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Chen CW, Lin PY, Lai YM, Lin MH, Lin SY, Hsu CC. TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics. Mol Cell Proteomics 2024; 23:100762. [PMID: 38608839 PMCID: PMC11098956 DOI: 10.1016/j.mcpro.2024.100762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Protein post-translational modifications (PTMs) are crucial in plant cellular processes, particularly in protein folding and signal transduction. N-glycosylation and phosphorylation are notably significant PTMs, playing essential roles in regulating plant responses to environmental stimuli. However, current sequential enrichment methods for simultaneous analysis of phosphoproteome and N-glycoproteome are labor-intensive and time-consuming, limiting their throughput. Addressing this challenge, this study introduces a novel tandem S-Trap-IMAC-HILIC (S-Trap: suspension trapping; IMAC: immobilized metal ion affinity chromatography; HILIC: hydrophilic interaction chromatography) strategy, termed TIMAHAC, for simultaneous analysis of plant phosphoproteomics and N-glycoproteomics. This approach integrates IMAC and HILIC into a tandem tip format, streamlining the enrichment process of phosphopeptides and N-glycopeptides. The key innovation lies in the use of a unified buffer system and an optimized enrichment sequence to enhance efficiency and reproducibility. The applicability of TIMAHAC was demonstrated by analyzing the Arabidopsis phosphoproteome and N-glycoproteome in response to abscisic acid (ABA) treatment. Up to 1954 N-glycopeptides and 11,255 phosphopeptides were identified from Arabidopsis, indicating its scalability for plant tissues. Notably, distinct perturbation patterns were observed in the phosphoproteome and N-glycoproteome, suggesting their unique contributions to ABA response. Our results reveal that TIMAHAC offers a comprehensive approach to studying complex regulatory mechanisms and PTM interplay in plant biology, paving the way for in-depth investigations into plant signaling networks.
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Affiliation(s)
- Chin-Wen Chen
- Institution of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pei-Yi Lin
- Institution of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ying-Mi Lai
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Miao-Hsia Lin
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shu-Yu Lin
- Academia Sinica Common Mass Spectrometry Facilities for Proteomics and Protein Modification Analysis, Academia Sinica, Taipei, Taiwan
| | - Chuan-Chih Hsu
- Institution of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
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Wang Y, Sun Y, Wang Y, Jia S, Qiao Y, Zhou Z, Shao W, Zhang X, Guo J, Song X, Niu X, Peng D. Urine metabolomics phenotyping and urinary biomarker exploratory in mild cognitive impairment and Alzheimer's disease. Front Aging Neurosci 2023; 15:1273807. [PMID: 38187356 PMCID: PMC10768723 DOI: 10.3389/fnagi.2023.1273807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/20/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction Alzheimer's disease is a prevalent disease with a heavy global burden and is suggested to be a metabolic disease in the brain in recent years. The metabolome is considered to be the most promising phenotype which reflects changes in genetic, transcript, and protein profiles as well as environmental effects. Aiming to obtain a comprehensive understanding and convenient diagnosis of MCI and AD from another perspective, researchers are working on AD metabolomics. Urine is more convenient which could reflect the change of disease at an earlier stage. Thus, we conducted a cross-sectional study to investigate novel diagnostic panels. Methods We first enrolled participants from China-Japan Friendship Hospital from April 2022 to November 2022, collected urine samples and conducted an LC-MS/MS analysis. In parallel, clinical data were collected and clinical examinations were performed. After statistical and bioinformatics analyzes, significant risk factors and differential urinary metabolites were determined. We attempt to investigate diagnostic panels based on machine learning including LASSO and SVM. Results Fifty-seven AD patients, 43 MCI patients and 62 CN subjects were enrolled. A total of 2,140 metabolites were identified among which 125 significantly differed between the AD and CN groups, including 46 upregulated ones and 79 downregulated ones. In parallel, there were 93 significant differential metabolites between the MCI and CN groups, including 23 upregulated ones and 70 downregulated ones. AD diagnostic panel (30 metabolites+ age + APOE) achieved an AUC of 0.9575 in the test set while MCI diagnostic panel (45 metabolites+ age + APOE) achieved an AUC of 0.7333 in the test set. Atropine, S-Methyl-L-cysteine-S-oxide, D-Mannose 6-phosphate (M6P), Spiculisporic Acid, N-Acetyl-L-methionine, 13,14-dihydro-15-keto-tetranor Prostaglandin D2, Pyridoxal 5'-Phosphate (PLP) and 17(S)-HpDHA were considered valuable for both AD and MCI diagnosis and defined as hub metabolites. Besides, diagnostic metabolites were weakly correlated with cognitive functions. Discussion In conclusion, the procedure is convenient, non-invasive, and useful for diagnosis, which could assist physicians in differentiating AD and MCI from CN. Atropine, M6P and PLP were evidence-based hub metabolites in AD.
