Metal–organic framework-based affinity materials in proteomics

Designed Nanomaterials-Assisted Proteomics and Metabolomics Analysis for In Vitro Diagnosis

In vitro diagnosis (IVD) is pivotal in modern medicine, enabling early disease detection and treatment optimization. Omics technologies, particularly proteomics and metabolomics, offer profound insights into IVD. Despite its significance, omics analyses for IVD face challenges, including low analyte concentrations and the complexity of biological environments. In addition, the direct omics analysis by mass spectrometry (MS) is often hampered by issues like large sample volume requirements and poor ionization efficiency. Through manipulating their size, surface charge, and functionalization, as well as the nanoparticle-fluid incubation conditions, nanomaterials have emerged as a promising solution to extract biomolecules and enhance the desorption/ionization efficiency in MS detection. This review delves into the last five years of nanomaterial applications in omics, focusing on their role in the enrichment, separation, and ionization analysis of proteins and metabolites for IVD. It aims to provide a comprehensive update on nanomaterial design and application in omics, highlighting their potential to revolutionize IVD.

Peptide-derived coordination frameworks for biomimetic and selective separation

Peptide-derived metal-organic frameworks (PMOFs) have emerged as a class of biomimetic materials with attractive performances in analytical and bioanalytical chemistry. The incorporation of biomolecule peptides gives the frameworks conformational flexibility, guest adaptability, built-in chirality, and molecular recognition ability, which greatly accelerate the applications of PMOFs in enantiomeric separation, affinity separation, and the enrichment of bioactive species from complicated samples. This review focuses on the recent advances in the engineering and applications of PMOFs in selective separation. The unique biomimetic size-, enantio-, and affinity-selective performances for separation are discussed along with the chemical structures and functions of MOFs and peptides. Updates of the applications of PMOFs in adaptive separation of small molecules, chiral separation of drug molecules, and affinity isolation of bioactive species are summarized. Finally, the promising future and remaining challenges of PMOFs for selective separation of complex biosamples are discussed.

Recent trends in glycoproteomics by characterization of intact glycopeptides

This trends article provides an overview of the state of the art in the analysis of intact glycopeptides by proteomics technologies based on LC-MS analysis. A brief description of the main techniques used at the different steps of the analytical workflow is provided, giving special attention to the most recent developments. The topics discussed include the need for dedicated sample preparation for intact glycopeptide purification from complex biological matrices. This section covers the common approaches with a special description of new materials and innovative reversible chemical derivatization strategies, specifically devised for intact glycopeptide analysis or dual enrichment of glycosylation and other post-translational modifications. The approaches are described for the characterization of intact glycopeptide structures by LC-MS and data analysis by bioinformatics for spectra annotation. The last section covers the open challenges in the field of intact glycopeptide analysis. These challenges include the need of a detailed description of the glycopeptide isomerism, the issues with quantitative analysis, and the lack of analytical methods for the large-scale characterization of glycosylation types that remain poorly characterized, such as C-mannosylation and tyrosine O-glycosylation. This bird's-eye view article provides both a state of the art in the field of intact glycopeptide analysis and open challenges to prompt future research on the topic.

Human serum N-glycome profiling via the newly developed asparagine immobilized cellulose/polymer nanohybrid

Human serum N-linked glycans expression levels change during the disease progression. The low abundance, structural diversity, and coexisting matrices hinder their detection in mass spectrometry analysis. Considering the hydrophilic nature of N-glycans, cellulose/polymer (1,2-Epoxy-5-hexene) nanohybrid is fabricated with oxirane groups functionalized of asparagine to develop solid phase extraction based hydrophilic interaction liquid chromatography sorbent (cellulose/1,2-Epoxy-5-hexene/asparagine). The morphology, elemental analysis, and surface properties are studied through scanning electron microscopy, energy dispersive X-ray spectroscopy, and Fourier-transform infrared spectroscopy. The large surface area of cellulose/polymer nanohybrid (2.09 × 10²  m² /g) facilitates the high density of asparagine immobilization resulting in better hydrophilic interaction liquid chromatography enrichment under optimized conditions. The enrichment capability of nanohybrid/asparagine is assessed by the N-Linked glycans released from ovalbumin and immunoglobulin G where 23 and 13 N-glycans are detected respectively. The nanohybrid/asparagine shows selectivity of 1:1200 with spiked bovine serum albumin and sensitivity down to 100 attomole. Human serum profiling for N-glycans identifies 52 glycan structures. This new enrichment strategy enriches serum N-linked glycans in the presence of salts, proteins, endogenous serum peptides, and so forth.

