Metal Oxide Affinity Chromatography Research Articles

Glycan-Tailored Glycoproteomic Analysis Reveals Serine is the Sole Residue Subjected to O-Linked Glycosylation in Acinetobacter baumannii.

Protein glycosylation is a ubiquitous process observed across all domains of life. Within the human pathogen Acinetobacter baumannii, O-linked glycosylation is required for virulence; however, the targets and conservation of glycosylation events remain poorly defined. In this work, we expand our understanding of the breadth and site specificity of glycosylation within A. baumannii by demonstrating the value of strain specific glycan electron-transfer/higher-energy collision dissociation (EThcD) triggering for bacterial glycoproteomics. By coupling tailored EThcD-triggering regimes to complementary glycopeptide enrichment approaches, we assessed the observable glycoproteome of three A. baumannii strains (ATCC19606, BAL062, and D1279779). Combining glycopeptide enrichment techniques including ion mobility (FAIMS), metal oxide affinity chromatography (titanium dioxide), and hydrophilic interaction liquid chromatography (ZIC-HILIC), as well as the use of multiple proteases (trypsin, GluC, pepsin, and thermolysis), we expand the known A. baumannii glycoproteome to 33 unique glycoproteins containing 42 glycosylation sites. We demonstrate that serine is the sole residue subjected to glycosylation with the substitution of serine for threonine abolishing glycosylation in model glycoproteins. An A. baumannii pan-genome built from 576 reference genomes identified that serine glycosylation sites are highly conserved. Combined this work expands our knowledge of the conservation and site specificity of A. baumannii O-linked glycosylation.

Abstract B070: Global proteomics and phosphoproteomics profiling of prostate cancer patient derived xenografts tumors from the LuCaP series

Abstract Castration Resistant Prostate Cancer (CRPC) is a form of prostate cancer (PCa) that is resistant to androgen deprivation therapies. Resistance to these therapies leads to metastatic CRPC of adenocarcinoma (AD) origin and can transform to emergent aggressive variant prostate cancer (AVPC) which has genetic aberration features similar to neuroendocrine (NE) phenotypes. Understanding and identifying the underlying mechanisms of resistance and genetic transformations leading to protein alterations will enable us to develop novel therapeutic methods to counteract this resistance and improve outcomes for men with lethal metastatic prostate cancer. To this end, we used patient-derived xenografts (PDXs), an in-vivo clinically relevant model from advanced prostate cancer (PC) patients, to investigate the biology, identify novel protein targets and evaluate new treatment modalities. We aimed to identify known and novel protein kinase targets that might be phospho-regulated unique between CRPC, in AD and AVPC in NE. To pursue this, we applied a mass spectrometry base phosphoproteomics analysis. We processed 48 PDX samples, which included 15 non-castrated (NCR), 18 castration resistant (CR), which are the AD samples and 15 AVPC, the NE tumors. To enrich for global phosphorylated residues, we used sequential metal oxide affinity chromatography. We sequenced peptides from each sample using liquid chromatography in tandem with Orbitrap Eclipse Tribid MS and FAIMS technology for 2 hour gradients. To normalize and calibrate the LC method and to compare across all 48 runs, we spiked-in 400 femtomol of internal standards (iRT) to each sample. For peptide sequence and search analysis, we used Maxquant search algorithm. Using a > 0.75 probability phospho-residue cut-off and 5% FDR, we identified more than 9,700 phospho-residues. We identified RET, ASCL1, CHGA and SYP in NEPC and Androgen Receptor (AR), FOXA1, HOXB13, NKX3.1 and TACSTD2 in the adenocarcinoma PDX LuCap tumor samples, which confirms that our approach detected specific proteins already previously established. We subsequently performed a kinase substrate enrichment analysis and identified GSK-3, ERK1, ERK2, CDK5 kinases to be significantly enriched in the NE tumors while ATM kinase and PKC alpha and beta were enriched in the AD PDX tumor samples. Hierarchical clustering analysis across NE versus AD tumor samples indicated that samples within each group clustered uniquely where we observed intra and inter sample variability. We generated pathway enrichment and GSEA analysis, identified novel targets for therapeutic treatments and novel surface proteins. In conclusion, we have performed a global mass spectrometry based proteomic analysis and created an important first global phosphoproteomics and proteomics database that provides insights into the differentially regulated protein and phosphoproteins between AD and NE PDX tumors and provide a protein database source to develop new hypothesis. Citation Format: Zoi E. Sychev, Gabbrianne E. Larson, Hannah E. Bergom, Abderrahman E. Day, Megan E. Ludwig, Atef E. Ali, Eva Corey, Stephen R. Plymate, Justin E. Hwang, Justin M. Drake. Global proteomics and phosphoproteomics profiling of prostate cancer patient derived xenografts tumors from the LuCaP series [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B070.