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Affiliation(s)
- Yuye Wang
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Yu Sun
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Yu Wang
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Shuhong Jia
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Yanan Qiao
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Zhi Zhou
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Wen Shao
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Xiangfei Zhang
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Jing Guo
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | - Xincheng Song
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Xiaoqian Niu
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Dantao Peng
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Neurology, China-Japan Friendship Hospital, Beijing, China
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
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Wang D, Huang J, Zhang H, Ma M, Xu M, Cui Y, Shi X, Li L. ATP-Coated Dual-Functionalized Titanium(IV) IMAC Material for Simultaneous Enrichment and Separation of Glycopeptides and Phosphopeptides. J Proteome Res 2023; 22:2044-2054. [PMID: 37195130 PMCID: PMC11138137 DOI: 10.1021/acs.jproteome.3c00118] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protein glycosylation and phosphorylation are two of the most common post-translational modifications (PTMs), which play an important role in many biological processes. However, low abundance and poor ionization efficiency of phosphopeptides and glycopeptides make direct MS analysis challenging. In this study, we developed a hydrophilicity-enhanced bifunctional Ti-IMAC (IMAC: immobilized metal affinity chromatography) material with grafted adenosine triphosphate (denoted as epoxy-ATP-Ti4+) to enable simultaneous enrichment and separation of common N-glycopeptides, phosphopeptides, and M6P glycopeptides from tissue/cells. The enrichment was achieved through a dual-mode mechanism based on the electrostatic and hydrophilic properties of the material. The epoxy-ATP-Ti4+ IMAC material was prepared from epoxy-functionalized silica particles via a convenient two-step process. The ATP molecule provided strong and active phosphate sites for binding phosphopeptides in the conventional IMAC mode and also contributed significantly to the hydrophilicity, which permitted the enrichment of glycopeptides via hydrophilic interaction chromatography. The two modes could be implemented simultaneously, allowing glycopeptides and phosphopeptides to be collected sequentially in a single experiment from the same sample. In addition to standard protein samples, the material was further applied to glycopeptide and phosphopeptide enrichment and characterization from HeLa cell digests and mouse lung tissue samples. In total, 2928 glycopeptides and 3051 phosphopeptides were identified from the mouse lung tissue sample, supporting the utility of this material for large-scale PTM analysis of complex biological samples. Overall, the newly developed epoxy-ATP-Ti4+ IMAC material and associated fractionation method enable simple and effective enrichment and separation of glycopeptides and phosphopeptides, offering a useful tool to study potential crosstalk between these two important PTMs in biological systems. The MS data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD029775.
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Affiliation(s)
- Danqing Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Haoran Zhang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Meng Xu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xudong Shi
- Department of Surgery, University of Wisconsin–Madison, Madison, WI 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
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4
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Wang K, Yu A, Gao Y, Chen M, Yuan H, Zhang S, Ouyang G. A nitrogen-doped graphene tube composite based on immobilized metal affinity chromatography for the capture of phosphopeptides. Talanta 2023; 261:124617. [PMID: 37187026 DOI: 10.1016/j.talanta.2023.124617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023]
Abstract
A novel immobilized metal affinity chromatography (IMAC) functional composite, mNi@N-GrT@PDA@Ti4+, was fabricated based on ultrathin magnetic nitrogen-doped graphene tube (mNi@N-GrT) after chelated Ti4+ with polydopamine, following as a magnetic solid-phase extraction sorbent for rapidly selective enrichment and mass spectrometry identification of phosphorylated peptides. After optimized, the composite exhibited high specificity in the enrichment of phosphopeptides from the digest mixture of β-casein and bovine serum albumin (BSA). The robust method presented the low detection limits (1 fmol, 200 μL) and excellent selectivity (1:100) in the molar ration mixture of β-casein and BSA digests. Furthermore, the selective enrichment of phosphopeptides in the complex bio-samples, was successfully carried out. The results showed that 28 phosphopeptides were finally detected in mouse brain, and 2087 phosphorylated peptides were identified in the HeLa cells extracts with specific selectivity of 95.6%. The enrichment performance of mNi@N-GrT@PDA@Ti4+ was satisfactory, suggesting that the functional composite provided a potential application in the enrichment of trace phosphorylated peptides from the complex biological matrix.
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Affiliation(s)
- Kexuan Wang
- College of Chemistry, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China
| | - Ajuan Yu
- College of Chemistry, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China.
| | - Yu Gao
- High & New Technology Research Center of Henan Academy of Sciences, Zhengzhou, Henan Province, 450002, PR China
| | - Miao Chen
- College of Chemistry, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China
| | - Hang Yuan
- Center of Advanced Analysis and Gene Sequencing, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China
| | - Shusheng Zhang
- Center of Advanced Analysis and Gene Sequencing, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China.
| | - Gangfeng Ouyang
- Center of Advanced Analysis and Gene Sequencing, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China
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Cao W, Bruening ML. Analysis of Protein Glycosylation after Rapid Digestion Using Protease-Containing Membranes in Spin Columns. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37127550 DOI: 10.1021/jasms.3c00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Glycosylation is an important protein post-translational modification that plays a pivotal role in the bioactivity of therapeutic proteins and in the infectivity of viral proteins. Liquid chromatography with tandem mass spectrometry readily identifies protein glycans with site specificity. However, the overnight incubation used in conventional in-solution proteolysis leads to high turnaround times for glycosylation analysis, particularly when sequential in-solution digestions are needed for site-specific glycan identification. Using bovine fetuin as a model glycoprotein, this work first shows that in-membrane digestion in ∼3 min yields similar glycan identification and quantitation when compared to overnight in-solution digestion. Protease-containing membranes in a spin column enable digestion of therapeutic proteins (trastuzumab and erythropoietin) and a viral protein (SARS-CoV-2 receptor binding domain) in ∼30 s. Glycan identification is similar after in-solution and in-membrane digestion, and limited in-membrane digestion enhances the identification of high-mannose glycans in trastuzumab. Finally, stacked membranes containing trypsin and chymotrypsin allow fast sequential proteolytic digestion to site-specifically identify the glycans of SARS-CoV-2 receptor binding domain. One can easily assemble the protease-containing membranes in commercial spin columns, and spinning multiple columns simultaneously will facilitate parallel analyses.
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Affiliation(s)
- Weikai Cao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Merlin L Bruening
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Chemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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A combination of surface-initiated atom transfer radical polymerization and photo-initiated "thiol-ene" click chemistry: Fabrication of functionalized macroporous adsorption resins for enrichment of glycopeptides. J Chromatogr A 2023; 1689:463774. [PMID: 36630850 DOI: 10.1016/j.chroma.2023.463774] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
A hydrophilic adsorbent (Cys@poly(AMA)@MAR) was successfully prepared for the enrichment of N-glycopeptides via surface-initiated atom transfer radical polymerization (SI-ATRP) and photo-initiated "thiol-ene" reaction using monodisperse macroporous adsorbent resin (MAR) as adsorption matrix. Due to the presence of electron-deficient acrylic groups and electron-rich vinyl groups in allyl methacrylate (AMA), both of them can participate in free radical reaction. Therefore, the polymerization time of SI-ATRP was optimized. The resulting poly(AMA)@MAR was modified with l-cysteine (L-Cys) via photo-initiated "thiol-ene" reaction, and the amount of vinyl retained was determined by measuring the adsorption of Cu2+. The Cys@poly(AMA)@MAR pendant brushes with high density of amine and carboxyl groups could capture N-glycopeptides from IgG digest and human serum digest by hydrophilic interaction. The 22 N-glycopeptides were identified from IgG digest and the limit of detection reached 10 fmol. The 319 N-glycosylation sites and 583 N-glycopeptides were identified from 2 μL human serum digest and mapped to 147 glycoproteins. It demonstrates great potential and commercialization prospects for the enrichment of N-glycopeptides.
