Facile synthesis of titanium (IV) ion immobilized adenosine triphosphate functionalized silica nanoparticles for highly specific enrichment and analysis of intact phosphoproteins

Polyoxometalate functionalized magnetic metal-organic framework with multi-affinity sites for efficient enrichment of phosphopeptides

The reasonable design of metal-organic framework (MOF)-derived nanomaterial has important meaning in increasing the enrichment efficiency in the study of protein phosphorylation. In this work, a polyoxometalate (POM) functionalized magnetic MOF nanomaterial (Fe3O4@MIL-125-POM) was designed and fabricated. The nanomaterial with multi-affinity sites (unsaturated metal sites and metal oxide clusters) was used for the enrichment of phosphopeptides. Fe3O4@MIL-125-POM had high-efficient enrichment performance towards phosphopeptides (selectivity, a mass ratio of bovine serum albumin/α-casein/β-casein at 5000:1:1; sensitivity, 0.1 fmol; satisfactory repeatability, ten times). Furthermore, Fe3O4@MIL-125-POM was employed to enrich phosphopeptides from non-fat milk digests, saliva, serum, and A549 cell lysate. The enrichment results illustrated the great potential of Fe3O4@MIL-125-POM for efficient identification of low-abundance phosphopeptides.

One-step enrichment and stepwise elution of glycoproteins and phosphoproteins by hydrophilic Ti4+-immobilized dendrimer poly(glycidyl methacrylate) microparticles functionalized with polyethylenimine and phytic acid

Glycosylation and phosphorylation rank as paramount post-translational modifications, and their analysis heavily relies on enrichment techniques. In this work, a facile approach was developed for the one-step simultaneous enrichment and stepwise elution of glycoproteins and phosphoproteins. The core of this approach was the application of the novel titanium (IV) ion immobilized poly(glycidyl methacrylate) microparticles functionalized with dendrimer polyethylenimine and phytic acid. The microparticles possessed dual enrichment capabilities due to their abundant titanium ions and hydroxyl groups on the surface. They demonstrate rapid adsorption equilibrium (within 30 min) and exceptional adsorption capacity for β-casein (1107.7 mg/g) and horseradish peroxidase (438.6 mg/g), surpassing that of bovine serum albumin (91.7 mg/g). Furthermore, sodium dodecyl sulfate-polyacrylamide gel electrophoresis was conducted to validate the enrichment capability. Experimental results across various biological samples, including standard protein mixtures, non-fat milk, and human serum, demonstrated the remarkable ability of these microparticles to enrich low-abundance glycoproteins and phosphoproteins from biological 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.

Profiling of phosphorylated metabolites from lung cancer by zeolite loaded Mg-Al-Ce ternary hydroxide (Zeolite@MAC) composite

Phosphorylated metabolites are linked to metabolism, and the dysregulation of metabolic reactions brings cancer. Dysregulated levels lead to hyperactivation of glycolytic and mitochondrial oxidative phosphorylation pathways. Abnormal concentrations are the indicators of energy-related disorders. In this work, Zeolite-loaded Mg-Al-Ce hydroxides (Zeolite@MAC) are prepared by co-precipitation and characterized through FTIR, XRD, SEM, BET, AFM, TEM, and DLS. Magnesium-Aluminum-Cerium-Zeolite particles enrich phosphate-containing small molecules. These ternary hydroxides carried out the main adsorption mechanism, which swapped the surface hydroxyl group ligands for phosphate and the inner-sphere complex of CePO₄. XH₂O. Cerium plays a significant role in the complexation of phosphate, and adding Mg and Al further helps disperse Ce and increase the surface charge on the adsorbent. ΑTP and AMP are the standard molecules for parameter optimization. Zeolite@MAC enriches phosphorylated metabolites followed by their desorption via UV-vis spectrophotometry. MS profiles for healthy and lung cancer serum samples are obtained for phosphorylated metabolites. Characteristic phosphorylated metabolites have been detected in lung cancer samples with high expression. The role of phosphorylated metabolites is explored for abnormal metabolic pathways in lung cancer. The fabricated material is sensitive, selective, and highly enriched for identifying phosphate-specific biomarkers.

Advances in proteomics sample preparation and enrichment for phosphorylation and glycosylation analysis

As the common and significant chemical modifications, post-translational modifications (PTMs) play a key role in the functional proteome. Affected by the signal interference, low concentration, and insufficient ionization efficiency of impurities, the direct detection of PTMs by mass spectrometry (MS) still faces many challenges. Therefore, sample preparation and enrichment are an indispensable link before MS analysis of PTMs in proteomics. The rapid development of functionalized materials with diverse morphologies and compositions provides an avenue for sample preparation and enrichment for PTMs analysis. In this review, we summarize recent advances in the application of novel functionalized materials in sample preparation for phosphoproteomes and glycoproteomes analysis. In addition, this review specifically discusses the design and preparation of functionalized materials based on different enrichment mechanisms, and proposes research directions and potential challenges for proteomic PTMs research.

