Dual-ligand hydrogen-bonded organic framework: Tailored for mono-phosphopeptides and glycopeptides analysis

Hydrogen-bonded organic frameworks (HOFs) have emerged as a promising class of materials for applications of separation and enrichment. Utilizing multiple-ligands to construct HOFs is a promising avenue towards the development of structurally stable and functionally diverse frameworks, offering opportunities to create customized binding sites for selective recognition of biomolecules. In recent years, due to the crucial role that protein post-translational modifications (PTMs) play in maintaining protein function and regulating signaling pathways, and the growing recognition of the extensive cross-talk that can occur between PTMs, simultaneous analysis of different types of PTMs represents a requirement of a new generation of enrichment materials. Here, for the first attempt, we report a dual-ligand HOF constructed from borate anion and guanidinium cation for the simultaneous identification of glycopeptides and phosphopeptides, especially mono-phosphopeptides. According to theoretical calculations, the HOF functional sites display a synergistic "matching" effect with mono-phosphopeptides, resulting in a stronger enrichment effect for mono-phosphopeptides as compared to multi-phosphopeptides. Also, due to its high hydrophilicity and boronate affinity, this material can efficiently capture glycoproteins. HOF is set to become an active research direction in the development of highly efficient simultaneous protein enrichment materials, and offers a new approach for comprehensive PTMs analysis.

Titania Nanosheet as a Matrix for Surface-Assisted Laser Desorption/Ionization Mass Spectrometry Analysis and Imaging

Surface-assisted laser desorption/ionization (SALDI) acts as a soft desorption/ionization technique, which has been widely recognized in small-molecule analysis owing to eliminating the requirement of the organic matrix. Herein, titania nanosheets (TiO₂ NSs) were applied as novel substrates for simultaneous analysis and imaging of low-mass molecules and lipid species. A wide variety of representative analytes containing amino acids, bases, drugs, peptides, endogenous small molecules, and saccharide-spiked urine were examined by the TiO₂ NS-assisted LDI mass spectrometry (MS). Compared with conventional organic matrices and substrates [Ag nanoparticles (NPs), Au NPs, carbon nanotubes, carbon NPs, CeO₂ microparticles, and P25 TiO₂], the TiO₂ NS-assisted LDI MS method shows higher sensitivity and less spectral interference. Repeatability was evaluated with batch-to-batch relative standard deviations for 5-hydroxytryptophan, glucose-spiked urine, and glucose with addition of internal standard, which were 17.4, 14.9, and 2.8%, respectively. The TiO₂ NS-assisted LDI MS method also allows the determination of blood glucose levels in mouse serum with a linear range of 0.5-10 mM. Owing to the nanoscale size and uniform deposition of the TiO₂ NS matrix, spatial distributions of 16 endogenous small molecules and 16 lipid species from the horizontal section of the mouse brain tissue can be visualized at a 50 μm spatial resolution. These successful applications confirm that the TiO₂-assisted LDI MS method has promising prospects in the field of life science.

Removal of adsorption sites on the external surface of mesoporous adsorbent for eliminating the interference of proteins in enrichment of phosphopeptides/nucleotides

Various mesoporous adsorbents are of great promise for enriching small molecules from biological samples based on the size-exclusion effect. At present, the mesoporous adsorbents have adsorption sites distributed uniformly on the internal and external surfaces of mesopores. However, the adsorption sites on the external surface can adsorb proteins, interfering with the enrichment of small molecules. Herein, a novel immobilized-Ti⁴⁺ magnetic mesoporous adsorbent removing the adsorption sites on the external surface was facile prepared via the coupling chemistry of isocyanate with amine and consequent hydrolysis of urea linkage by urease. The adsorbent enables fast and selective enrichment of phosphopeptides and nucleotides from biological samples. In addition, sensitive detection methods for phosphopeptides and nucleotides in human serum are developed by coupling the magnetic solid-phase extraction with matrix-assisted laser desorption/ionization time of flight mass spectrometry and liquid chromatography-mass spectrometer, respectively. Under optimal conditions, response is linear (R² ≥ 0.9923), limits of detection are low (0.41-9.48 ng mL^-1), and reproducibility is acceptable (inter- and intra-day assay RSDs of≤15.0%) for six nucleotides. The developed strategy offers an effective method to eliminate the interference of proteins in the enrichment of small molecules from real biological samples.

