Enrichment and detection of peptides from biological systems using designed periodic mesoporous organosilica microspheres

Oriented assembly of hydrophilic nanochains modified by porous zirconium-based coordination polymers for glycopeptides analysis

Mass spectrometry (MS)-based glycoproteomics research requires additional sample pretreatment to improve the effective identification of low-abundance glycopeptides without interference from non-glycoproteins. Herein, an attractive strategy using resorcinol-formaldehyde (RF) resin and zirconium-based coordination polymer (Zr-BCP) was established to prepare one-dimensional porous coordination polymer composites for glycopeptide enrichment before MS analysis. The obtained Fe3O4@RF@Zr-BCP nanochains feature excellent magnetic response (42.26 emu/g), high hydrophilicity (16.0°), and large specific surface area (140.84 m2/g), which provides abundant affinity sites for specific capture of glycopeptides. The materials exhibit outstanding performance in the enrichment of glycopeptides in terms of sensitivity (15 fmol/μL IgG), selectivity (1:200, molar ratio of IgG/BSA), loading capacity (200 mg/g) and recovery (106.4 ± 3.5%). In addition, the developed method based on Fe3O4@RF@Zr-BCP has been successfully applied to capture glycopeptides in tryptic digest of mouse teratoma cell extracts. It is worth emphasizing that compared with dispersed nanoparticles, the one-dimensional chain structure brings extraordinary reusability to Fe3O4@RF@Zr-BCP nanochains, which is conducive to the rapid cyclic enrichment of glycopeptides. This present work provides a potential enrichment platform for comprehensive glycoprotein analysis, and opens a new avenue for the application of oriented-assembly nanochains.

Integrative Serum Metabolic Fingerprints Based Multi-Modal Platforms for Lung Adenocarcinoma Early Detection and Pulmonary Nodule Classification

Identification of novel non-invasive biomarkers is critical for the early diagnosis of lung adenocarcinoma (LUAD), especially for the accurate classification of pulmonary nodule. Here, a multiplexed assay is developed on an optimized nanoparticle-based laser desorption/ionization mass spectrometry platform for the sensitive and selective detection of serum metabolic fingerprints (SMFs). Integrative SMFs based multi-modal platforms are constructed for the early detection of LUAD and the classification of pulmonary nodule. The dual modal model, metabolic fingerprints with protein tumor marker neural network (MP-NN), integrating SMFs with protein tumor marker carcinoembryonic antigen (CEA) via deep learning, shows superior performance compared with the single modal model Met-NN (p < 0.001). Based on MP-NN, the tri modal model MPI-RF integrating SMFs, tumor marker CEA, and image features via random forest demonstrates significantly higher performance than the clinical models (Mayo Clinic and Veterans Affairs) and the image artificial intelligence in pulmonary nodule classification (p < 0.001). The developed platforms would be promising tools for LUAD screening and pulmonary nodule management, paving the conceptual and practical foundation for the clinical application of omics tools.

Nanostructure stable hydrophilic hierarchical porous metal-organic frameworks for highly efficient enrichment of glycopeptides

Protein glycosylation plays a vital role in many physiological activities in organisms. Due to the low abundance of glycopeptides and the interference of numerous non-glycopeptides in biological samples, selective enrichment of glycopeptides is of great significance for their successful identification. Metal organic frameworks (MOFs) materials are appropriate for glycopeptides enrichment by virtue of their large specific surface area and outstanding hydrophilic properties. However, the instability of hydrophilic MOFs in acidic solutions have severely limited their applications. In this work, a rational facile strategy was established to synthesize a stable hydrophilic hierarchical porous MOF (denoted as HP-MOF-Arg@mSiO₂). This new material improved the selectivity and sensitivity of enrichment for glycopeptides via modification of arginine groups. More importantly, the mesoporous silica layer was introduced to enhance the stability of MOFs in aqueous solution and achieve the size exclusion effect of large-size proteins in complex samples. Overall, owing to the unique hierarchical porous and the hydrophilic modification, the synthesized HP-MOF-Arg@mSiO₂ materials showed excellent hydrophilicity and hydrolytic stability, resulting in outstanding specific separation capacity in glycopeptides enrichment. A total of 521 and 342 glycopeptides were respectively captured from 2 μL human serum digests and mouse testis tissue digests, revealing the potential of the materials in the study of glycoproteomics in complex biological samples.

