Highly efficient enrichment of N-glycopeptides by two-dimensional Hf-based metal-organic framework nanosheets.

Highly efficient enrichment of target glycopeptides plays a crucial role in glycoproteome research. Owing to their large surface area and excellent hydrophilicity, 2-D Hf-BTB nanosheets showed effective and selective enrichment of 78 glycopeptides derived from 29 glycoproteins with 90 N-glycosylation sites from just 2 µL of human serum.

Highly Selective Capture of Monophosphopeptides by Two-Dimensional Metal-Organic Framework Nanosheets.

Separation of monophosphopeptides from multi-phosphopeptides in complex biological samples is significant in the study of protein kinase signal transduction pathways. To the best of our knowledge, very few materials have been reported that could selectively enrich monophosphopeptides because of the chemical difficulty in retaining the intermediate monophosphopeptides and excluding both non-phosphopeptides and multi-phosphopeptides in acidic conditions, which requires unique interactions to balance the metallic affinity and the hydrophobicity. With the large surface area, abundant accessible active sites, and ultrathin structures, two-dimensional (2-D) metal-organic framework (MOF) Hf-1,3,5-tris(4-carboxyphenyl)benzene (BTB) nanosheets were rationally selected. Due to the elongated organic ligands and the balance between metallic affinity of clusters and hydrophobicity from ligands, the 2-D Hf-BTB nanosheets exhibited unique enrichment selectivity toward monophosphopeptides. The 2-D MOF nanosheets demonstrated excellent sensitivity (detection limit of 0.4 fmol µL-1) and selectivity [1:1000 molar ratios of ß-casein/BSA (bovine serum albumin)] in model phosphopeptides enrichment. The nanosheets were implemented for the analysis of nonfat milk and human saliva samples as well as in situ isotope labeling for dysregulated phosphopeptides from patients' serum with anal canal inflammation, exhibiting 6.6-fold upregulation of serum phosphopeptide HS4 (ADpSGEGDFLAEGGGVR) compared to the control healthy serum. The proteomics analysis of mouse brain cortical samples associated with Alzheimer's disease, which were from Akt (protein kinase B) conditional knockout mouse and littermate control mouse, was further established with 2-D Hf-BTB nanosheets. With high capture efficiency for monophosphopeptides, this method was capable of distinguishing the difference of monophosphopeptides from microtubule-associated protein τ (MAPT/τ) between the Akt knockout sample and control sample.

Recent applications of metal-organic frameworks in matrix-assisted laser desorption/ionization mass spectrometry.

Metal-organic frameworks (MOFs) have drawn great interest in recent decades due to their fascinating structures, unusual physical properties, versatile modification strategies, and biological compatibilities. In this review, we describe recent progress in the application of MOFs to matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Owing to their high porosities, specific affinities, and photon absorption capacities, MOFs can be used as solid adsorbents to selectively capture peptides (including endogenous peptides, phosphopeptides, and glycopeptides) and as matrices in MALDI MS. Current developments in and future prospects for this field of research are also discussed.

Enrichment of Phosphorylated Peptides with Metal-Organic Framework Nanosheets for Serum Profiling of Diabetes and Phosphoproteomics Analysis.

Capturing phosphopeptides from complicated biological samples is essential for the discovery of new post-translational modification sites and disease diagnostics. Although several two-dimensional (2-D) materials have been used for phosphopeptides capturing, metal-organic framework (MOF) nanosheets have not been reported. The Ti-based MOF nanosheets have well-defined 2-D morphology, high density of active sites, large surface area, and an ultrathin structure. Phosphopeptides can be efficiently extracted and superior detection limits of 0.1 fmol µL-1 can be achieved even for an extremely low molar ratio of phosphoprotein/nonphosphoprotein (1:10000) mixtures. The selectivity over nonphosphopeptides can be enhanced further by pretreatment with a 10 mM salt solution (ß-glycerophosphate disodium, NaCl, or KCl). The performance of 2-D Ti-based MOF nanosheets is much better than Zr-based MOF (Zr-BTB) nanosheets or any other Ti-based 3-D MOF counterpart, such as MIL-125 and NH2-MIL-125. The nanosheets were used for in situ isotope labeling for abnormally regulated phosphopeptides analysis from serum samples of type 2 diabetes patients. The relative quantitative results showed that three of the phosphorylated fibrinogen peptides A (FPA, DpSGEGDFLAEGGGV, DpSGEGDFLAEGGGVR, and ADpSGEGDFLAEGGGVR) were down-regulated, while the other isoform (ADpSGEGDFLAEGGGV) was up-regulated in the serum samples of type 2 diabetes patients compared with those of healthy volunteers. Finally, proteomics analysis showed selective enrichment of phosphopeptides with 2-D Ti-based MOF nanosheets from real samples, including tryptic digests of mouse brain neocortex lysate, mouse spinal cord lysate, and mouse testis lysate, followed by LC-MS/MS analysis. Total numbers of 2601, 3208, and 2866 phosphopeptides were successfully identified from the three samples, respectively. The 2-D Ti-based MOF nanosheets significantly improved sample preparation for mass spectrometric analysis in phosphopeptides and phosphoproteomics research.