Two-dimensional magnetic bimetallic organic framework nanosheets for highly efficient enrichment of phosphopeptides

Highly selective enrichment and sensitive detection of phosphopeptides is pivotal for comprehensive phosphoproteomics analysis; however, it also poses a long-standing challenge. Here, a novel two-dimensional (2D) magnetic bimetallic organic framework (MOF) nanosheet with Zr-O clusters and Ti-O clusters (denoted as the Fe₃O₄@Zr-Ti BPDC nanosheet) is prepared via a solvothermal method and in situ deposition of Fe₃O₄ nanoparticles for the first time. Taking advantage of the abundant dual affinities of Zr-O and Ti-O clusters for phosphopeptides, large surface area and high chemical stability, the Fe₃O₄@Zr-Ti BPDC nanosheets exhibit excellent enrichment performance for phosphopeptides. Within the framework of density functional theory, the interaction between Zr-O clusters, Ti-O clusters and phosphorylated molecules was studied to find the possible reason behind the superior adsorption performance of the bimetallic MOF nanosheets. We found that electrons would migrate from Ti to Zr spontaneously after doping Ti element and enhance the electrostatic traction between Zr species and phosphorylated molecules, demonstrating that the synergistic effect of Zr-Ti was helpful to improve the enrichment efficiency for phosphopeptides. Furthermore, the Fe₃O₄@Zr-Ti BPDC nanosheets showed good enrichment performance in complex bio-samples, including nonfat milk, human saliva, and a breast cancer cell lysate, indicating their tremendous potential in the analysis of trace phosphorylated biomolecules in complex bio-samples.

Epitaxial Growth of Guanidyl-Functionalized Magnetic Metal-Organic Frameworks with Multiaffinity Sites for Selective Capture of Global Phosphopeptides

The flexible and controlled synthesis of metal-organic framework (MOF)-derived hybrid nanostructures is of great significance in fine tuning of their enrichment performance in large-scale and in-depth phosphoproteome analysis. Herein, a magnetic guanidyl-functionalized MOF hybrid coating with multiaffinity sites, denoted as Fe₃O₄@G-ZIF-8, was fast fabricated via a one-pot epitaxial growth strategy for the first time and applied for selective and highly efficient enrichment of global phosphopeptides. The intrinsic unsaturated metal sites of ZIF-8 endow the surface-mounted MOF coatings with immobilized metal ion affinity chromatography interaction with multiphosphorylated peptides. The oriented anchoring of bifunctional guanidineacetic acid on the magnetic MOF nanospheres provides additional affinity sites (guanidyl groups) for specific recognition of phosphopeptides by "salt bridge" interaction, as well as active site carboxyl groups for the coordination with the metal ions. The as-prepared Fe₃O₄@G-ZIF-8 exhibits large surface area (382.5 m² g^-1), good superparamagnetic property (41.6 emu g^-1) and stability, and size-exclusion effect (1.73 nm), which can serve as a specific adsorbent for global phosphopeptide analysis with satisfactory selectivity, great detection sensitivity (1 fmol), and rapid magnetic separation. Moreover, the successful application of Fe₃O₄@G-ZIF-8 for selective capture of both multi- and mono-phosphopeptides from human saliva and serum demonstrated the great potential of magnetic surface-mounted MOF coatings in effective identification of low-abundance phosphopeptides by matrix-assisted laser desorption ionization time-of-flight mass spectrometry from complicated biological matrices.

Current Sample Preparation Methodologies for Determination of Catecholamines and Their Metabolites

Catecholamines (CAs) and their metabolites play significant roles in many physiological processes. Changes in CAs concentration in vivo can serve as potential indicators for the diagnosis of several diseases such as pheochromocytoma and paraganglioma. Thus, the accurate quantification of CAs and their metabolites in biological samples is quite important and has attracted great research interest. However, due to their extremely low concentrations and numerous co-existing biological interferences, direct analysis of these endogenous compounds often suffers from severe difficulties. Employing suitable sample preparation techniques before instrument detection to enrich the target analytes and remove the interferences is a practicable and straightforward approach. To date, many sample preparation techniques such as solid-phase extraction (SPE), and liquid-liquid extraction (LLE) have been utilized to extract CAs and their metabolites from various biological samples. More recently, several modern techniques such as solid-phase microextraction (SPME), liquid-liquid microextraction (LLME), dispersive solid-phase extraction (DSPE), and chemical derivatizations have also been used with certain advanced features of automation and miniaturization. There are no review articles with the emphasis on sample preparations for the determination of catecholamine neurotransmitters in biological samples. Thus, this review aims to summarize recent progress and advances from 2015 to 2021, with emphasis on the sample preparation techniques combined with separation-based detection methods such capillary electrophoresis (CE) or liquid chromatography (LC) with various detectors. The current review manuscript would be helpful for the researchers with their research interests in diagnostic analysis and biological systems to choose suitable sample pretreatment and detection methods.