Coating of a MALDI target with metal oxide nanoparticles by droplet-free electrospraying – A versatile tool for in situ enrichment of human globin adducts of halogen-containing drug metabolites

The strategies for integration of different orthogonal analytical procedures directly on the targets for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) are being intensively developed over the last two decades. This methodology, which is usually referred to as “lab-on-a-plate”, proved to be the method of choice for fast and reproducible sample preparation prior to MALDI-MS analysis. To date, numerous “lab-on-a-plate” protocols for enrichment of phosphorylated peptides by metal oxide affinity chromatography (MOAC) are established. However, despite this, a straightforward and efficient implementation of the on-target workflow for selective MOAC-based enrichment of the protein adducts formed by halogen-containing xenobiotics is still missing. Therefore, here we present a successful application of droplet-free electrospraying under normal conditions for efficient deposition of metal oxide (MeOx) nanoparticles on the MALDI target. Here we employed oxides of four transition metals – Fe(III), Co(II/III), Ni(II) and Cu(II). These materials were synthesized by the microwave-assisted sol–gel approach and electrosprayed post-synthetically on a stainless steel MALDI target. Thus, stable coating of the target could be achieved without heating and any damage of its surface. As a case study, MALDI targets were deposited with MeOx nanoparticles, and human globin adducts with in vitro generated diclofenac (DCL) metabolites were enriched on spot from the tryptic digests of the protein treated with DCL oxidation mixture. This extraction procedure gave access to efficient, selective and reliable identification of the human globin adduct with decarboxylation oxidation product of DCL. The developed approach appears to be promising for in situ enrichment of halogen-containing adducts of proteins due to simplifying the sample treatment and minimizing sample losses.

Magnetic Ti3C2 MXene Nanosheets Prepared for Enrichment of Phosphopeptides

MXenes have received lots of attention since discovered and have been applied in various fields. In this work, Ti3C2-Fe3O4 composites with exposed non-modified Ti3C2 MXene nanosheets were designed and prepared by an in situ growth strategy and then applied in the enrichment of phosphopeptides. The two-dimensional composites could interact with the phosphopeptides through a metal oxide affinity chromatography mechanism provided by Ti-O and Fe-O bonds and a hydrophilic interaction chromatography mechanism by surface hydroxyl groups. This magnetic nanomaterial with a specific surface area of 66.1 m2·g-1 had high sensitivity to phosphopeptides (0.5 nmol·L-1) and high selectivity (1:1000 of the molar ratio of β-casein to bovine serum albumin). Non-fat milk was adopted as a real sample to preliminarily examine the applicability of the Ti3C2-Fe3O4-based protocol. Subsequently, Qingkailing injection, a kind of traditional Chinese medicine injection, was introduced to further explore the suitability of the nanocomposites for phosphopeptide enrichment from more complex matrices and satisfactory results were obtained.

Ti(IV) immobilized bisphosphate fructose-modified magnetic Zr metal organic framework (MOF) for specific enrichment of phosphopeptides

Highly selective enrichment of low abundance phosphopeptides from intricate biological samples before mass spectrometry detection is a vital prerequisite for in-depth phosphoproteomics. Herein, a magnetic material mMOF-FBP-Ti4+ is fabricated by grafting UiO-66-NH2 metal–organic framework (Zr-MOF) onto the surface of Fe3O4, and subsequently immobilizing Ti(IV) on the mMOF with fructose 1,6-bisphosphate as chelating ligands. The obtained mMOF-FBP-Ti4+ showed large specific surface area (202.4 m2 g−1) and superparamagnetism (47.5 emu/g). The intrinsic Zr − O clusters of mMOF and the immobilized Ti(IV) ions on the surface of mMOF could interact with phosphopeptides as metal oxide affinity chromatography (MOAC) and immobilized metal affinity chromatography (IMAC), respectively. The introduction of fructose 1,6-bisphosphate also improved the hydrophilicity of the material, which enhanced the hydrophilic chromatography interaction (HILIC) between mMOF-FBP-Ti4+ and phosphopeptides. The above strong affinities provided low limit of detection (0.2 fmol μL−1), high selectivity (α-/β-casein/BSA tryptic digests with a mass ratio of 1:1:500), great reusability (three times circles) and good postenrichment recovery (90.2 %) towards phosphopeptides. Furthermore, the mMOF-FBP-Ti4+ was successfully applied to capture phosphopeptides from non-fat milk tryptic digest and human saliva, indicating its great potential for highly efficient enrichment of low-abundance phosphopeptides in complex biological samples.