Two-Dimensional Metal-Organic Framework Nanosheets: A Rapidly Growing Class of Versatile Nanomaterials for Gas Separation, MALDI-TOF Matrix and Biomimetic Applications.

Two-dimensional (2D) metal-organic framework (MOF) nanosheets, as an emerging type of 2D materials, attract numerous attention due to their unique properties. First, the ultrathin thickness and nanoscale of the materials results in homogeneous dispersion in aqueous solution, giving the materials more opportunities to be utilized in solution chemistry, especially beneficial to the biomimetic catalysis and bio-related analytical applications. Second, the large surface area and accessible active sites of the MOF nanosheets are favorable to the binding between materials and the substrate, leading to their superior performance in catalysis, sensing and enzyme inhibition. Third, the suitable sizes of nanopores on the 2D MOF nanosheets give them the abilities to act as membranes for highly selective and energy-saving gas separation. This minireview covers the synthesis, characterization as well as bio-related and separation applications of 2D MOF nanosheets.

An Exfoliated 2D Egyptian Blue Nanosheet for Highly Selective Enrichment of Multi-phosphorylated Peptides in Mass Spectrometric Analysis.

Phosphopeptide enrichment is essential for the phosphoprotein profiling, due to the low abundance in complex biological samples. Moreover, selective binding of multi-phosphopeptides over mono-phosphopeptides is rarely established, but strongly needed in real sample analysis, especially for the investigation of cell behaviors with the multisite phosphorylation cascades. Here two-dimensional (2D) nanosheets were synthesized of Egyptian blue (CaCuSi4 O10 ), the well-known ancient pigment, and its analogues (SrCuSi4 O10 and BaCuSi4 O10 ), which were employed in the enrichment of phosphopeptides for the first time. Surprisingly, the 2D CaCuSi4 O10 nanosheet was highly selective towards multi-phosphopeptides without enriching the mono-phosphorylated peptides in a wide range of acidic conditions or buffer compositions. Meanwhile, the SrCuSi4 O10 and BaCuSi4 O10 nanosheet analogues do not exhibit this unique selectivity. Moreover, the ultrathin and well-defined 2D morphology, with abundant CaII , of Egyptian blue nanosheet was applied in cortical samples of forebrain specific PDK1 conditional knockout mice and their age-matched littermate controls, that are associated with Alzheimer's disease. The as-prepared 2D CaCuSi4 O10 nanosheet not only showed specific selectivity, but also exhibited high sensitivity (detection limit of 4×10-7 m).

Triazine-structured covalent organic framework nanosheets with inherent hydrophilicity for the highly efficient and selective enrichment of glycosylated peptides.

Protein glycosylation plays a crucial role in various biological processes and is related to various diseases. Highly specific enrichment of glycopeptides before mass spectrometry detection is crucial for comprehensive glycoproteomic analysis. However, it still remains a great challenge due to the absence of affinity materials with excellent enrichment efficiency. In this work, a triazine structure linked by a -NH- bond of two-dimensional (2-D) covalent organic framework (COF) nanosheets was synthesized as an affinity adsorbent for the selective capture of glycopeptides. In particular, by introducing hydrophilic monomers via a bottom-up approach, the 2-D COF (denoted as NENP-1) nanosheets were provided with abundant amino groups and inherent hydrophilicity. Owing to the specific surface area and excessive accessible sites for hydrophilicity, the resulting NENP-1 nanosheets exhibited an outstanding glycopeptide enrichment efficiency from standard samples with a superior detection sensitivity (1 × 10-10 M), good enrichment selectivity (1 : 800, HRP tryptic digest to BSA protein), excellent binding capacity (100 mg g-1), great reusability, and recovery (60.2%). Furthermore, using the NENP-1 nanosheet adsorbent, twenty-four endogenous glycopeptides in the serum of patients with gastric cancer were successfully identified by LC-MS/MS technology, which illustrates a promising prospective of hydrophilic COF nanosheets in glycoproteomics research.

Three-Dimensional MAX-Ti3 AlC2 Nanomaterials for Dual-Selective and Highly Efficient Enrichment of Phosphorylated and Glycosylated Peptides.