Ti4+-immobilized hierarchically porous zirconium-organic frameworks for highly efficient enrichment of phosphopeptides

Ti⁴⁺-immobilized hierarchically porous zirconium-organic frameworks (denoted as THZr-MOFs) was prepared for phosphopeptide enrichment. The THZr-MOFs showed high specific surface area of 185.28 m² g^-1, wide pore-size distribution of 3 ~ 20 nm, good chemical stability and excellent hydrophilicity. Introduction of hierarchical pores in MOFs not only facilitated the accessibility of phosphopeptides to the internal metal affinity sites and reduce their mass transfer resistance, but also increased the exposure sites of metal affinity interaction and binding energies of Zr and Ti elements. Benefited from these advantages, the THZr-MOFs showed high adsorption capacity (79.8 μg mg^-1) towards standard phosphopeptide. A low detection limit (0.05 fmol μL^-1) and high enrichment selectivity (β-casein/BSA with a molar ratio of 1:5000) were also obtained by MALDI-TOF MS. The THZr-MOFs were applied to analyze complex samples including nonfat milk, human serum, and HeLa cell lysate. In total, 1432 phosphopeptides derived from 762 phosphoproteins were identified from human HeLa cell lysate. Schematic representation of the application of Ti⁴⁺-immobilized hierarchically porous zirconium-organic frameworks (denoted as THZr-MOFs) in high-efficiency and selective enrichment of low-abundance phosphopeptides from the tryptic digest of human HeLa cell lysate.

C18-functionalized magnetic nanocomposites fabricated by one-step aqueous coating of tailored oligopeptides for enrichment of low-abundance peptides

Screening and monitoring endogenous peptides from complicated biosamples is still a major challenge in mass spectrometry-based proteomics research, mainly due to their low concentration and the interference of high-abundance proteins and other contaminants in biological samples. Herein, a facile and novel approach was described for rapid fabrication of C₁₈-functionalized magnetic nanocomposites (C₁₈-MNCs) based on one-step aqueous coating of C₁₈-Val-Lys-Val-Lys-Val-Lys (C₁₈-VK-VI) for the highly selective enrichment of low-abundance endogenous peptides from biological samples. C₁₈-VK-VI can readily self-assemble into complete monolayers mainly composed of β-sheets with C₁₈ hydrophobic chains erecting on the surface of GO@Fe₃O₄ MNCs under the physiological conditions. The resulting C₁₈VK-VI-GO@Fe₃O₄ MNCs exhibited good performance for peptides enrichment from digests of standard protein (myoglobin, MYO) and human serum, such as high sensitivity (0.05 fmol μL^-1) and selectivity (mass ratio of MYO digests and MYO = 1:500), rapid separation, and good reproducibility. Such a simple mild and rapid one-step aqueous coating method on the basis of oligopeptides self-assembly showed great potential in surface functionalization of various nanoadsorbents for proteome/peptidome researches.

Targeted immobilization of titanium (IV) on magnetic mesoporous nanomaterials derived from metal-organic frameworks for high-efficiency phosphopeptide enrichment in biological samples

A selectively modified porous metal/carbon nanocomposite was fabricated to enhance the enrichment of low-abundance phosphopeptides from biological samples. The carbon matrix derived from the metal-organic framework provides a suitable pore size to allow the diffusion of peptides, while the deliberately modified metal nanoparticles within the pores enhance their interaction with the phosphopeptides. This nanocomposite shows extremely high enrichment selectivity for phosphopeptides in the MALDI-TOF MS detection, even when the molar ratio of α-casein digests versus bovine serum albumin digests was up to about 1:20,000. By combining such nanocomposite with nano-LC-MS/MS, 4556 unique phosphopeptides were identified with high selectivity (95.2%) from HeLa cell extracts. Furthermore, phosphopeptides from prostate tissue digests were also determined. A total of 277 and 1242 phosphopeptides were identified from normal and tumor tissues of a patient with prostate cancer, respectively. This indicates that phosphorylation and prostate cancer can be related to each other.