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Shao X, Zhu J, Shi Y, Fang H, Chen J, Zhang Y, Wang J, Jian H, Lan S, Jiang F, Zhong F, Zhang Y, Cao C. Upregulated UBE4B expression correlates with poor prognosis and tumor immune infiltration in hepatocellular carcinoma. Aging (Albany NY) 2022; 14:9632-9646. [PMID: 36470669 PMCID: PMC9792214 DOI: 10.18632/aging.204414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/23/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a major human health concern. Increasing evidence has demonstrated that ubiquitin ligase E4B (UBE4B) may be involved in the occurrence and development of various human cancers and may affect prognosis. However, the specific role and mechanism of UBE4B in HCC is unclear. METHODS A pan-cancer analysis of UBE4B expression, clinicopathological features, and prognosis was performed using bioinformatics techniques. Subsequently, the expression, prognosis, and correlation of UBE4B and its upstream miRNAs and lncRNAs were analyzed. We investigated the relationship between UBE4B expression and immune cell infiltration, immunomodulatory factors, and chemokines in HCC. The expression levels of UBE4B and its upstream lncRNAs (FGD5-AS1, LINC00858, and SNHG16) and miRNAs (hsa-miR-22-3p) were evaluated in HCC cell lines using qRT-PCR. RESULTS UBE4B expression increased in HCC and was correlated with a poor survival rate in patients with HCC. A ceRNA network was established to identify the UBE4B-hsa-miR-22-3p-FGD5-AS1/LINC00858/SNHG16 regulatory axis in HCC. UBE4B expression was significantly associated with immune cell infiltration, immunomodulators, chemokines, and their receptors in HCC. The mRNA expression of FGD5-AS1, LINC00858, SNHG16, and UBE4B was higher in the HCC cell lines (7721 and HepG2) than in the normal hepatocyte line (LO2), and the expression of hsa-miR-22-3p mRNA showed a decreasing trend. CONCLUSIONS Our findings showed that upregulation of UBE4B was associated with poor prognosis and tumor immune infiltration in HCC. These findings will aid in understanding the relevant functions of UBE4B and provide new strategies for drug development and exploration of prognosis-related biomarkers.
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Affiliation(s)
- Xuyang Shao
- Graduate School of Bengbu Medical College, Bengbu 233000, Anhui Province, China,Department of General Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing 314000, Zhejiang Province, China
| | - Jun Zhu
- Department of Oncology, Fuyang Hospital of Anhui Medical University, Fuyang 236000, Anhui Province, China
| | - Yanlong Shi
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210003, Jiangsu Province, China
| | - Hanlu Fang
- Institute of Medical and Health Science of HeBMU, Hebei Medical University, Shijiazhuang 050017, Hebei Province, China
| | - Jingsi Chen
- Department of Intensive Care Unit, Fuyang Women and Children’s Hospital, Fuyang 236000, Anhui Province, China
| | - Yixiao Zhang
- The First Clinical College of Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang Province, China
| | - Jingyan Wang
- Department of Anesthesia, Shaoxing People’s Hospital, Shaoxing 312000, Zhejiang Province, China
| | - Haokun Jian
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan Province, China
| | - Sheng Lan
- The Second Clinical College of Guangzhou Medical University, Guangzhou 510030, Guangdong Province, China
| | - Fei Jiang
- Department of General Surgery, Fuyang Hospital of Anhui Medical University, Fuyang 236000, Anhui Province, China
| | - Fei Zhong
- Department of Oncology, Fuyang Hospital of Anhui Medical University, Fuyang 236000, Anhui Province, China,Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, Anhui Province, China
| | - Yewei Zhang
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210003, Jiangsu Province, China
| | - Chenxi Cao
- Graduate School of Bengbu Medical College, Bengbu 233000, Anhui Province, China,Department of General Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing 314000, Zhejiang Province, China
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Chen Z, Wang D, Yu Q, Johnson J, Shipman R, Zhong X, Huang J, Yu Q, Zetterberg H, Asthana S, Carlsson C, Okonkwo O, Li L. In-Depth Site-Specific O-Glycosylation Analysis of Glycoproteins and Endogenous Peptides in Cerebrospinal Fluid (CSF) from Healthy Individuals, Mild Cognitive Impairment (MCI), and Alzheimer's Disease (AD) Patients. ACS Chem Biol 2022; 17:3059-3068. [PMID: 34964596 PMCID: PMC9240109 DOI: 10.1021/acschembio.1c00932] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Site-specific O-glycoproteome mapping in complex biological systems provides a molecular basis for understanding the structure-function relationships of glycoproteins and their roles in physiological and pathological processes. Previous O-glycoproteome analysis in cerebrospinal fluid (CSF) focused on sialylated glycoforms, while missing information on other glycosylation types. In order to achieve an unbiased O-glycosylation profile, we developed an integrated strategy combining universal boronic acid enrichment, high-pH fractionation, and electron-transfer and higher-energy collision dissociation (EThcD) for enhanced intact O-glycopeptide analysis. We applied this strategy to analyze the O-glycoproteome in CSF, resulting in the identification of 308 O-glycopeptides from 110 O-glycoproteins, covering both sialylated and nonsialylated glycoforms. To our knowledge, this is the largest data set of O-glycoproteins and O-glycosites reported for CSF to date. We also developed a peptidomics workflow that utilized the EThcD and a three-step database searching strategy for comprehensive PTM analysis of endogenous peptides, including N-glycosylation, O-glycosylation, and other common peptide PTMs. Interestingly, among the 1411 endogenous peptides identified, 89 were O-glycosylated, and only one N-glycosylated peptide was found, indicating that CSF endogenous peptides were predominantly O-glycosylated. Analyses of the O-glycoproteome and endogenous peptidome PTMs were also conducted in the CSF of MCI and AD patients to provide a landscape of glycosylation patterns in different disease states. Our results showed a decreasing trend in fucosylation and an increasing trend of endogenous peptide O-glycosylation, which may play an important role in AD progression.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Danqing Wang
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Jillian Johnson
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Richard Shipman
- Applied Science Program, University of Wisconsin-Stout, Menomonie, WI 54751, USA
| | - Xiaofang Zhong
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 43180, Mölndal, Sweden,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, 43180, Mölndal, Sweden,Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, United Kingdom,UK Dementia Research Institute at UCL, London, WC1E 6BT, United Kingdom
| | - Sanjay Asthana
- School of Medicine and Public Health, University of Wisconsin, Madison, WI 53726, USA
| | - Cynthia Carlsson
- School of Medicine and Public Health, University of Wisconsin, Madison, WI 53726, USA
