrich phosphopeptides from standard protein digest solutions exhibited a high selectivity (β-casein:bovine serum albumin = 1:1000), a low detection limit (4 fmol), and a high loading capacity (400 mg/g). At the same time, the experimental results proved that G@PDA@ZrO₂ had great recyclability (five cycles), stability, and reproducibility. Subsequently, G@PDA@ZrO₂ was applied to enrich phosphopeptides from human saliva and human serum, in which 25 and 4 phosphopeptide peaks, respectively, were detected.

CONCLUSIONS

This novel MOAC affinity probe (G@PDA@ZrO₂ ) showed good performance in enriching phosphopeptides. Thus, G@PDA@ZrO₂ has good potential in phosphopeptidomics analysis.

Coupling hydrophilic interaction chromatography materials with immobilized Fe3+ for phosphopeptide and glycopeptide enrichment and separation

Simultaneous profiling of protein phosphorylation and glycosylation is very important to elucidate the bio-functions of these proteins. However, simultaneous enrichment of glyco- and phosphopeptides is the bottleneck in proteomics because of the low abundance of these species and ion suppression from non-modified peptides in mass spectrometry (MS). In this study, Fe³⁺ immobilized hydrophilic interaction chromatography (HILIC) materials (termed polySD-SiO₂, recently reported in our lab) and polySD-SiO₂ in the HILIC mode were employed for the simultaneous enrichment and subsequent separation of glyco- and phosphopeptides. The Fe³⁺ immobilized polySD-SiO₂ could selectively enrich glycopeptides and phosphopeptides and the co-enriched peptides were further fractionated with polySD-SiO₂ in the HILIC mode. With the established method, glyco- and phosphopeptides were well enriched and divided into two fractions even from tryptic digests of a-casein, fetuin and BSA at a molar ratio of 1 : 2 : 400. Application of the established method to HeLa cell lysate resulted in a total of 1903 phosphopeptides and 141 glycosylation sites. These results demonstrate that the established method could selectively and simultaneously enrich and fractionate glyco- and phosphopeptides from complex peptide mixtures.

Simultaneous profiling of protein phosphorylation and glycosylation is very important to elucidate the bio-functions of these proteins.

Ni(II)-decorated porous titania microspheres as a stationary phase for column chromatography applications: Highly selective purification of hemoglobin from human blood

Titania (TiO₂)-based monodisperse-porous stationary phase/sorbent was synthesized by decoration of Ni(II) ions onto TiO₂ microspheres 4.2 µm in size, obtained by a staged-shape template hydrolysis and condensation protocol. Ni(II) ions were attached onto iminodiacetic acid-3-glycidoxypropyltrimethoxysilane (IDA-GPTMS) bound-titania microspheres by metal-chelate complex formation. The appropriate mean size, sufficiently high surface area and high porosity providing an appropriate column permeability make Ni(II)-decorated TiO₂ microspheres a good sorbent/stationary phase for batch/continuous-column chromatography applications. Ni(II)-decorated TiO₂ microspheres were investigated as a sorbent for purification of a typical histidine-rich protein, hemoglobin (Hb) via immobilized metal affinity chromatography (IMAC) in batch fashion, by including bovine serum albumin (BSA) as reference. The saturation capacities of batch adsorption runs performed with bovine Hb and BSA were determined as 137 ± 9 and 45 ± 3 mg/g, respectively. Human Hb with the purity of > 95% was recovered from whole blood by IMAC conducted in batch-fashion. Ni(II)-decorated microspheres were also evaluated as a stationary phase in a microfluidic-IMAC system, in which, human Hb was recovered from whole blood with a purity of 85%. The microfluidic-IMAC system constructed here, based on monodisperse-porous TiO₂ microspheres, is a promising tool for genomics/proteomics applications involving isolation of valuable biomolecules from low-volume samples.

Aptamer-Functionalized Magnetic Conjugated Organic Framework for Selective Extraction of Traces of Hydroxylated Polychlorinated Biphenyls in Human Serum

A solid-phase extraction adsorbent based on an aptamer-functionalized magnetic conjugated organic framework (COF) was developed for selective extraction of traces of hydroxylated polychlorinated biphenyls. This material has advantages such as superparamagnetism of the magnetic core, high surface area and porous structure of the COF, and high specific affinity of the aptamer. In combination with HPLC-MS, the aptamer-functionalized magnetic COF was used for the capture of hydroxy-2',3',4',5,5'-pentachlorobiphenyl in human serum. The method provided a linear range of 0.01-40 ng mL^-1 with a good correlation coefficient (R² =0.9973). The limit of detection was as low as 2.1 pg mL^-1 . Furthermore, the material showed good reusability and could be applied in at least ten extraction cycles with recoveries greater than 90 %.

A magnetic hydrazine-functionalized dendrimer embedded with TiO2 as a novel affinity probe for the selective enrichment of low-abundance phosphopeptides from biological samples

Dendrimers exhibit tunable terminal functionality and bio-friendly nature, making them of being promising materials for applications in the field of separation and enrichment. In this work, we prepared magnetic hydrazide-functionalized poly-amidoamine (PAMAM) dendrimer embedded with TiO₂ for the enrichment of phosphopeptides. The novel affinity probe possessed superparamagnetism, realizing its rapid separation from sample solution. Electrostatic attraction and hydrogen bonding existed between PAMAM and phosphopeptides while Lewis acid-base interaction was originated between TiO₂ and the targets. The combined synergistic strength of multiple binding interactions contributed to the highly selective enrichment of phosphopeptides. The specificity for the capture of phosphopeptides was reflected in quantities as low as 1:1000 mass ratio of phosphopeptides to non-phosphopeptides. The detection limit of β-casein digests was low to 0.4 fmol, indicating the high sensitivity of the developed method. Fifteen and four phosphopeptides could be selectively captured from non-fat milk digests and human serum samples, which further confirmed the great potential of the affinity probe in the extraction of low-abundance phosphopeptides from real complex biological samples.