New insights into the structure-performance relationships of mesoporous materials in analytical science

Mesoporous materials are ideal carriers for guest molecules and they have been widely used in analytical science. The unique mesoporous structure provides special properties including large specific surface area, tunable pore size, and excellent pore connectivity. The structural properties of mesoporous materials have been largely made use of to improve the performance of analytical methods. For instance, the large specific surface area of mesoporous materials can provide abundant active sites and increase the probability of contact between analytes and active sites to produce stronger signals, thus leading to the improvement of detection sensitivity. The connections between analytical performances and the structural properties of mesoporous materials have not been discussed previously. Understanding the "structure-performance relationship" is highly important for the development of analytical methods with excellent performance based on mesoporous materials. In this review, we discuss the structural properties of mesoporous materials that can be optimized to improve the analytical performance. The discussion is divided into five sections according to the analytical performances: (i) selectivity-related structural properties, (ii) sensitivity-related structural properties, (iii) response time-related structural properties, (iv) stability-related structural properties, and (v) recovery time-related structural properties.

Fabrication of a new superparamagnetic metal-organic framework with core-shell nanocomposite structures: Characterization, biocompatibility, and drug release study

The Superparamagnetic CoFe₂O₄NPs@Mn-Organic Framework core-shell nanocomposites that had potential application in targeted drug-delivery were synthesized by layer to layer method. The structure and composition of the obtained microspheres were characterized by SEM, TEM, DLS, XRD, VSM, FTIR, and TG analysis. Results showed that the structures have a high degree crystalline, high temperature stability, magnetics and core-shell nanocomposites. Therefore, it is an excellent candidate for drug delivery systems. Afterwards, Daunorubicin (as a drug model) was laden in the MOFs by a Simple stirring. For comparison of magnetic properties of MOFs for drug delivery, an external magnetic field applied to the plate to evaluate the efficiency. The external magnetic field significantly increases anti-tumor activity of formulation (drug+ MOFs). The results showed that MOFs are biocompatible, which endue MOFs great potential in targeting drug-delivery systems with enhanced efficiency.

A Plasmonic Mass Spectrometry Approach for Detection of Small Nutrients and Toxins

Nutriology relies on advanced analytical tools to study the molecular compositions of food and provide key information on sample quality/safety. Small nutrients detection is challenging due to the high diversity and broad dynamic range of molecules in food samples, and a further issue is to track low abundance toxins. Herein, we developed a novel plasmonic matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) approach to detect small nutrients and toxins in complex biological emulsion samples. Silver nanoshells (SiO₂@Ag) with optimized structures were used as matrices and achieved direct analysis of ~ 6 nL of human breast milk without any enrichment or separation. We performed identification and quantitation of small nutrients and toxins with limit-of-detection down to 0.4 pmol (for melamine) and reaction time shortened to minutes, which is superior to the conventional biochemical method currently in use. The developed approach contributes to the near-future application of MALDI MS in a broad field and personalized design of plasmonic materials for real-case bio-analysis.

Gold nanorod embedded large-pore mesoporous organosilica nanospheres for gene and photothermal cooperative therapy of triple negative breast cancer

To date, clinicians still lack an effective strategy to treat triple negative breast cancer (TNBC). In this work, we design for the first time a gold nanorod embedded large-pore mesoporous organosilica (GNR@LPMO) nanoplatform for gene and photothermal cooperative therapy of TNBC. The synthesized GNR@LPMOs possess a uniform size (175 nm), high surface area (631 m2 g-1), large pore size, excellent photothermal efficiency, and good biocompatibility. Thanks to the large-pore mesoporous organosilica layer, the GNR@LPMO nanoplatforms display much higher loading capacity of siRNA compared with traditional liposome and bare gold nanorods. Thus, functional siRNA can be efficiently delivered into TNBC cells by GNR@LPMOs, causing much higher cell apoptosis through knocking down the PLK1 proteins. By combining the effective gene delivery and photothermal abilities, the GNR@LPMO nanoplatforms are further used for gene and photothermal cooperative therapy of TNBC, which induce a 15 fold higher mice tumor inhibition rate than sole therapy modality, indicating the potential clinical use of this novel nanoplatform in treating TNBC.