| | - Ozioma Okonkwo
- School of Medicine and Public Health, University of Wisconsin, Madison, WI 53726, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA,School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA,Correspondence: Professor Lingjun Li, School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, , Fax: +1-608-262-5345, Phone: +1-608-265-8491
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9
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Materials, workflows and applications of IMAC for phosphoproteome profiling in the recent decade: A review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Wang D, Ma M, Huang J, Gu TJ, Cui Y, Li M, Wang Z, Zetterberg H, Li L. Boost-DiLeu: Enhanced Isobaric N, N-Dimethyl Leucine Tagging Strategy for a Comprehensive Quantitative Glycoproteomic Analysis. Anal Chem 2022; 94:11773-11782. [PMID: 35960654 PMCID: PMC9966376 DOI: 10.1021/acs.analchem.2c01773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Intact glycopeptide analysis has been of great interest because it can elucidate glycosylation site information and glycan structural composition at the same time. However, mass spectrometry (MS)-based glycoproteomic analysis is hindered by the low abundance and poor ionization efficiency of glycopeptides. Relatively large amounts of starting materials are needed for the enrichment, which makes the identification and quantification of intact glycopeptides from samples with limited quantity more challenging. To overcome these limitations, we developed an improved isobaric labeling strategy with an additional boosting channel to enhance N,N-dimethyl leucine (DiLeu) tagging-based quantitative glycoproteomic analysis, termed as Boost-DiLeu. With the integration of a one-tube sample processing workflow and high-pH fractionation, 3514 quantifiable N-glycopeptides were identified from 30 μg HeLa cell tryptic digests with reliable quantification performance. Furthermore, this strategy was applied to human cerebrospinal fluid (CSF) samples to differentiate N-glycosylation profiles between Alzheimer's disease (AD) patients and non-AD donors. The results revealed processes and pathways affected by dysregulated N-glycosylation in AD, including platelet degranulation, cell adhesion, and extracellular matrix, which highlighted the involvement of N-glycosylation aberrations in AD pathogenesis. Moreover, weighted gene coexpression network analysis (WGCNA) showed nine modules of glycopeptides, two of which were associated with the AD phenotype. Our results demonstrated the feasibility of using this strategy for in-depth glycoproteomic analysis of size-limited clinical samples. Taken together, we developed and optimized a strategy for the enhanced comprehensive quantitative intact glycopeptide analysis with DiLeu labeling, showing significant promise for identifying novel therapeutic targets or biomarkers in biological systems with a limited sample quantity.
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Affiliation(s)
- Danqing Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ting-Jia Gu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Miyang Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zicong Wang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 43141, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 43130, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, WC1N 3BG, U.K.,UK Dementia Research Institute at UCL, London, WC1N 3BG, U.K.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.,To whom correspondence should be addressed. . Phone: +1-(608)-265- 8491, Fax: +1-(608)-262-5345. Mailing Address: 5125 Rennebohm Hall, 777 Highland Avenue, Madison, WI 53705, USA
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11
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Yi L, Fu M, Shao Y, Tang K, Yan Y, Ding CF. Bifunctional super-hydrophilic mesoporous nanocomposite: a novel nanoprobe for investigation of glycosylation and phosphorylation in Alzheimer's disease. J Chromatogr A 2022; 1676:463236. [PMID: 35709605 DOI: 10.1016/j.chroma.2022.463236] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 10/18/2022]
Abstract
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.
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Affiliation(s)
- Linhua Yi
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Mengyao Fu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yifan Shao
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Keqi Tang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
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12
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Seo J, Oh DB. Mannose-6-phosphate glycan for lysosomal targeting: various applications from enzyme replacement therapy to lysosome-targeting chimeras. Anim Cells Syst (Seoul) 2022; 26:84-91. [PMID: 35784393 PMCID: PMC9246025 DOI: 10.1080/19768354.2022.2079719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Affiliation(s)
- Jinho Seo
- Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Doo-Byoung Oh
- Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Korea
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13
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Du Z, Yang Q, Liu Y, Chen S, Zhao H, Bai H, Shao W, Zhang Y, Qin W. A New Strategy for High-Efficient Tandem Enrichment and Simultaneous Profiling of N-Glycopeptides and Phosphopeptides in Lung Cancer Tissue. Front Mol Biosci 2022; 9:923363. [PMID: 35685241 PMCID: PMC9171396 DOI: 10.3389/fmolb.2022.923363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
N-glycosylation and phosphorylation, two common posttranslational modifications, play important roles in various biological processes and are extensively studied for biomarker and drug target screening. Because of their low abundance, enrichment of N-glycopeptides and phosphopeptides prior to LC–MS/MS analysis is essential. However, simultaneous characterization of these two types of posttranslational modifications in complex biological samples is still challenging, especially for tiny amount of samples obtained in tissue biopsy. Here, we introduced a new strategy for the highly efficient tandem enrichment of N-glycopeptides and phosphopeptides using HILIC and TiO2 microparticles. The N-glycopeptides and phosphosites obtained by tandem enrichment were 21%–377% and 22%–263% higher than those obtained by enriching the two PTM peptides separately, respectively, using 160–20 μg tryptic digested peptides as the starting material. Under the optimized conditions, 2798 N-glycopeptides from 434 N-glycoproteins and 5130 phosphosites from 1986 phosphoproteins were confidently identified from three technical replicates of HeLa cells by mass spectrometry analysis. Application of this tandem enrichment strategy in a lung cancer study led to simultaneous characterization of the two PTM peptides and discovery of hundreds of differentially expressed N-glycosylated and phosphorylated proteins between cancer and normal tissues, demonstrating the high sensitivity of this strategy for investigation of dysregulated PTMs using very limited clinical samples.