Zinc-Based Metal-Organic Frameworks in Drug Delivery, Cell Imaging, and Sensing

The design and structural frameworks for targeted drug delivery of medicinal compounds and improved cell imaging have been developed with several advantages. However, metal-organic frameworks (MOFs) are supplemented tremendously for medical uses with efficient efficacy. These MOFs are considered as an absolutely new class of porous materials, extensively used in drug delivery systems, cell imaging, and detecting the analytes, especially for cancer biomarkers, due to their excellent biocompatibility, easy functionalization, high storage capacity, and excellent biodegradability. While Zn-metal centers in MOFs have been found by enhanced efficient detection and improved drug delivery, these Zn-based MOFs have appeared to be safe as elucidated by different cytotoxicity assays for targeted drug delivery. On the other hand, the MOF-based heterogeneous catalyst is durable and can regenerate multiple times without losing activity. Therefore, as functional carriers for drug delivery, cell imaging, and chemosensory, MOFs' chemical composition and flexible porous structure allowed engineering to improve their medical formulation and functionality. This review summarizes the methodology for fabricating ultrasensitive and selective Zn-MOF-based sensors, as well as their application in early cancer diagnosis and therapy. This review also offers a systematic approach to understanding the development of MOFs as efficient drug carriers and provides new insights on their applications and limitations in utility with possible solutions.

Metal Organic Framework Nanomaterial-Based Extraction and Proteome Analysis of Membrane and Membrane-Associated Proteins

Membrane proteins (MPs) play a key role in various biological processes, while difficulties still exist in the extraction because of their inherent low abundance and poor solubility caused by high hydrophobicity. Metal organic framework (MOF) materials with good hydrophobic properties have the ability to absorb MPs, especially zeolitic imidazolate framework (ZIF) materials. Here, two MOF materials (ZIF-8 and ZIF-67) were compared for MP extraction, and our results revealed that higher yield was obtained with ZIF-67. After method development, the optimal enrichment effect was obtained when the mass ratio of proteins and ZIF-67 reached 1:20 with 100 mM NaCl in 20% ethanol at 4 °C and pH 9.0. When compared with a commercial kit, the extraction yield increased by 88.11% and the average number of identified MPs elevated by 29.17% with the developed ZIF method. Normal lung cell MRC5 was employed to verify the effectiveness of the ZIF method. Results showed 45.13% increase in yield and 22.88% increase in average number of identified MPs by the ZIF method. Our method was further applied to the enrichment of MPs for high-metastatic (95D) and low-metastatic (95C) human lung cancer cells. A total of 1732 (95D) and 1711 (95C) MPs were identified, among which 710 MPs were dysregulated significantly; 441 upregulated MPs in 95D cells were found to be closely related to the growth, proliferation, and migration of lung cancer cells. Our results collectively demonstrated that ZIF-67 was an ideal material for MP extraction, which might be helpful for analysis of cancer proteomics and discovery of cancer migration associated MPs.

Material-assisted mass spectrometric analysis of low molecular weight compounds for biomedical applications

Low molecular weight compounds play an important role in encoding the current physiological state of an individual. Laser desorption/ionization mass spectrometry (LDI MS) offers high sensitivity with low cost for molecular detection, but it is not able to cover small molecules due to the drawbacks of the conventional matrix. Advanced materials are better alternatives, showing little background interference and high LDI efficiency. Herein, we first classify the current materials with a summary of compositions and structures. Matrix preparation protocols are then reviewed, to enhance the selectivity and reproducibility of MS data better. Finally, we highlight the biomedical applications of material-assisted LDI MS, at the tissue, bio-fluid, and cellular levels. We foresee that the advanced materials will bring far-reaching implications in LDI MS towards real-case applications, especially in clinical settings.