Dual-selective enrichment of phosphopeptides and glycopeptides of post-translational modifications (PTMs) in the complex biological samples are challenging. In this work, considering the versatile properties including surface abundant metal sites and electrostatic attraction between Ti3 C2 -layers and Al-layers, layered ternary carbides Ti3 AlC2 nanomaterials was successfully applied for the first time as an affinity adsorbent for the dual-selective capture of phosphopeptides and glycopeptides. Especially, the Ti3 AlC2 nanomaterials had an excellent detection sensitivity for phosphopeptides (1×10-11  M) and a good selectivity for glycopeptides with a low molar ratio of 1 : 500 of HRP (horseradish peroxidase) to BSA (bovine serum albumin). Furthermore, Ti3 AlC2 nanomaterials was also applied for dual-selective enrichment of phosphopeptides and glycopeptides from mouse brain neocortex lysate and human serum lysate respectively before mass spectrometry (MS) analysis, yielding twenty-two unique phosphopeptides from thirteen phosphoproteins and fifty-three unique glycopeptides from thirty-seven glycoproteins, respectively. This work will open a new avenue and will greatly promote sample preparation for mass spectrometric analysis in phosphoproteomics and glycoproteomics research.

Two-dimensional materials as solid-state nanopores for chemical sensing.

Solid-state nanopores as a versatile alternative to biological nanopores have grown tremendously over the last two decades. They exhibit unique characteristics including mechanical robustness, thermal and chemical stability, easy modifications and so on. Moreover, the pore size of a solid-state nanopore could be accurately controlled from sub-nanometers to hundreds of nanometers based on the experimental requirements, presenting better adaptability than biological nanopores. Two-dimensional (2D) materials with single layer thicknesses and highly ordered structures have great potential as solid-state nanopores. In this perspective, we introduced three kinds of substrate-supported 2D material solid-state nanopores, including graphene, MoS2 and MOF nanosheets, which exhibited big advantages compared to traditional solid-state nanopores and other biological counterparts. Besides, we suggested the fabrication and modulation of 2D material solid-state nanopores. We also discussed the applications of 2D materials as solid-state nanopores for ion transportation, DNA sequencing and biomolecule detection.

Sn-based metal-organic framework for highly selective capture of monophosphopeptides.

Sn-based metal-organic framework (MOF) was utilized to effectively capture monophosphopeptides due to the unique affinity. The Sn-based MOF demonstrated the good sensitivity and selectivity in the model phosphoproteins enrichment and was successfully applied in the biological fluids.

A hydrophilic two-dimensional titanium-based metal-organic framework nanosheets for specific enrichment of glycopeptides.

A hydrophilic two-dimensional titanium-based metal-organic framework (MOF) nanosheets were prepared and applied to improve the glycopeptides enrichment efficiency. Seventeen N-linked glycopeptides from horseradish peroxidase (HRP) tryptic digests were readily identified and the results showed highly improved signal intensities. As the molar ratio of the mixture of tryptic digests of HRP, glycoprotein (HRP), and nonglycoprotein (BSA) reached 1:800:800, good selectivity of the Ti-MOF nanosheets were still clearly observed. As to human serum samples, 41 glycoproteins and 66 glycopeptides corresponding to 68 N-glycosylation sites were finally detected, which showed the good ability of the nanosheets material to enrich N-linked glycopeptides from complex human serum samples. Moreover, the Ti-MOF nanosheets exhibited unique stability and reusability even after being regenerated and reused for five times. It also performed a high sensitivity (1 × 10-10 M HRP), a good enrichment capacity (250 mg/g) for glycopeptides enrichment and a high enrichment recovery of 78%, suggesting a great application prospect for the enrichment of N-linked glycopeptides and the analysis glycoproteomic research.

Ultrahigh efficient laser desorption ionization of saccharides by Ti-based metal-organic frameworks nanosheets.

We proposed some exfoliated Ti-based metal-organic frameworks (MOFs) nanosheets as matrices with ultrahigh ionization efficiency, free matrix background, significant dispersibility and acidic resistance. Combining the features between MOFs and 2-D nanomaterials, the NTU-9 nanosheets matrix also demonstrated suitable band gap energy and superior photoabsorption properties, much better than other representative MOFs. A wide range of small molecules that involving low mass region were also analyzed with NTU-9 nanosheets as the matrices in both positive-ion and negative-ion reflector modes. The ultra-efficient NTU-9 nanosheets matrix was successfully applied to serum for quantitative determination of glucose as a clinical diagnosis indicator of diabetes mellitus.