Newly Fabricated Magnetic Lanthanide Oxides Core–Shell Nanoparticles in Phosphoproteomics

Temporally and spatially resolved molecular profiling in fingerprint analysis using indium vanadate nanosheets-assisted laser desorption ionization mass spectrometry

This study presents the first-ever synthesis of samarium-doped indium vanadate nanosheets (IVONSs:Sm) via microemulsion-mediated solvothermal method. The nanosheets were subsequently utilized as a nano-matrix in laser desorption/ionization mass spectrometry (LDI-MS). It was discovered that the as-synthesized IVONSs:Sm possessed the following advantages: improved mass spectrometry signal, minimal matrix-related background, and exceptional stability in negative-ion mode. These qualities overcame the limitations of conventional matrices and enabled the sensitive detection of small biomolecules such as fatty acids. The negative-ion LDI mechanism of IVONSs:Sm was examined through the implementation of density functional theory simulation. Using IVONSs:Sm-assisted LDI-MS, fingerprint recognitions based on morphology and chemical profiles of endogenous/exogenous compounds were also achieved. Notably, crucial characteristics such as the age of an individual's fingerprints and their physical state could be assessed through the longitudinal monitoring of particular biomolecules (e.g., ascorbic acid, fatty acid) or the specific biomarker bilirubin glucuronide. Critical information pertinent to the identification of an individual would thus be facilitated by the analysis of the compounds underlying the fingerprint patterns.

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.

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.

Ionic liquid modification of metal-organic framework endows high selectivity for phosphoproteins adsorption

Zr-based metal-organic framework, UiO-66-NH₂, provides favorable adsorption capacity to phosphoproteins, however, it exhibits obvious nonspecific adsorption to other proteins. In the present work, we report a facile strategy to reduce the nonspecific adsorption of nonphosphoproteins by modifying UiO-66-NH₂ with imidazolium ionic liquids (ILs). With respect to bare UiO-66-NH₂, the modified counterpart, UiO@IL, exhibits much improved selectivity to phosphoproteins while maintains comparable adsorption performance. The surface of UiO@IL presents a strong hydrophilicity due to the modification of ILs. Hydrophobic and electrostatic interaction between the absorbent and nonphosphoprotein is significantly reduced. In addition, the interaction between imidazole group of ILs moiety and phosphate group in phosphoprotein ensures the favorable adsorption capacity of UiO@IL for phosphoproteins. Anionic moieties of ILs, i.e., Cl^-, Br^-, BF₄^-, CF₃SO₃^-, play negligible effect in the adsorption process. As a representative, phosphoprotein β-casein (β-ca) is selectively enriched at a mass ratio of BSA:β-ca = 100:1. UiO@IL was further applied for the selective enrichment of phosphoprotein in milk.

Phosphate-imprinted magnetic nanoparticles using phenylphosphonic acid as a template for excellent recognition of tyrosine phosphopeptides

The tyrosine phosphorylation of proteins and peptides plays a vital role in cell signal transduction pathways, and it is very important to assay them for understanding their action mechanism. Due to the low levels of the tyrosine phosphopeptides (pTyr) in cells, it is a challenge to enrich them with traditional sorbents, therefore, development of specific and selective sorbents is urgent and necessary. In this work, the phosphate-imprinted magnetic nanoparticles (PMNPs) to enrich the pTyr with high efficiency and selectivity have been fabricated using the phenylphosphonic acid as a template for the "epitope" of pTyr. The magnetic nanoparticles have been functionalized with TiO₂ and then the imprinting silica shells have been coated on the surface of the functional core to obtain the PMNPs sorbents. The PMNPs can obviously shorten the enrichment time and improve the adsorption efficiency for pTyr, and the epitope imprinting films provide an excellent selective recognition ability to target. The recognition capability of PMNPs for pTyr is 90.3 μg/mg and the imprinting factor of the sorbents can reach 24.4. The results indicate that the PMNPs can enrich the pTyr from the tryptic digest of β-casein samples with high specificity, and the spiking recoveries of the pTyr range from 85.1% to 93.8% with the RSD from 0.04 to 3.73. With the high adsorption capacity, rapid separation, excellent specificity and recyclability, the PMNPs sorbents show great potential for analysis of the phosphorylation of peptides in biological and medical fields.

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.

Facile Preparation of Titanium(IV)-Immobilized Hierarchically Porous Hybrid Monoliths

Hierarchically porous materials have become a key feature of biological materials and have been widely applied for adsorption or catalysis. Herein, we presented a new approach to directly prepare a phosphate-functionalized hierarchically porous hybrid monolith (HPHM), which simultaneously contained mesopores and macropores. The design was based on the copolymerization of polyhedral oligomeric vinylsilsesquioxanes (vinylPOSS) and vinylphosphonic acid (VPA) by adding degradable polycaprolactone (PCL) additive. The phosphate groups could be directly introduced into the hybrid monoliths. This approach was simple and time-saving, and overcame the defect of a rigorous, complex process for preparing traditional Ti⁴⁺-immobilized metal ion affinity chromatography (IMAC) materials. The specific surface area of an optimal hybrid monolith could reach 502 m²/g obtained by nitrogen adsorption/desorption measurements, which originated from the degradation of PCL. Meanwhile, the characterization of scanning electron microscopy (SEM) and mercury intrusion porosimetry (MIP) also suggested that the macropores existed in the hybrid monoliths. The size of macropores could be controlled by the content of PCL in the polymerization mixture. The prepared Ti⁴⁺-IMAC HPHMs exhibited high adsorption capacity (63.6 mg/g for pyridocal 5'-phosphatemonohydrate), and excellent enrichment specificity (tryptic digest of β-casein/BSA at a molar ratio of 1:1000) and sensitivity (tryptic digest of 5 fmol of β-casein). Moreover, the Ti⁴⁺-IMAC HPHMs provided effective enrichment ability of low-abundance phosphopeptides from human serum and HeLa cell digests.

Formation of Core-Shell Nanoparticles Composed of Magnetite and Samarium Oxide in Magnetospirillum magneticum Strain RSS-1

Magnetotactic bacteria (MTB) synthesize magnetosomes composed of membrane-enveloped magnetite (Fe₃O₄) or greigite (Fe₃S₄) particles in the cells. Recently, several studies have shown some possibilities of controlling the biomineralization process and altering the magnetic properties of magnetosomes by adding some transition metals to the culture media under various environmental conditions. Here, we successfully grow Magnetospirillum magneticum strain RSS-1, which are isolated from a freshwater environment, and find that synthesis of magnetosomes are encouraged in RSS-1 in the presence of samarium and that each core magnetic crystal composed of magnetite is covered with a thin layer of samarium oxide (Sm₂O₃). The present results show some possibilities of magnetic recovery of transition metals and synthesis of some novel structures composed of magnetic particles and transition metals utilizing MTB.

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.