Graphene oxide-metal oxide nanocomposites for on-target enrichment and analysis of phosphorylated biomolecules

The surface of matrix-assisted laser desorption/ionization mass spectrometry target is modified for improved signal strength and detection of analytes. The developed method includes on-target enrichment and detection of phosphopeptides/phospholipids using graphene oxide-lanthanide metal oxides (samarium, gadolinium, dysprosium, and erbium) nanocomposites. Enriched phosphopeptides are detected using material enhanced laser desorption/ionization mass spectrometry and phospholipids by laser desorption/ionization-mass spectrometry. Nanocomposites are prepared using graphene oxide with respective metal salts at high pH. They are characterized for nano-morphology, chemistry, porosity, composition, crystallinity, and thermal stability. Phosphopeptides enrichment protocol is developed and optimized for tryptic β-casein digest and that of phospholipids by phosphatidylcholine standard. Statistical analyses of phosphopeptides and phospholipids from milk show overlapping results for gadolinium, dysprosium, and erbium oxide nanocomposites. GO-Gd₂ O₃ has better enrichment efficiency and application as LDI material. Selectivity for GO-Dy₂ O₃ is 1:2500, for GO-Sm₂ O₃ is 1:3500, and 1:4000 for GO-Gd₂ O₃ . GO-Er₂ O₃ has a sensitivity of 25 fmol, whereas the highest sensitivity is down to 0.5 fmol for GO-Gd₂ O₃ . On-target enrichment is batch to batch reproducible with a standard deviation of <1, reduced time of enrichment to 10 min, and ease of operation compared to solid-phase batch extraction. The developed method enriches serum phosphopeptides characteristic of cancer-related phosphoproteins.

Metal-organic frameworks as advanced materials for sample preparation of bioactive peptides

Development of novel affinity materials and separation techniques is crucial for the progress of modern proteomics and peptidomics. Detection of peptides and proteins from complex matrices still remains a challenging task due to the highly complicated biological composition, low abundance of target molecules, and large dynamic range of proteins. As an emerging area of analytical science, metal-organic framework (MOF)-based separation of proteins and peptides is attracting growing interest. This minireview summarizes the recent advances in MOF-based affinity materials for the sample preparation of proteins and peptides. Some newly emerging MOF nanoreactors for the degradation of peptides and proteins are introduced. An update of MOF-based affinity materials for the isolation of glycopeptides, phosphopeptides and low-abundance endogenous peptides in the last two years is focused on. The separation mechanism is discussed along with the chemical structures of MOFs. Finally, the remaining challenges and future development of MOFs in analyzing peptides and proteins in complicated biological samples are discussed.

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.

Melamine foam assisted in-tip packed amine-functionalized titanium metal-organic framework for the selective enrichment of endogenous glycopeptides

Endogenous glycopeptides are significantly important in diverse pathological and physiological systems, but their direct analysis is severely hampered by their low abundance and presence of interfering species in biological fluids. In this study, we synthesized the amine-functionalized titanium metal-organic framework (NH₂-MIL-125(Ti)) by a simple hydrothermal method, characterized and used for glycopeptides enrichment. The designed separation media is highly hydrophilic and stable which is suitable for hydrophilic interaction chromatography (HILIC). To make the process smooth, simple, reliable, and robust, NH₂-MIL-125(Ti) crystals were packed in pipette-tip using hydrophilic melamine foam, as supporting frit. Free amine groups, present in the structure imparted hydrophilicity and a unique pattern of porosity, contributing to the size exclusion effect that excluded the large-sized proteins up to 1:700 peptide to protein ratio. The prepared MOF particles possessed regular porosity, high surface area, good hydrophilicity, and offered an in-tip flow-based set-up enhanced the enrichment performance for N-linked glycopeptides. The affinity material showed a detection limit of 1 fmol.µL^-1 and selectivity up to 1:1000 (HRP digest to BSA digest). Moreover, repeatability and reusability were evaluated up to five rounds of enrichment using the same affinity tip, and scanning electron microscopic images revealed no structural changes in the MOF crystals. Finally, the MOF packed in pipette tip was applied to selectively capture the N-linked endogenous glycopeptides from a healthy saliva sample and 64 unique endogenous glycopeptides were identified. These results demonstrated the excellent potential of NH₂-MIL-125(Ti) based affinity tip for glycopeptides which can be used to enrich trace glycopeptide biomarkers from the biological fluids.