Phytic acid functionalized magnetic bimetallic metal-organic frameworks for phosphopeptide enrichment

Highly specific enrichment of phosphopeptides from complex biological samples was a precondition for further studying its physiological and pathological processes due to the important and trace amounts of phosphopeptides. In this work, phytic acid (PA) functionalized magnetic cerium and zirconium bimetallic metal-organic framework nanocomposites (denoted as Fe3O4@SiO2@Ce-Zr-MOF@PA) were fabricated by a facile yet efficient method. The as-prepared nanomaterial exhibited high sensitivity (0.1 fmol μL-1), high selectivity toward phosphopeptides from β-casein tryptic digests/BSA (1 : 800), and good reusability of five cycles for enriching phosphopeptides. This affinity probe was applied to biological samples, and 19, 4 and 15 phosphopeptides were identified from non-fat milk, human serum and human saliva, respectively. The above marked advantages are attributed to the strong affinity of the abundant Ce-O and Zr-O nanoclusters on the surface of the MOF shell with the improved hydrophilicity from a great number of phosphate groups. Therefore, the novel Fe3O4@SiO2@Ce-Zr-MOF@PA nanospheres could not only enrich phosphopeptides effectively, but also reduce the adsorption of phosphopeptides, manifesting great potential in the identification and further analysis of low abundance phosphopeptides in complex biological samples.

PAMAM–PMAA brush-functionalized magnetic composite nanospheres: a smart nanoprobe with tunable selectivity for effective enrichment of mono-, multi-, or global phosphopeptides

A novel PAMAM–PMAA brush functionalized magnetic composite nanosphere was successfully prepared for selective enrichment of mono-, multi-, or global phosphopeptides by modulating buffer polarity and acidity.

Multi-affinity sites of magnetic guanidyl-functionalized metal-organic framework nanospheres for efficient enrichment of global phosphopeptides

Magnetic guanidyl-functionalized metal-organic framework (MOF) nanospheres with multi-affinity sites composed of an inherent Zn-O cluster based on MOAC and specific recognized groups (amino group and guanidyl group) were for the first time synthesized by a combination strategy of epitaxial growth and post-synthetic modification of magnetic amino-derived MOFs, and they exhibit great potential for efficient enrichment of global phosphopeptides.

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.

Hydrazide functionalized monodispersed silica microspheres: a novel probe with tunable selectivity for a versatile enrichment of phosphopeptides with different numbers of phosphorylation sites in MS analysis

Hydrazide functionalized monodispersed silica microspheres (HFMSM) were developed for the enrichment of phosphopeptides for the first time.

Magnetite/Ceria-Codecorated Titanoniobate Nanosheet: A 2D Catalytic Nanoprobe for Efficient Enrichment and Programmed Dephosphorylation of Phosphopeptides

Global characterization and in-depth understanding of phosphoproteome based on mass spectrometry (MS) desperately needs a highly efficient affinity probe during sample preparation. In this work, a ternary nanocomposite of magnetite/ceria-codecorated titanoniobate nanosheet (MC-TiNbNS) was synthesized by the electrostatic assembly of Fe3O4 nanospheres and in situ growth of CeO 2 nanoparticles on pre-exfoliated titanoniobate and eventually utilized as the probe and catalyst for the enrichment and dephosphorylation of phosphopeptides. The two-dimensional (2D) structured titanoniobate nanosheet not only promoted the efficacy of capturing phosphopeptides with enlarged surface area, but also functioned as a substrate for embracing the magnetic anchor Fe3O4 to enable magnetic separation and mimic phosphatase CeO2 to produce identifying signatures of phosphopeptides. Compared to single-component TiNbNS or CeO2 nanoparticles, the ternary nanocomposite provided direct evidence of the number of phosphorylation sites while maintaining the enrichment efficiency. Moreover, by altering the on-sheet CeO2 coverage, the dephosphorylation activity could be fine-tuned, generating continuously adjustable signal intensities of both phosphopeptides and their dephosphorylated tags. Exhaustive detection of both mono- and multiphosphorylated peptides with precise counting of their phosphorylation sites was achieved in the primary mass spectra in the cases of digests of standard phosphoprotein and skim milk, as well as a more complex biological sample, human serum. With the resulting highly informative mass spectra, this multifunctional probe can be used as a promising tool for the fast and comprehensive characterization of phosphopeptides in MS-based phosphoproteomics.

Phosphonate-modified metal oxides for the highly selective enrichment of phosphopeptides

Phosphonate-modified metal oxides display higher selectivity than unmodified ones for the effective enrichment of phosphopeptides.