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Affiliation(s)
- Zhuokun Du
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Qianying Yang
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Yuanyuan Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Sijie Chen
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Hongxian Zhao
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Haihong Bai
- Phase I Clinical Trial Center, Beijing Shijitan Hospital of Capital Medical University, Beijing, China
| | - Wei Shao
- School of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Yangjun Zhang
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
- *Correspondence: Yangjun Zhang, ; Weijie Qin,
| | - Weijie Qin
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
- *Correspondence: Yangjun Zhang, ; Weijie Qin,
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14
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Tabang DN, Wang D, Li L. A Spin-Tip Enrichment Strategy for Simultaneous Analysis of N-Glycopeptides and Phosphopeptides from Human Pancreatic Tissues. J Vis Exp 2022:10.3791/63735. [PMID: 35604151 PMCID: PMC9186302 DOI: 10.3791/63735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2024] Open
Abstract
Mass spectrometry can provide deep coverage of post-translational modifications (PTMs), although enrichment of these modifications from complex biological matrices is often necessary due to their low stoichiometry in comparison to non-modified analytes. Most enrichment workflows of PTMs on peptides in bottom-up proteomics workflows, where proteins are enzymatically digested before the resulting peptides are analyzed, only enrich one type of modification. It is the entire complement of PTMs, however, that leads to biological functions, and enrichment of a single type of PTM may miss such crosstalk of PTMs. PTM crosstalk has been observed between protein glycosylation and phosphorylation, the two most common PTMs in human proteins and also the two most studied PTMs using mass spectrometry workflows. Using the simultaneous enrichment strategy described herein, both PTMs are enriched from post-mortem human pancreatic tissue, a complex biological matrix. Dual-functional Ti(IV)-immobilized metal affinity chromatography is used to separate various forms of glycosylation and phosphorylation simultaneously in multiple fractions in a convenient spin tip-based method, allowing downstream analyses of potential PTM crosstalk interactions. This enrichment workflow for glyco- and phosphopeptides can be applied to various sample types to achieve deep profiling of multiple PTMs and identify potential target molecules for future studies.
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Affiliation(s)
| | - Danqing Wang
- Department of Chemistry, University of Wisconsin-Madison
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison; School of Pharmacy, University of Wisconsin-Madison;
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15
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Glyco-Decipher enables glycan database-independent peptide matching and in-depth characterization of site-specific N-glycosylation. Nat Commun 2022; 13:1900. [PMID: 35393418 PMCID: PMC8990002 DOI: 10.1038/s41467-022-29530-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 03/16/2022] [Indexed: 12/20/2022] Open
Abstract
Glycopeptides with unusual glycans or poor peptide backbone fragmentation in tandem mass spectrometry are unaccounted for in typical site-specific glycoproteomics analysis and thus remain unidentified. Here, we develop a glycoproteomics tool, Glyco-Decipher, to address these issues. Glyco-Decipher conducts glycan database-independent peptide matching and exploits the fragmentation pattern of shared peptide backbones in glycopeptides to improve the spectrum interpretation. We benchmark Glyco-Decipher on several large-scale datasets, demonstrating that it identifies more peptide-spectrum matches than Byonic, MSFragger-Glyco, StrucGP and pGlyco 3.0, with a 33.5%-178.5% increase in the number of identified glycopeptide spectra. The database-independent and unbiased profiling of attached glycans enables the discovery of 164 modified glycans in mouse tissues, including glycans with chemical or biological modifications. By enabling in-depth characterization of site-specific protein glycosylation, Glyco-Decipher is a promising tool for advancing glycoproteomics analysis in biological research. Poor peptide fragmentation and unusual glycan structures limit mass spectrometry-based analysis of intact N-glycopeptides. Here, the authors develop Glyco-Decipher, a glycan-independent peptide search tool, to tackle these issues and improve the coverage of site-specific glycan analysis.
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16
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Li X, Ma S, Tang R, Ou J. Interface-Engineered Hollow Nanospheres with Titanium(IV) Binding Sites and Microwindows as Affinity Probes for Ultrafast and Enhanced Phosphopeptides Enrichment. Anal Chem 2022; 94:5159-5166. [PMID: 35300494 DOI: 10.1021/acs.analchem.2c00164] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Enrichment and identification of phosphopeptides in real biological samples are of great significance in many aspects. Herein, Ti4+-immobilized silica hollow nanospheres were tailored via chelating with phosphonic acid groups produced from dealkylation of phosphonate ester functionalized silica hollow nanospheres, which were synthesized through a single micelle templated method with diethylphosphatoethyltriethoxysilane (DPTES) and tetramethoxysilane (TMOS) as silane precursors under neutral conditions. The characterization results of transmission electron microscopy (TEM), nitrogen sorption isotherms, FT-IR, and energy-dispersive X-ray (EDX) spectroscopy confirmed the successful preparation of Ti4+-immobilized silica hollow nanospheres (SHS-Ti; approximately 17 nm particle size), which possessed a 10 nm hollow cavity with 1.6 nm micropores on the thin shell (about 3.5 nm). Attributed to the immobilized Ti4+ and high specific area (396 m2/g), SHS-Ti was applied as a Ti4+-immobilized metal affinity chromatography (Ti-IMAC) material and showed good specificity, a low limit of detection (5 fmol), high selectivity (tryptic digestion mixture of bovine serum albumin/β-casein, 1000:1 molar ratio), high binding capacity (120 mg/g for pyridoxal 5'-phosphate), and a high binding constant (1.30 × 103 L/mg). Particularly, benefiting from the unique hollow structure with microwindows on the thin shell, a short transport path, and small mass transfer resistance, SHS-Ti exhibited excellent enrichment speed in which both phosphopeptide loading and elution could be completed in 1 min. The 5298 unique phosphopeptides from 1618 unique phosphoproteins were identified after enrichment by SHS-Ti from 100 μg Jurkat cell lysates within three independent replicates. The results showed that SHS-Ti could be utilized as a novel and promising enrichment probe for phosphopeptide characterization in MS-based phosphoproteomics and related fields.