Phosphorylated Proteins from Serum: A Promising Potential Diagnostic Biomarker of Cancer.

Cancer is a fatal disease worldwide. Each year ten million people are diagnosed around the world, and more than half of patients eventually die from it in many countries. A majority of cancer remains asymptomatic in the earlier stages, with specific symptoms appearing in the advanced stages when the chances of adequate treatment are low. Cancer screening is generally executed by different imaging techniques like ultrasonography (USG), mammography, CT-scan, and magnetic resonance imaging (MRI). Imaging techniques, however, fail to distinguish between cancerous and non-cancerous cells for early diagnosis. To confirm the imaging result, solid and liquid biopsies are done which have certain limitations such as invasive (in case of solid biopsy) or missed early diagnosis due to extremely low concentrations of circulating tumor DNA (in case of liquid biopsy). Therefore, it is essential to detect certain biomarkers by a noninvasive approach. One approach is a proteomic or glycoproteomic study which mostly identifies proteins and glycoproteins present in tissues and serum. Some of these studies are approved by the Food and Drug Administration (FDA). Another non-expensive and comparatively easier method to detect glycoprotein biomarkers is by ELISA, which uses lectins of diverse specificities. Several of the FDA approved proteins used as cancer biomarkers do not show optimal sensitivities for precise diagnosis of the diseases. In this regard, expression of phosphoproteins is associated with a more specific stage of a particular disease with high sensitivity and specificity. In this review, we discuss the expression of different serum phosphoproteins in various cancers. These phosphoproteins are detected either by phosphoprotein enrichment by immunoprecipitation using phosphospecific antibody and metal oxide affinity chromatography followed by LC-MS/MS or by 2D gel electrophoresis followed by MALDI-ToF/MS analysis. The updated knowledge on phosphorylated proteins in clinical samples from various cancer patients would help to develop these serum phophoproteins as potential diagnostic/prognostic biomarkers of cancer.

Application of smart responsive materials in phosphopeptide and glycopeptide enrichment

蛋白质的磷酸化和糖基化作为研究最广泛的两种翻译后修饰(PTMs),在疾病的早期无创诊断、预后和治疗评估中表现出越来越大的潜力。蛋白质的异常磷酸化和糖基化经常被用于临床蛋白质组学研究和疾病相关生物标志物的发现。目前已有多种材料被开发用于磷酸化肽和糖肽的富集研究,其中,智能响应材料由于具有独特的响应特性,已被陆续报道用于磷酸化肽和糖肽的富集。智能响应材料可对外界刺激做出响应,发生结构和性质上的变化,将光、电、热、机械等信号转化为生物化学信号。响应分子是决定智能响应材料响应特性的先决条件,它们在不同刺激条件下(如温度、pH、光、机械应力、电磁场等)的可逆异构化将导致材料的宏观物理和化学性质的动态变化。与传统材料相比,智能响应材料可以可逆地“打开”和“关闭”,具有更好的可调控性。由于引起智能材料响应的刺激信号对其性能具有重要的影响,综述根据施加的刺激种类对智能响应材料进行分类,具体分为外源性响应材料和内源性响应材料,且分别总结了外源性响应材料、内源性响应材料以及内外源共同响应材料在磷酸化肽和糖肽富集方面的工作。此外,综述对智能响应材料在磷酸化肽和糖肽富集方面的发展前景进行了展望,并且提出了智能响应材料在其他蛋白质翻译后修饰方面的应用中存在的挑战。

Design of two-dimensional molybdenum trioxide-immobilized magnetic graphite nitride nanocomposites with multiple affinity sites for phosphopeptide enrichment

Here, two-dimensional magnetic graphite nitride nanosheets were synthesized, over which molybdenum trioxide was distributed evenly. The magnetic nanocomposite served as an enrichment platform for phosphopeptides based on metal oxide affinity chromatography and anion-exchange chromatography. Owing to the abundant affinity sites, positive electricity, and large surface area, the nanocomposite had high selectivity (α-casein/β-casein/bovine serum albumin, 1:1:5000), sensitivity (0.1 fmol), quantitative recovery (91.3%), and good recyclability (10 cycles). The nanocomposite also showed good enrichment performance for phosphopeptides from non-fat milk, human serum, saliva, and A549 cell lysate. The results demonstrated the value of this material in phosphorylated proteomics.