A Two-Dimensional Affinity Capture and Separation Mini-Platform for the Isolation, Enrichment, and Quantification of Biomarkers and Its Potential Use for Liquid Biopsy

Biomarker detection for disease diagnosis, prognosis, and therapeutic response is becoming increasingly reliable and accessible. Particularly, the identification of circulating cell-free chemical and biochemical substances, cellular and subcellular entities, and extracellular vesicles has demonstrated promising applications in understanding the physiologic and pathologic conditions of an individual. Traditionally, tissue biopsy has been the gold standard for the diagnosis of many diseases, especially cancer. More recently, liquid biopsy for biomarker detection has emerged as a non-invasive or minimally invasive and less costly method for diagnosis of both cancerous and non-cancerous diseases, while also offering information on the progression or improvement of disease. Unfortunately, the standardization of analytical methods to isolate and quantify circulating cells and extracellular vesicles, as well as their extracted biochemical constituents, is still cumbersome, time-consuming, and expensive. To address these limitations, we have developed a prototype of a portable, miniaturized instrument that uses immunoaffinity capillary electrophoresis (IACE) to isolate, concentrate, and analyze cell-free biomarkers and/or tissue or cell extracts present in biological fluids. Isolation and concentration of analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. When compared to other existing methods, the process of this affinity capture, enrichment, release, and separation of one or a panel of biomarkers can be carried out on-line with the advantages of being rapid, automated, and cost-effective. Additionally, it has the potential to demonstrate high analytical sensitivity, specificity, and selectivity. As the potential of liquid biopsy grows, so too does the demand for technical advances. In this review, we therefore discuss applications and limitations of liquid biopsy and hope to introduce the idea that our affinity capture-separation device could be used as a form of point-of-care (POC) diagnostic technology to isolate, concentrate, and analyze circulating cells, extracellular vesicles, and viruses.

Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials

Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.

Polycarbonate Microchip Containing CuBTC-Monopol Monolith for Solid-Phase Extraction of Dyes

In the present study, preparation of CuBTC-monopol monoliths for use within the microchip solid phase extraction was undertaken through a 20-min UV lamp-assisted polymerization for 2,2-dimethoxy-2-phenyl acetophenone (DMPA), butyl methacrylate (BMA), and ethylene dimethacrylate (EDMA) alongside inclusion of the porogenic solvent system (1-propanol and methanol (1 : 1)). The resultant coating underwent coating using CuBTC nanocrystals in ethanolic solution of ethanolic solution of 1,3,5-benzenetricarboxylic acid (H₃BTC, 10 mM) and 10 mM copper(II) acetate Cu(CH₃COO)₂. This paper reports enhanced extraction, characterization, and synthesis studies for porous CuBTC metal organic frameworks that are marked by different methods including SEM/EDAX analysis, atomic force microscopy (AFM), and Fourier-transform infrared spectroscopy (FT-IR). The evaluation of the microchip's performance was undertaken as sorbent through retrieval of six toxic dyes (anionic and cationic dyes). Various parameters (desorption and extraction step flow rates, volume of desorption solvent, volume of sample, and type of desorption solvent) were examined to optimize dye extraction using fabricated microchips. The result indicated that CuBTC-monopol monoliths were permeable with the ability of removing impurities and attained high toxic dye extraction recovery (83.4-99.9%). The assessment of reproducibility for chip-to-chip was undertaken by computing the relative standard deviations (RSDs) of the six dyes in extraction. The interbatch and intrabatch RSDs ranged between 3.8 and 6.9% and 2.3 and 4.8%. Such features showed that fabricated CuBTC-monopol monolithic disk polycarbonate microchips have the potential of extracting toxic dyes that could be utilized for treating wastewater.

Metal organic framework/chitosan foams functionalized with polyethylene oxide as a sorbent for enrichment and analysis of bisphenols in beverages and water

MIL-53(Al)/CS/PEO foam as a sorbent for the vortex assisted solid phase extraction of a trace amount of five bisphenols in beverages and water.

Advances in hydrophilic nanomaterials for glycoproteomics

Owing to the formidable challenge posed by microheterogeneities in glycosylation sites, macroheterogeneity of the modification number of glycans, and low abundance and ionization efficiency of glycosylation, the crucial premise for conducting in-depth profiling of the glycoproteome is to develop highly efficient technology for separation and enrichment. The appearance of hydrophilic interaction chromatography (HILIC) has considerably accelerated the progress in glycoproteomics. In particular, additional hydrophilic nanomaterials have been developed for glycoproteomics research in the recent years. In this review, we mainly summarize the recent progresses made in the design and synthesis of different hydrophilic nanomaterials, as well as their applications in glycoproteomics, according to the classification of the main hydrophilic functional molecules on the surface. Further, we briefly illustrate the potential retention mechanism of the HILIC mode and discuss the limits and barriers of hydrophilic nanomaterials in glycoproteomics, as well as propose their possible development trends in the future.