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Affiliation(s)
- Xiaowei Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shujuan Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Ruizhi Tang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Junjie Ou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Design and fabrication of reusable core–shell composite microspheres based on nanodiamond for selective enrichment of phosphopeptides. Mikrochim Acta 2022; 189:124. [DOI: 10.1007/s00604-022-05234-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/16/2022] [Indexed: 10/19/2022]
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18
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Zhu T, Gu Q, Liu Q, Zou X, Zhao H, Zhang Y, Pu C, Lan M. Nanostructure stable hydrophilic hierarchical porous metal-organic frameworks for highly efficient enrichment of glycopeptides. Talanta 2021; 240:123193. [PMID: 34979462 DOI: 10.1016/j.talanta.2021.123193] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 12/22/2022]
Abstract
Protein glycosylation plays a vital role in many physiological activities in organisms. Due to the low abundance of glycopeptides and the interference of numerous non-glycopeptides in biological samples, selective enrichment of glycopeptides is of great significance for their successful identification. Metal organic frameworks (MOFs) materials are appropriate for glycopeptides enrichment by virtue of their large specific surface area and outstanding hydrophilic properties. However, the instability of hydrophilic MOFs in acidic solutions have severely limited their applications. In this work, a rational facile strategy was established to synthesize a stable hydrophilic hierarchical porous MOF (denoted as HP-MOF-Arg@mSiO2). This new material improved the selectivity and sensitivity of enrichment for glycopeptides via modification of arginine groups. More importantly, the mesoporous silica layer was introduced to enhance the stability of MOFs in aqueous solution and achieve the size exclusion effect of large-size proteins in complex samples. Overall, owing to the unique hierarchical porous and the hydrophilic modification, the synthesized HP-MOF-Arg@mSiO2 materials showed excellent hydrophilicity and hydrolytic stability, resulting in outstanding specific separation capacity in glycopeptides enrichment. A total of 521 and 342 glycopeptides were respectively captured from 2 μL human serum digests and mouse testis tissue digests, revealing the potential of the materials in the study of glycoproteomics in complex biological samples.
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Affiliation(s)
- Tianyi Zhu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Qinying Gu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Qiannan Liu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xia Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Hongli Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China.
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Chenlu Pu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China; Research Center of Analysis and Test, East China University of Science and Technology, Shanghai, 200237, PR China.
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19
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Li Z, Li S, Luo M, Jhong JH, Li W, Yao L, Pang Y, Wang Z, Wang R, Ma R, Yu J, Huang Y, Zhu X, Cheng Q, Feng H, Zhang J, Wang C, Hsu JBK, Chang WC, Wei FX, Huang HD, Lee TY. dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications. Nucleic Acids Res 2021; 50:D471-D479. [PMID: 34788852 PMCID: PMC8728263 DOI: 10.1093/nar/gkab1017] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 01/02/2023] Open
Abstract
Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version. Due to the increasing number of studies on the mechanism of PTMs in the past few years, a great deal of upstream regulatory proteins of PTM substrate sites have been revealed. The updated dbPTM thus collates regulatory information from databases and literature, and merges them into a protein-protein interaction network. To enhance the understanding of the association between PTMs and molecular functions/cellular processes, the functional annotations of PTMs are curated and integrated into the database. In addition, the existing PTM-related resources, including annotation databases and prediction tools are also renewed. Overall, in this update, we would like to provide users with the most abundant data and comprehensive annotations on PTMs of proteins. The updated dbPTM is now freely accessible at https://awi.cuhk.edu.cn/dbPTM/.
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Affiliation(s)
- Zhongyan Li
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen 518172, China.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Shangfu Li
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Mengqi Luo
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Jhih-Hua Jhong
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Wenshuo Li
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Lantian Yao
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yuxuan Pang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Zhuo Wang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Rulan Wang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Renfei Ma
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Jinhan Yu
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yuqi Huang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Xiaoning Zhu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Qifan Cheng
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Hexiang Feng
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Jiahong Zhang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chunxuan Wang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Justin Bo-Kai Hsu
- Department of Medical Research, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Wen-Chi Chang
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan 701, Taiwan
| | - Feng-Xiang Wei
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen 518172, China.,Department of Cell Biology, Jiamusi University, Jiamusi 154007, China.,Shenzhen Children's Hospital of China Medical University, Shenzhen 518172, China
| | - Hsien-Da Huang
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen 518172, China.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Tzong-Yi Lee
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
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20
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Chen Y, Fang Z, Zhou J, Qin H, Ye M. Mirror-Cutting-Based Digestion Strategy Enables the In-Depth and Accuracy Characterization of N-Linked Protein Glycosylation. J Proteome Res 2021; 20:4948-4958. [PMID: 34636569 DOI: 10.1021/acs.jproteome.1c00333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
N-linked glycosylation plays important roles in multiple physiological and pathological processes, while the analysis coverage is still limited due to the insufficient digestion of glycoproteins, as well as incomplete ion fragments for intact glycopeptide determination. Herein, a mirror-cutting-based digestion strategy was proposed by combining two orthogonal proteases of LysargiNase and trypsin to characterize the macro- and micro-heterogeneity of protein glycosylation. Using the above two proteases, the b- or y-ion series of peptide sequences were, respectively, enhanced in MS/MS, generating the complementary spectra for peptide sequence identification. More than 27% (489/1778) of the site-specific glycoforms identified by LysargiNase digestion were not covered by trypsin digestion, suggesting the elevated coverage of protein sequences and site-specific glycoforms by the mirror-cutting method. Totally, 10,935 site-specific glycoforms were identified from mouse brain tissues in the 18 h MS analysis, which significantly enhanced the coverage of protein glycosylation. Intriguingly, 27 mannose-6-phosphate (M6P) glycoforms were determined with core fucosylation, and 23 of them were found with the "Y-HexNAc-Fuc" ions after manual checking. This is hitherto the first report of M6P and fucosylation co-modifications of glycopeptides, in which the mechanism and function still needs further exploration. The mirror-cutting digestion strategy also has great application potential in the exploration of missing glycoproteins from other complex samples to provide rich resources for glycobiology research.