Post-modified porous hollow nanospheres incorporating multiple strategies for comprehensive phosphoproteomics analysis of serum of Alzheimer's disease

Alzheimer's disease (AD), as a neurodegenerative disease, has become a major disease threatening the physical and mental health of the elderly. In order to find potential cost-effective and valuable AD biomarkers from human serum, we developed and designed a post-modified functional nanomaterial denoted as H–CeO2@PEI-Ti with a porous hollow structure modified with polyethyleneimine (PEI) and Ti4+. This post-modified porous hollow nanomaterial integrated multiple enrichment strategies, including immobilized metal ion affinity chromatography (IMAC) and metal oxide affinity chromatography (MOAC) with electrostatic interaction synergy and hydrogen bond assistance was applied to the phosphoproteomics for the first time. The experimental results demonstrated good performance in the enrichment of standard phosphoprotein tryptic digests, such as extremely low detection limit (0.02 fmol), excellent selectivity (1:5000 M ratio of β-casein and BSA), given that the large specific surface area created by the special porous hollow structure. In serum analyses, 49 phosphopeptides corresponding to 31 phosphoproteins were identified in the serum of the normal controls, and 49 phosphopeptides corresponding to 32 phosphoproteins in AD patients. More importantly, some functional items based on Gene Ontology (GO) analysis after enrichment for human serum supported the molecular biological processes that may be related to the pathogenesis of AD, including copper ion binding, heparin binding and retinoid metabolism.

Bifunctional super-hydrophilic mesoporous nanocomposite: a novel nanoprobe for investigation of glycosylation and phosphorylation in Alzheimer's disease

Alzheimer's disease (AD) is a common neurodegenerative disease. Abnormal glycosylation and phosphorylation modification in AD may be closely related to its pathology. It is of substantial practical significance to simultaneously investigate the roles of phosphorylation and glycosylation in AD. In this work, a bifunctional super-hydrophilic mesoporous nanocomposite (denoted mTiO2@AuCG) was prepared, which combined hydrophilic interaction chromatography (HILIC) and metal oxide affinity chromatography (MOAC) enrichment strategies to enrich phosphopeptides and glycopeptides, respectively or simultaneously. The mTiO2@AuCG exhibited excellent performance on the high-efficiency enrichment of glycopeptides (selectivity, 5000:1 molar ratios of BSA/HRP; sensitivity, 0.1 fmol HRP; satisfactory recovery rate; loading capacity, 200 mg/g) and phosphopeptides (selectivity, 1000:1 molar ratios of BSA/β-casein; sensitivity, 0.2 fmol β-casein; satisfactory recovery rate; loading capacity, 200 mg/g). Using these advantages, after single-step enrichment of mTiO2@AuCG, a total of 209 glycopeptides related to 93 glycoproteins, and 17 phosphopeptides related to 13 phosphoproteins were detected from normal human serum. By contrast, 167 glycopeptides related to 88 glycoproteins, and 14 phosphopeptides related to 12 phosphoproteins were found in AD serum.

Robust Dual-Biomimetic Titanium Dioxide-Cellulose Monolith for Enrichment of Phosphopeptides.

