Fabrication of hydrophilic multilayer magnetic probe for salivary glycopeptidome analysis

Super-hydrophilic sulfonate-modified covalent organic framework nanosheets for efficient separation and enrichment of glycopeptides

Highly efficient extraction of glycopeptides prior to mass spectrometry detection is extremely crucial for glycoproteomic research, especially in disease biomarker research. Reported here is the first time by applying two-dimensional (2D) covalent organic framework (COFs) nanosheets for highly efficient enrichment of glycopeptides. Particularly, by incorporating hydrophilic monomers through a bottom-up strategy, the 2D COF nanosheets (denoted as NUS-9) displayed an ultra-high graft density of sulfonic groups and super-hydrophilicity. In addition, because of the large surface area, low steric hindrance, high chemical stability, and abundant accessibility sites of 2D COF nanosheets, NUS-9 exhibited remarkable efficiency for glycopeptide enrichment, involving excellent detection sensitivity (0.01 fmol μL^-1), outstanding enrichment capability, and good enrichment selectivity (1:1500, horseradish peroxidase (HRP) tryptic digest to bovine serum albumin (BSA) tryptic digest), and recovery (92.2 ± 2.0%). Moreover, the NUS-9 was able to unambiguously detect 631 endogenous glycopeptides from human saliva, demonstrating an unparalleled high efficiency in glycopeptide enrichment. Gene ontology analyses of proteins from human saliva enriched by NUS-9 demonstrated its potential for comprehensive glycoproteome analysis.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.

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.

A Novel BODIPY Quaternary Ammonium Salt-Based Fluorescent Probe: Synthesis, Physical Properties, and Live-Cell Imaging

The development of biological fluorescent probes is of great significance to the field of cancer bio-imaging. However, most current probes within the bulky hydrophobic group have limited application in aqueous medium and restricted imaging under physiological conditions. Herein, we proposed two efficient molecules to study their physical properties and imaging work, and the absorption and fluorescence intensity were collected with varying ions attending in aqueous medium. We enhance the water solubility through the quaternization reaction and form a balance between hydrophilic and hydrophobicity with dipyrrome-theneboron difluoride (BODIPY) fluorophore. We introduced pyridine and dimethylaminopyridine (DMAP) by quaternization and connected the BODIPY fluorophore by ethylenediamine. The final synthesized probes have achieved ideal affinity with HeLa cells (human cervical carcinoma cell line) in live-cell imaging which could be observed by Confocal Microscope. The probes also have a good affinity with subcutaneous tumor cells in mice in in vivo imaging, which may make them candidates as oncology imaging probes.

Recognition of urinary N-linked glycopeptides in kidney cancer patients by hydrophilic carbohydrate functionalized magnetic metal organic framework combined with LC-MS/MS

A hydrophilic carbohydrate functionalized magnetic metal organic framework (Mag Zr-MOF@G6P) was synthesized via a facile one-step modification strategy for selective glycopeptide capture in virtue of hydrophilic interaction chromatography technique. The inherently hydrophilic Zr-MOF layer not only provides selective size-sieving pore structures but also offers large specific surface area to afford abundant affinity sites. Hydroxyl-rich glucose-6-phosphate was immobilized onto the Zr-MOF via a straightforward coordination manner to regulate its surface property, for the purpose of enhancing its hydrophilicity. Benefitting from the merits of Zr-MOF and glucose-6-phosphate, the as-designed composite exhibits good selectivity (the mass ratio of HRP digests to BSA digests was up to1:200) and low limit of detection (0.1 fmol μL^-1) towards the recognition of glycopeptides from standard samples. More excitingly, glycopeptides in urine of healthy people and patients with kidney cancer were successfully enriched and identified by the combined liquid chromatography-mass spectrometry/mass spectrometry technology (LC-MS/MS). Further gene ontology analysis of molecular function and biological process revealed that 13 original glycoproteins of the identified glycopeptides from urine of patients significantly participate in diverse cancer-associated events, including collagen binding, immunoglobulin receptor binding, antigen binding, and complement activation process. Graphical abstract.

Facile preparation of polymer-grafted ZIF-8-modified magnetic nanospheres for effective identification and capture of phosphorylated and glycosylated peptides

As a member of MOFs, Zn-MOFs (ZIF-8) are seldom used in phosphopeptide enrichment because ZIF-8 is soluble in acid solutions. Therefore, properly designing a novel strategy to overcome the defect of ZIF-8 is necessary. In this study, a novel multifunctional nanoprobe was designed by uniting magnetic core, titania shell and hydrophilic metal-organic frameworks (named as Fe3O4@PDA@mTiO2@PEI-g-ZIF-8). Integrating the strategies of hydrophilic interaction affinity chromatography (HILIC), immobilized metal ion affinity chromatography (IMAC) and metal oxide affinity chromatography (MOAC), the Fe3O4@PDA@mTiO2@PEI-g-ZIF-8 mesoporous microspheres can enrich phosphorylated peptides and glycosylated peptides simultaneously. Fe3O4@PDA@mTiO2@PEI-g-ZIF-8 has high selectivity (maximum molar ratio β-casein/HRP : BSA = 1 : 1000), low detection limit (2 fmol) towards phosphopeptides and glycopeptides. Besides, the Fe3O4@PDA@mTiO2@PEI-g-ZIF-8 also exhibited a fine performance in the actual sample detection. In the experiment, taking saliva as a sample, 16 phosphorylated peptides were identified, and from a human serum sample, 4 phosphorylated peptides were selectively identified. All in all, the materials show great potential in the future study of phosphoproteomics and glycoproteomics.

Glutathione-Functionalized Magnetic Covalent Organic Framework Microspheres with Size Exclusion for Endogenous Glycopeptide Recognition in Human Saliva

Endogenous glycopeptides have been confirmed to play a significant role in multifarious pathological and physiological processes. The low abundance of endogenous glycopeptides and abundant interferents (e.g., large-size proteins and heteropeptides) in complex biological matrices render the direct analysis of endogenous glycopeptides difficult. Reported here is a novel glutathione-functionalized magnetic covalent organic framework microsphere (denoted as MCNC@COF@GSH) endowed with size-exclusion effect and strong hydrophilicity for selective and efficient enrichment of N-linked glycopeptides. The as-prepared MCNC@COF@GSH microspheres possessed fast magnetic responsiveness, regular porosity, large surface areas, and good hydrophilicity, resulting in remarkable performances in N-linked glycopeptide enrichment with low detection limit (0.01 fmol μL^-1), high selectivity (1:5000, human immunoglobulin G (IgG) digests to bovine serum albumin digests), excellent size-exclusion effect (IgG digests/IgG/bovine serum albumin (BSA), 1:500:500), and reusability (at least five times). More excitingly, 143 endogenous N-linked glycopeptides were clearly identified from 10 μL sample of human saliva treated with the MCNC@COF@GSH microspheres, which is the unprecedented high efficiency in endogenous N-linked glycopeptide enrichment from human saliva. In addition to providing a strategy for versatile functionalization of magnetic covalent organic frameworks (COFs), this study may be used to develop application of endogenous glycoproteome analysis.

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.