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Affiliation(s)
- Yao Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahua Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
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21
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Tabang DN, Cui Y, Tremmel DM, Ford M, Li Z, Sackett SD, Odorico JS, Li L. Analysis of pancreatic extracellular matrix protein post-translational modifications via electrostatic repulsion-hydrophilic interaction chromatography coupled with mass spectrometry. Mol Omics 2021; 17:652-664. [PMID: 34318855 PMCID: PMC8511275 DOI: 10.1039/d1mo00104c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The pancreas is a vital organ with digestive and endocrine roles, and diseases of the pancreas affect millions of people yearly. A better understanding of the pancreas proteome and its dynamic post-translational modifications (PTMs) is necessary to engineer higher fidelity tissue analogues for use in transplantation. The extracellular matrix (ECM) has major roles in binding and signaling essential to the viability of insulin-producing islets of Langerhans. To characterize PTMs in the pancreas, native and decellularized tissues from four donors were analyzed. N-Glycosylated and phosphorylated peptides were simultaneously enriched via electrostatic repulsion-hydrophilic interaction chromatography and analyzed with mass spectrometry, maximizing PTM information from one workflow. A modified surfactant and chaotropic agent assisted sequential extraction/on-pellet digestion was used to maximize solubility of the ECM. The analysis resulted in the confident identification of 3650 proteins, including 517 N-glycoproteins and 148 phosphoproteins. We identified 214 ECM proteins, of which 99 were N-glycosylated, 18 were phosphorylated, and 9 were found to have both modifications. Collagens, a major component of the ECM, were the most highly glycosylated of the ECM proteins and several were also heavily phosphorylated, raising the possibility of structural and thus functional changes resulting from these modifications. To our knowledge, this work represents the first characterization of PTMs in pancreatic ECM proteins. This work provides a basal profile of PTMs in the healthy human pancreatic ECM, laying the foundation for future investigations to determine disease-specific changes such as in diabetes and pancreatic cancer, and potentially helping to guide the development of tissue replacement constructs. Data are available via ProteomeXchange with identifier PXD025048.
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Affiliation(s)
- Dylan Nicholas Tabang
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
| | - Daniel M Tremmel
- Department of Surgery, Division of Transplantation, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Megan Ford
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zihui Li
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
| | - Sara Dutton Sackett
- Department of Surgery, Division of Transplantation, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jon S Odorico
- Department of Surgery, Division of Transplantation, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
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22
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[Recent advances in glycopeptide enrichment and mass spectrometry data interpretation approaches for glycoproteomics analyses]. Se Pu 2021; 39:1045-1054. [PMID: 34505426 PMCID: PMC9404232 DOI: 10.3724/sp.j.1123.2021.06011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
蛋白质糖基化是生物体内最重要的翻译后修饰之一,在蛋白质稳定性、细胞内和细胞间信号转导、激素活化或失活和免疫调节等生理过程和病理进程中发挥重要作用。而异常的蛋白质糖基化往往和多种疾病的发生发展密切相关,目前应用于临床检测的多种肿瘤生物标志物大多属于糖蛋白或者糖抗原。因此在组学层次系统分析蛋白质糖基化的变化对阐明生物体内糖基化修饰的调控机理和发现新型疾病标志物都非常重要。基于质谱的蛋白质组学技术为全面分析蛋白质及其修饰提供了有效的分析手段。在自下而上的蛋白质组学研究中,由于完整糖基化肽段同时存在性质各异的肽段骨架和糖链结构、糖肽的相对丰度和离子化效率较低以及糖基化修饰有高度异质性等特点,完整糖肽的分析比其他翻译后修饰更加困难。近年来,为了更全面、系统地分析蛋白质糖基化,研究人员发展了一些新技术,包括完整糖肽的富集技术、质谱的碎裂模式和数据采集模式、质谱数据的解析方法和定量策略等等,大力推进了该领域的研究水平,也为研究蛋白质糖基化相关的生物标志物提供了技术支持。该篇综述主要关注近年来基于质谱的糖蛋白质组学研究中的新进展,重点介绍针对完整N-和O-糖基化肽段的富集新技术和谱图解析新方法,并讨论其在肿瘤早期诊断方面的应用潜力。
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23
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Huang J, Liu X, Wang D, Cui Y, Shi X, Dong J, Ye M, Li L. Dual-Functional Ti(IV)-IMAC Material Enables Simultaneous Enrichment and Separation of Diverse Glycopeptides and Phosphopeptides. Anal Chem 2021; 93:8568-8576. [PMID: 34100586 PMCID: PMC8245321 DOI: 10.1021/acs.analchem.1c01324] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Simultaneous enrichment and fractionation of diverse proteins/peptides possessing different post-translational modifications (PTMs) from the same biological samples is highly desirable to reduce sample consumption, avoid complicated sample processing, and enable studies of potential crosstalks between different PTMs. In this work, we report a new approach to enable simultaneous enrichment and separation of glycopeptides, phosphopeptides, and mannose-6-phosphate (M6P) glycopeptides by using a dual-functional Ti(IV)-IMAC material. Moreover, we also made the separation of neutral and sialyl glycopeptides and mono- and multi-phosphopeptides possible by performing different elution processes according to the differences in their electrostatic or hydrophilic properties. These separations are effective and efficient to eliminate the signal suppression from neutral glycopeptides for sialyl glycopeptide detection, allowing separation of mono-phosphopeptides from multi-phosphopeptides, as well as detection of M6P glycopeptides that are free from the abovementioned modifications. This new strategy significantly improves the coverage and identification numbers of glycopeptides, phosphopeptides, and M6P glycopeptides by 1.9, 2.3, and 4.3-fold compared with the conventional method, respectively. This is the first report on simultaneous enrichment and separation of neutral and sialyl glycopeptides, mono- and multi-phosphopeptides, and M6P glycopeptides via dual-functional Ti(IV)- IMAC, revealing novel insights into potential crosstalk among these important PTMs.