Metal oxide affinity chromatography (MOAC) is considered to be one of the most effective methods for phosphopeptide enrichment. However, most of the materials used in the method are powder; frequent centrifugation is necessitated during the enrichment process, and potential risks of loss of peptides and materials and clogging of the column employed for liquid chromatography-mass spectrometry (LC-MS) arise. Moreover, the reusability of these materials to achieve sustainability was hardly investigated. To overcome these limitations, herein, inorganic titanium dioxide (TiO2) was coated onto the skeletal surface of the organic cellulose monolith (CM) material with a coral-like structure via a sol-gel method. This produced an organic-inorganic hybrid TiO2-CM material, which contained a combination of organic and inorganic substances, making it mimic the mollusk shell in terms of composition. The prepared TiO2-CM material as monolith exhibited excellent mechanical strength and did not break during the enrichment process; thus, the tedious implementation of multiple centrifugation cycles was prevented, thereby streamlining the experimental procedure and avoiding the loss of peptides and materials. Moreover, a large amount of TiO2 was introduced onto the surface of the CM material, and thus, the resultant TiO2-CM material exhibited a large surface area. As a result, the fabricated TiO2-CM material was successfully applied to the enrichment of phosphopeptides obtained from the tryptic digests of a BSA/β-casein (mass ratio, 500/1) mixture. The results were superior to those achieved for commercial TiO2 beads, confirming that TiO2-CM has excellent selectivity for phosphopeptides and reusability. Furthermore, 9287 unique phosphopeptides derived from the 2661 phosphoproteins were successfully identified from two milligrams of tryptic digests of Hela cell exosomes obtained through five independent replications after enriching using the TiO2-CM material. The results indicated that the material has good application prospects in the analysis of protein phosphorylation. Furthermore, TiO2-CM consists of green and cheap cellulose as the skeleton, and its synthesis process is environment-friendly, simple, and inexpensive.

Layer-by-layer assembly of multilayereddouble hydroxides/polyoxometalate-coated magnetic nanoparticles for highly efficient phosphopeptide enrichment.

Alayer-by-layer (LbL) assembly strategy was developed to prepare multilayered double hydroxide/polyoxometalate shell-coated magnetic nanoparticles. The introduction of functional shells not only offered abundant affinity sites of metal oxide and metal ions but also increased the surface area for thecontact with targets. By combining the enrichment strategies of immobilized metal ion affinity chromatography and metal oxide affinity chromatography, the nanomaterial can capture phosphopeptides via a synergistic effect. The method presented a low detection limit of 0.1 fmol in combination withmatrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis. The nanomaterial showed satisfactory selectivity (1:1:5000M ratio of α-/β-casein/bovine serum albumin), goodrecovery (92.07%), highadsorption capacity (117.6mgg-1), and ten timesreusability for capturing phosphopeptides.

Synergistic synthesis of hydrophilic hollow zirconium organic frameworks for simultaneous recognition and capture of phosphorylated and glycosylated peptides

Highly efficient extraction of phospho- and glycopeptides from complicated biological samples is extremely crucial for comprehensive characterization of protein phosphorylation and glycosylation based on mass spectrometry (MS). In this work, a new synergistic strategy that combined surface covalent modification and alkaline etching was developed to synthesize hydrophilic hollow zirconium-organic frameworks (HHZr-MOFs) for simultaneous recognition and capture of phospho- and N-glycopeptides. The unique properties including high specific surface area, mesoporous shell and hollow cavity endowed HHZr-MOFs with facilitated mass transport and abundant accessible active sites. Benefited from the maltose modified on the external surface and Zr–O clusters retained on the internal surface, HHZr-MOFs could act as a highly efficient bifunctional probe for simultaneous enrichment of phospho- and N-glycopeptides based on hydrophilic interaction chromatography (HILIC) and metal oxide affinity chromatography (MOAC), respectively. Finally, a total of 98 endogenous phosphopeptides and 216 endogenous N-glycopeptides were simultaneously captured by HHZr-MOFs from saliva samples of patients with oral inflammation, and several phospho- and glycoproteins related with coagulation, bacterial defense and immune response for oral inflammation were identified by Gene ontology (GO) analyses, confirming the great potential of HHZr-MOFs in rapid detection of clinical biomarkers and comprehensive profiling of phosphoproteomic and glycoproteomic for complex biological samples. This work not only provides an alternative method to precisely design and synthesize sophisticated hollow MOFs with multifunctionalities, but also offers a novel concept of multifunctional material design for bioseparation and analysis in modification-specific proteomics.