TiO2 with Confined Water Boosts Ultrahigh Selective Enrichment of Phosphorylated Proteins

In the selective enrichment of phosphorylated proteins (PPs) from biological samples, the non-phosphorylated proteins (NPPs) adhered onto enrichment adsorbents due to the hydrophobic interaction, resulting in poor selectivity and low recovery of target PPs. Herein, superhydrophilic TiO₂-coated porous SiO₂ microspheres are prepared and boost remarkable selectivity toward standard PP spiked with 2000 mass-fold NPP interference. The outstanding performance of the superhydrophilic microspheres is attributed to the coordination interaction between TiO₂ and PPs, and the confined water layer generated from superhydrophilicity avoids the irreversible adsorption of NPPs by keeping NPP inner hydrophobic regions in a compact structure, which is verified by single molecule force spectroscopy, circular dichroism, and quartz crystal microbalance. This strategy for enrichment is expected to solve the challenge in proteomics and sheds light on the interactions between biomolecules and superwettability.

Development of dual-ligand titanium (IV) hydrophilic network sorbent for highly selective enrichment of phosphopeptides

A hydrophilic metal-organic network based on Ti⁴⁺ and dual natural ligand, tannic acid (TA) and phytic acid (PA), has been developed to enrich phosphopeptides from complex bio-samples prior to liquid chromatography-mass spectrometric analysis. Due to the strong chelation ability of TA and PA, abundant Ti⁴⁺ can be immobilized in the material, forming hydrophilic network by one-step coordination-driven self-assembly approach. The sorbent, TA-Ti-PA@Fe₃O₄, exhibited satisfactory selectivity for the phosphopeptides in the tryptic digest of β-casein, and can eliminate the interference components in 1000-fold excess of bovine serum albumin. The adsorption capacity of the sorbents for phosphopeptides was up to 35.2 mg g^-1 and the adsorbing equilibrium can be reached in 5 min. The adsorbing mechanism has been investigated and the results indicated that the Ti⁴⁺ in forms of [Ti(f-TA)(H₂O)₄]²⁺, [Ti(f-PA)(H₂O)₄]²⁺ and Ti(f-PA)₂(H₂O)₂ may play an important role in the adsorption process. The sorbent of the TA-Ti-PA@Fe₃O₄ has been applied to enrichment of the phosphopeptides in tryptic digest of rat liver lysate, and 3408 phosphopeptides have been identified, while the numbers of the identified phosphopeptides were 2730 and 1217 when the sample was enriched by the commercial TiO₂ and Fe³⁺-IMAC kit, respectively. This work provides a strategy to enrich phosphopeptides from complex samples and shows great potential application in phosphoproteome research.

Facile synthesis of titanium(IV) ion-immobilized arsenate-modified poly(glycidyl methacrylate) microparticles and the application to the specific enrichment of phosphoproteins

Selective separation and enrichment of phosphoproteins possess the distinct clinical and biological importance in the diagnosis, treatment, and management of several fatal human diseases. In this study, a facile synthesis of titanium(IV) ion-immobilized arsenate-modified poly(glycidyl methacrylate) microparticles (denoted as Ti⁴⁺-arsenate-PGMA-MPs) was developed for the efficient enrichment of intact phosphoproteins found in biologically complex protein samples. By virtue of the strong interaction between the titanium ions immobilized on the surface of Ti⁴⁺-arsenate-PGMA-MPs and phosphate groups of phosphoproteins, Ti⁴⁺-arsenate-PGMA-MPs had a high saturated adsorption capacity for phosphoproteins (901 mg/g for β-casein), which was much higher than that of non-phosphoproteins (73.5 mg/g for BSA). Ti⁴⁺-arsenate-PGMA-MPs were characterized by SEM, TEM, and FT-IR, and the average particle diameter was about 2.5 μm with good dispersibility. Besides, the application of Ti⁴⁺-arsenate-PGMA-MPs in real biological samples was investigated by SDS-PAGE analysis, and the results showed that Ti⁴⁺-arsenate-PGMA-MPs were able to enrich phosphoproteins efficiently.

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.

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.

Novel Ti4+-Chelated Polyoxometalate/Polydopamine Composite Microspheres for Highly Selective Isolation and Enrichment of Phosphoproteins

Selective isolation and enrichment of phosphoproteins play critical roles for identification of biomarkers in biological applications. Herein, a kind of polyoxometalate (P₅W₃₀)/polydopamine (PDA) composite microspheres is readily synthesized via an in situ polymerization way, followed by immobilization of Ti⁴⁺ on the surface of the microspheres to obtain P₅W₃₀/PDA-Ti⁴⁺. Due to metal affinity and π stacking interaction, this novel material exhibits high selectivity to β-casein (β-ca), and the theoretical maximum adsorption capacity is as high as 1250 mg g^-1, fitting well with the Langmuir model. The captured β-ca can be collected by using Britton-Robinson (B-R) buffer at pH 7.0, and a recovery of 81.5% is acquired. The enrichment factor is over 150 at a mass ratio of BSA/β-ca = 100:1, indicating that phosphoproteins can be purified by P₅W₃₀/PDA-Ti⁴⁺. Moreover, the application of P₅W₃₀/PDA-Ti⁴⁺ as sorbent in real biological samples has been investigated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis, and the consequences show that this kind of material is able to selectively isolate phosphoproteins from complex samples such as drinking milk and chicken egg white.