Multifunctional Magnetic Particles for Combined Circulating Tumor Cells Isolation and Cellular Metabolism Detection

We for the first time demonstrate multi-functional magnetic particles based rare cell isolation combined with the downstream laser desorption/ionization mass spectrometry (LDI-MS) to measure the metabolism of enriched circulating tumor cells (CTCs). The characterization of CTCs metabolism plays a significant role in understanding the tumor microenvironment, through exploring the diverse cellular process. However, characterizing cell metabolism is still challenging due to the low detection sensitivity, high sample complexity, and tedious preparation procedures, particularly for rare cells analysis in clinical study. Here we conjugate ferric oxide magnetic particles with anti-EpCAM on the surface for specific, efficient enrichment of CTCs from PBS and whole blood with cells concentration of 6-100 cells per mL. Moreover, these hydrophilic particles as matrix enable sensitive and selective LDI-MS detection of small metabolites (MW<500 Da) in complex bio-mixtures and can be further coupled with isotopic quantification to monitor selected molecules metabolism of ~50 CTCs. Our unique approach couples the immunomagnetic separation of CTCs and LDI-MS based metabolic analysis, which represents a key step forward for downstream metabolites analysis of rare cells to investigate the biological features of CTCs and their cellular responses in both pathological and physiological phenomena.

Binder-Free TiO2 Monolith-Packed Pipette Tips for the Enrichment of Phosphorylated Peptides

A macroporous TiO2 monolith-entrapped pipette-tip was developed through a binder-free packing method for convenient phosphorylated peptide enrichment. A detection limit of 1 ng mL–1 for phosphorylated peptide is achieved, showing a better enrichment efficiency compared with the commercial pure TiO2-embedded NuTip.

Recent advances in hybrid periodic mesostructured organosilica materials: opportunities from fundamental to biomedical applications

Periodic mesoporous organosilica nanostructures functionalized with various active functional groups: from design to biomedical applications.

Sensitive detection of human insulin using a designed combined pore approach

A unique combined pore approach to the sensitive detection of human insulin is developed. Through a systematic study to understand the impact of pore size and surface chemistry of nanoporous materials on their enrichment and purification performance, the advantages of selected porous materials are integrated to enhance detection sensitivity in a unified two-step process. In the first purification step, a rationally designed large pore material (ca. 100 nm in diameter) is chosen to repel the interferences from nontarget molecules. In the second enrichment step, a hydrophobically modified mesoporous material with a pore size of 5 nm is selected to enrich insulin molecules. A low detection limit of 0.05 ng mL(-1) in artificial urine is achieved by this advanced approach, similar to most antibody-based analysis protocols. This designer approach is efficient and low cost, and thus has great potential in the sensitive detection of biomolecules in complex biological systems.

A combo-pore approach for the programmable extraction of peptides/proteins

A novel combo-pore approach has been designed for the programmable purification, minimisation of sample complexity, enrichment and sensitive detection of peptides in biosamples. This approach has a superior performance to conventional protocols and commercial products.

Precisely designed rattle-type mTiO2@P(NIPAM-co-MBA) microspheres with screening gel network for highly selective extraction of phosphopeptidome

Rattle-type mTiO₂@P(NIPAM-co-MBA) microspheres with a screening gel network shell were elaborately designed and fabricated for highly selective extraction of endogenous phosphopeptidome.

Applications of nanomaterials in mass spectrometry analysis

Mass spectrometry (MS) based analyses have received intense research interest in a series of rapidly developing disciplines. Although current MS techniques have enjoyed great successes, several key challenges still remain in practical applications, especially for the detection of biomolecules in biological systems. The use of nanomaterials in MS based analysis provides a promising approach due to their unique physical and chemical properties. In this review, nanomaterials with different compositions and nanostructures employed in MS applications are summarised and classified by their functions. Such an integrated and wide reaching review will provide a comprehensive handbook to researchers with various backgrounds working in this exciting interdisciplinary area.