Synthesis of a metal oxide affinity chromatography magnetic mesoporous nanomaterial and development of a one-step selective phosphopeptide enrichment strategy for analysis of phosphorylated proteins

Protein phosphorylation is one of the most vital protein post-translational modifications, which regulates numerous biological processes including protein structure transformation, molecular interaction, cell proliferation and apoptosis, as well as various malignant diseases. Though mass spectrometry (MS)-based technologies provide a feasible strategy to analyze phosphorylated proteins, label-free quantitative analysis for phosphopeptides in biological samples is still a challenging task due to sample losses from complicated preparation and necessary phosphopeptide enrichment. In this study, magnetic mesoporous TiO2 microspheres, Fe3O4@nSiO2@mSiO2@TiO2, a metal oxide affinity chromatography material, were synthesized with uniform particle size of 500 nm. The synthesized material exhibited good selectivity (molar ratio of β-casein:BSA = 1:2000, great sensitivity (0.5 fmol μL−1β-casein), and good adsorption capacity (120 mg g−1). Moreover, the proper mesopores on the surface of the enrichment material displayed the unique property of size-exclusion, which could ‘capture’ the trypsin and form a temporary immobilized enzyme reactor, reducing the tryptic digestion procedure from at least 16 h to 2 h. Based on the synthesized material, a facile one-step selective phosphopeptide enrichment method was successfully developed and consisted with protein digestion and phosphopeptide enrichment, which was further applied to selectively enrich phosphopeptides from the complex biological samples of nonfat milk and HepG2 cells, indicating its great feasibility and potential of applications in real sample analysis. More importantly, combining with MS, a label-free phosphoproteomic quantitative strategy was established and performed for determination of the mixture samples containing BSA and various concentrations of β-casein. The results showed that the obtained calibration curve was linear with R = 0.9987 by plotting the intensities of unique phosphopeptide of β-casein (m/z 2061.77) versus the concentrations of β-casein. Our study will provide a novel analytical strategy for selective enrichment of phosphopeptides and facile label-free relative quantitative analysis of phosphorylated proteins.

Proteomics and phosphoproteomics of C3 to CAM transition in the common ice plant.

Among all post-translational modifications of proteins, phosphorylation is one of the most common and most studied. Since plants are sessile organisms, many physiological processes on which their survival depends are regulated by phosphorylation and dephosphorylation. Understanding the extent to which a plant proteome is phosphorylated at specific developmental stages and/or under certain environmental conditions is essential for identifying molecular switches that regulate physiological processes and responses. While most phosphoproteomic workflows proposed in the literature provide tools to exclusively analyze phosphorylated proteins, it is imperative to examine both the proteome and the phosphoproteome to reveal the true complexity of a biological process. Here we describe a mass spectrometry-based phosphoproteomics workflow to analyze both total and phosphorylated proteins. Our method includes phenol-based protein extraction, as well as techniques to measure the quantity and quality of protein extracts. In addition, we compare in detail the efficiency and suitability of in-gel and in-solution trypsin digestion methods. A metal oxide affinity chromatography technique for rapid and efficient enrichment of phosphorylated peptides and an LC-MS/MS method for analysis of the phosphorylated peptides are described. Finally, we present and discuss the results generated by applying this workflow to our study of the C3 to CAM transition in the common ice plant (Mesembryanthemum crystallinum). Overall, our workflow provides robust methods for the identification of phosphoproteins and total proteins. It can be broadly applied to many other organisms and sample types, and the results provide a more accurate picture of the molecular switches that regulate different biological processes.

Inherently hydrophilic mesoporous channel coupled with metal oxide for fishing endogenous salivary glycopeptides and phosphopeptides

Both glycosylation and phosphorylation exert crucial rule in multitudinous biological processes. For in-depth profiling of glycosylation and phosphorylation, a magnetic metal oxide is effectively coupled with inherently hydrophilic mesoporous channels (denoted as Fe3O4@TiO2@mSiO2-TSG). Based on the mechanism of hydrophilic interaction liquid chromatography (HILIC) and metal oxide affinity chromatography (MOAC), the Fe3O4@TiO2@mSiO2-TSG nanomaterial shows high capacity for simultaneously enriching glycopeptides and phosphopeptides. With human saliva collected in successive four days as practical biological sample, endogenous glycopeptides and phosphopeptides are efficiently enriched. Further gene ontology analysis reveals that the identified endogenous glycopeptides and phosphopeptides participate in diverse molecular functions and biological processes. This strategy is anticipated to promote variation analysis of salivary post-translational modifications.

Metal-Organic Framework-Derived Hollow and Hierarchical Porous Multivariate Metal-Oxide Microspheres for Efficient Phosphoproteomics Analysis.