Cooperative adsorption behavior of phosphopeptides on TiO2 leads to biased enrichment, detection and quantification

Novel data show that anomalous adsorption behavior and common washing procedures can lead to biased results in TiO₂-based phosphoproteomics.

Guanidyl-functionalized graphene as a bifunctional adsorbent for selective enrichment of phosphopeptides

This novel bi-functional gfg provides two enriching performances, one is for global phosphopeptides, and the other is for multi-phosphopeptides with consecutive phosphorylated residues.

On-target titanium dioxide-based enrichment for characterization of phosphorylations in the Adenovirus pIIIa protein

A recently developed titanium dioxide (TiO2) based on-target method for phosphopeptide enrichment and matrix assisted laser desorption-ionization mass spectrometry (MALDI MS) analysis was used to investigate phosphorylations in the Adenovirus type 2 structural protein pIIIa. Lysates of purified virus particles were separated on 1-D SDS-PAGE and the band for the pIIIa protein was excised for tryptic digestion into peptides that were enriched with the on-target method. The enrichment provided by the method clearly improved the detectability of phosphorylated peptides and the results show for the first time evidence for multi-phosphorylated peptides in pIIIa. Moreover, three novel phosphorylations were identified in the protein sequence, even though the precise positions could not be determined. These results illustrate the potential of the method for the characterization of novel phosphoproteomes in biological samples of medical relevance.

In-situ enrichment of phosphopeptides on MALDI plates modified by ambient ion landing

We report substantial in-situ enrichment of phosphopeptides in peptide mixtures using titanium and zirconium dioxide-coated matrix assisted laser desorption-ionization (MALDI) plates prepared by recently reported ambient ion landing deposition technique. The technique was able to modify four common materials currently used for MALDI targets (stainless steel, aluminum, indium-tin oxide glass and polymeric anchor chip). The structure of the deposited dioxide was investigated by electron microscopy, and different surfaces were compared and discussed in this study. Two standard proteins were used to test the enrichment capabilities of modified MALDI plates: casein and in-vitro phosphorylated trehalase. The enrichment of casein tryptic digest resulted in identification of 20 phosphopeptides (including miscleavages). Trehalase was used as a suitable model of larger protein that provided more complex peptide mixture after the trypsin digestion. All four possible phosphorylation sites in trehalase were identified and up to seven phosphopetides were found (including methionine oxidations and miscleavages). Two different mass spectrometers, MALDI-Fourier transform ion cyclotron resonance (FTICR) and MALDI-time of flight, were used to detect the phosphopeptides from modified MALDI plates after the enrichment procedure. It was observed that the desorption-ionization phenomena on the modified surfaces are not critically influenced by the parameters of the different MALDI ion sources (e.g. different pressure, different extraction voltages), and thus the presence of dioxide layer on the standard MALDI plate does not significantly interfere with the main MALDI processes. The detection of phosphopeptides after the enrichment could be done by both instruments. Desorption electrospray ionization coupled to the FTICR was also tested, but, unlike MALDI, it did not provide satisfactory results.

Bifunctional polymer brushes for low-bias enrichment of mono- and multi-phosphorylated peptides prior to mass spectrometry analysis

Polymer brushes orthogonally derivatized with oxotitanium and nitrilotriacetate-Fe(III) groups enrich both mono- and multi-phosphorylated peptides for mass spectrometry analysis.

Nanomaterial-assisted laser desorption ionization for mass spectrometry-based biomedical analysis

Nanomaterials have been widely used to assist laser desorption ionization of biomolecules for mass spectrometry analysis. Compared with classical matrix-assisted laser desorption ionization, strategies based on nanomaterial-assisted ionization generate a clean background, which is of great benefit for the qualitative and quantitative analysis of small biomolecules, such as therapeutic and diagnostic molecules. As label-free platforms, they have successfully been used for high-throughput enzyme activity/inhibition monitoring and also for tissue imaging to map in situ the distribution of peptides, metabolites and drugs. In addition to widely used porous silicon nanomaterials, gold nanoparticles can be easily chemically modified by thiol-containing compounds, opening novel interesting perspectives. Such functionalized nanoparticles have been used both as probes to extract target molecules and as matrices to assist laser desorption ionization for developing new enzyme immunoassays or for studying DNA hybridization. More recently, semiconductor nanomaterials or quantum dots acting as photosensitive centers to induce in-source redox reactions for proteomics and to investigate biomolecule oxidation for metabolomics have been shown to offer new analytical strategies.