Pre-enrichment of the biological samples is a crucial step in phosphoproteomics research. At present, metal-oxide affinity chromatography (MOAC) is one of the most recognized enrichment strategy. Therefore, the design and preparation of a MOAC-based affinity material with better enrichment properties will be of great significance for the phosphoproteomics study. In this work, we obtained a novel multivariate metal-oxide microsphere (NiFe2O4@C@TiO2) with a hollow and hierarchical porous structure through pyrolysis of TiO2-modified Fe/Ni-based metal-organic frameworks (MOFs). After pyrolysis, the carbon matrix derived from the MOFs provided support and porous properties. Meanwhile, multivariate metal oxides endowed the microspheres with an excellent magnetic response property and superior enrichment performance for phosphorylated biomolecules. The unique hollow and hierarchical porous structure greatly enhanced the diffusion of phosphorylated biomolecules. Therefore, the microspheres exhibited excellent enrichment performance for phosphorylated biomolecules: a large adsorption capacity (124 μmol g-1), excellent selectivity (α-casein/BSA, 1:5000, m/m), perfect size-exclusion performance (α-casein digests/α-casein/BSA, 1:500:500), and extremely low detection limit (2 fmol). Furthermore, the microspheres showed excellent enrichment performance in a series of real biological samples, such as nonfat milk, serum, saliva, rat brain tissue, and plasma exosomes of patients with esophageal cancer, which further demonstrated its huge application potential in MS-based phosphoproteomics research.

Integrated Phosphoproteomic and N-Glycoproteomic Landscape of Cutaneous T-Cell Lymphoma Reveals Distinctive Pathogenetic Insights and Therapeutic Vulnerabilities

Background: A critical goal of precision oncology is the identification of deregulated signaling pathways that serve as disease-specific biomarkers and vulnerabilities that may be exploited as therapeutic targets. Cutaneous T cell lymphomas (CTCLs) are heterogeneous neoplasms with variable clinical outcomes. Whereas the genomic landscapes of CTCLs are being characterized, a large scale analysis of their proteomic signatures and post-translational modifications (PTM) has not been performed. In this study, we sought to gain insights into the pathogenesis of CTCLs using high mass accuracy tandem mass spectrometry (HMA-MS/MS)-based phosphoproteomics and glycoproteomics.Methods: CTCL-derived cell lines representative of Sézary syndrome (SS, HUT78), mycosis fungoides (MF, HH), and ALK-negative anaplastic large cell lymphoma (ALCL) with PCM1-JAK2 or NPM1-TYK2 translocations (Mac1, Mac2a, and Myla) were analyzed in technical and biologic triplicates to perform unbiased proteome characterization. Phosphoproteins were enriched using metal oxide affinity chromatography and immunoprecipitation using 3 anti-phosphotyrosine antibodies and N-glycoproteins were enriched using solid phase extraction and hydrazide resin and an Orbitrap Fusion or LTQ OrbitrapXL in-line with a Paradigm MS2 HPLC. Precise site-mapping of the PTMs was assigned and quantitated using Maxquant. Hierarchical clustering was performed using Perseus. Whole exome sequencing (WES) was performed using an Illumina HiSeq 2500. Functional studies using tyrosine kinase inhibitors were performed to assess selective vulnerabilities.Results: Phosphoproteomic analysis identified 1899 tyrosine (Y) phosphoproteins and 6029 serine/threonine (S/T) phosphoproteins. Unsupervised hierarchical clustering of the Y-phosphoproteome data accurately grouped the CTCLs to those with and without underlying tyrosine kinase translocations. Unique driver kinase phosphosignaling signatures were identified in MYLA (NPM1-TYK2) and MAC1/2 (PCM1-JAK2) representing the ALCL subgroup, as well as close similarity between the signatures of MF and SS-derived cells (HH and HUT78). Notably, phosphoproteomic analysis of HUT78 (SS) yielded high spectral counts of Y-phosphorylated residues at IL2RG p.Y325, JAK3 p.Y980/Y981, and STAT5 p.Y699 indicative of constitutive activation of the JAK/STAT5 pathway corroborated by WES showing activating mutations in JAK3 p.A573V and JAK1 p.Y654F.Beyond driver kinases, oncogenic kinase-specific substrates with distinct site-specific phosphorylated residues were identified for each disease class. Phosphoproteins selectively expressed in MF/SS, (46 p-S/T and 25 p-Y proteins) included members of the killer-cell immunoglobulin-like receptor (KIR) family implicated in immune modulation through immune tyrosine-based inhibitor or TYRO protein tyrosine kinase binding domains for signal transduction. Additionally, proteins not previously associated with MF/SS including NKG2-D type integral membrane protein family members were discriminative of this subgroup. Phosphoprotein members of lysine demethylases (KDM family) and Aryl Hydrocarbon Receptor families were distinctively identified in MF/SS cells, while components of the T-cell receptor signaling pathways were common in all groups of CTCLs. By comparison, N-glycoproteomic analysis identified 811 unique N-glycoproteins. A total of 51 N-glycoproteins were found solely in HUT78 of which 46 were novel in their specificity and included 13 with a role in cell-adhesion while N-glycoproteins unique to HH revealed 12 novel candidate biomarkers (e.g. MERTK, CD97 and SLC44A2). Integrative phosphoproteomic and N-glycoproteomic analysis strikingly revealed convergent pathways implicating a prominent role for the KIR family proteins in SS. Orthogonal immunophenotyping by flow cytometry has shown high sensitivity (96%) detection of KIR3DL2 in primary human SS cases. Significantly, anti-KIR3DL2 inhibition using a humanized antibody revealed activity against SS cells. By comparison, TYK2-driven CTCL (MYLA) was sensitive to inhibitors of TYK2 and JAK.Conclusions: Integrated phosphoproteomic and N-glycoproteomic analysis identifies known and novel candidate biomarkers, unique PTM signatures, and therapeutic vulnerabilities implicating disease-specific pathogenetic mechanisms in CTCL. DisclosuresNo relevant conflicts of interest to declare.

Magnetic metal oxide affinity chromatography-based molecularly imprinted approach for effective separation of serous and urinary phosphoprotein biomarker

Many phosphoprotein biomarkers have been proved to exist in body fluids such as serum and urine, however, there is absence of rapid and efficient separation and identification method. In this study, we proposed to combine metal oxide affinity chromatography (MOAC), molecular imprinting technology (MIT) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to establish an effective approach to solve this problem. To verify the feasibility of this approach, we selected a typical phosphoprotein lysozyme (Lys) as template and magnetic TiO2 as substrate to prepare the molecularly imprinted nanoparticles (denoted as Fe3O4@TiO2@Lys MIPs). A point worth noting is that polydopamine (PDA) as polymer layer made Fe3O4@TiO2@Lys MIPs more hydrophilic and biocompatible. Thanks to the recognition sites of phosphate and the template-shaped cavities, Fe3O4@TiO2@Lys MIPs showed great sensitivity (0.01 ng*μL−1) and selectivity (Lysozyme: BSA: β-casein = 1:100:100, mass ratio) in standard phosphoprotein solution. At the end, the Fe3O4@TiO2@Lys MIPs showed great separation ability to lysozyme phosphoprotein in both human serum and urine samples. Therefore, the MOAC-based molecularly imprinted approach is worthy to be expected in effective separation of phosphoprotein biomarker in complex body fluid, which will be a promising one in future.

Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment.

Phosphopeptide enrichment is an essential step in large-scale, quantitative phosphoproteomics by mass spectrometry. Several phosphopeptide affinity enrichment techniques exist, such as immobilized metal-ion affinity chromatography (IMAC) and metal oxide affinity chromatography (MOAC). We compared zirconium(IV) IMAC (Zr-IMAC) magnetic microparticles to more commonly used titanium(IV) IMAC (Ti-IMAC) and TiO2 magnetic microparticles for phosphopeptide enrichment from simple and complex protein samples prior to phosphopeptide sequencing and characterization by mass spectrometry (liquid chromatography-tandem mass spectrometry, LC-MS/MS). We optimized sample-loading conditions to increase phosphopeptide recovery for Zr-IMAC-, Ti-IMAC-, and TiO2-based workflows by 22, 24, and 35%, respectively. The optimized protocol resulted in improved performance of Zr-IMAC over Ti-IMAC and TiO2 as well as high-performance liquid chromatography-based Fe(III)-IMAC with up to 23% more identified phosphopeptides. The different enrichment chemistries showed a high degree of overlap but also differences in phosphopeptide selectivity and complementarity. We conclude that Zr-IMAC improves phosphoproteome coverage and recommend that this complementary and scalable affinity enrichment method is more widely used in biological and biomedical studies of cell signaling and the search for biomarkers. Data are available via ProteomeXchange with identifier PXD018273.