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Affiliation(s)
- Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Xiaoyan Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Danqing Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Xudong Shi
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jing Dong
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Mingliang Ye
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA
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24
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Simultaneous enrichment and separation of neutral and sialyl glycopeptides of SARS-CoV-2 spike protein enabled by dual-functionalized Ti-IMAC material. Anal Bioanal Chem 2021; 413:7295-7303. [PMID: 34155551 PMCID: PMC8216326 DOI: 10.1007/s00216-021-03433-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a serious threat to human health all over the world. The development of effective vaccines has been focusing on the spike (S) glycoprotein, which mediates viral invasion to human cells through its interaction with the angiotensin-converting enzyme 2 (ACE2) receptor. In this work, we perform analytical characterization of N- and O-linked glycosylation of the SARS-CoV-2 S glycoprotein. We explore the novel use of dual-functionalized titanium (IV)-immobilized metal affinity chromatography (Ti-IMAC) material for simultaneous enrichment and separation of neutral and sialyl glycopeptides of a recombinant SARS-CoV-2 S glycoprotein from HEK293 cells. This strategy helps eliminate signal suppression from neutral glycopeptides for the detection of sialyl glycopeptides and improves the glycoform coverage of the S protein. We profiled 19 of its 22 potential N-glycosylated sites with 398 unique glycoforms using the dual-functional Ti-IMAC approach, which exhibited improvement of coverage by 1.6-fold compared to the conventional hydrophilic interaction chromatography (HILIC) glycopeptide enrichment method. We also identified O-linked glycosylation site that was not found using the conventional HILIC approach. In addition, we reported on the identification of mannose-6-phosphate (M6P) glycosylation, which substantially expands the current knowledge of the spike protein's glycosylation landscape and enables future investigation into the influence of M6P glycosylation of the spike protein on its cell entry.
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25
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Yue X, Qin H, Chen Y, Fang Z, Liu L, Zhu H, Liu X, Zhou J, Tian K, Qiao X, Ye M. Highly Efficient Enrichment of O-GalNAc Glycopeptides by Using Immobilized Metal Ion Affinity Chromatography. Anal Chem 2021; 93:7579-7587. [PMID: 34009939 DOI: 10.1021/acs.analchem.0c05236] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Proteomics analysis of O-GalNAc glycosylation is important for the screening of biomarkers and the assessment of therapeutic responses. However, its analysis still faces challenges due to the poor performance of currently available enrichment methods. In this study, an enrichment method was established on the basis of Ti-IMAC(IV) materials, which could enrich the intact O-GalNAc glycopeptides via both the hydrophilic interaction and affinity interaction. This method enabled nearly 200 intact O-GalNAc glycopeptides identified from only 0.1 μL of human serum. This was nearly 2-fold different from that of the HILIC method. An in-depth analysis of the O-GalNAc glycosylation was performed, and 2093 intact glycopeptides were identified from 7.2 μL of human serum samples. This is the largest O-GalNAc glycosylation database of human serum from a trace amount of sample. Furthermore, 52 significantly changed intact O-GalNAc glycopeptides were determined by the quantitative analysis of hepatocellular carcinoma (HCC) and control serum samples, indicating the potential applications of this enrichment method in biomarker discovery.
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Affiliation(s)
- Xuyang Yue
- College of Pharmacy, Hebei Province Key Laboratory of Analytical Science & Technology, MOE Key Laboratory of Medicinal Chemistry & Molecular Diagnosis, Hebei University, Baoding 071002, China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yao Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luyao Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - He Zhu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Jiahua Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kailu Tian
- College of Pharmacy, Hebei Province Key Laboratory of Analytical Science & Technology, MOE Key Laboratory of Medicinal Chemistry & Molecular Diagnosis, Hebei University, Baoding 071002, China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoqiang Qiao
- College of Pharmacy, Hebei Province Key Laboratory of Analytical Science & Technology, MOE Key Laboratory of Medicinal Chemistry & Molecular Diagnosis, Hebei University, Baoding 071002, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
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26
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Fan Z, Liu T, Zheng F, Qin W, Qian X. An Ultrafast N-Glycoproteome Analysis Method Using Thermoresponsive Magnetic Fluid-Immobilized Enzymes. Front Chem 2021; 9:676100. [PMID: 33981677 PMCID: PMC8107388 DOI: 10.3389/fchem.2021.676100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/06/2021] [Indexed: 12/02/2022] Open
Abstract
N-Glycosylation is one of the most common and important post-translational modification methods, and it plays a vital role in controlling many biological processes. Increasing discovery of abnormal alterations in N-linked glycans associated with many diseases leads to greater demands for rapid and efficient N-glycosylation profiling in large-scale clinical samples. In the workflow of global N-glycosylation analysis, enzymatic digestion is the main rate-limiting step, and it includes both protease digestion and peptide-N4–(N-acetyl-beta-glucosaminyl) asparagine amidase (PNGase) F deglycosylation. Prolonged incubation time is generally required because of the limited digestion efficiency of the conventional in-solution digestion method. Here, we propose novel thermoresponsive magnetic fluid (TMF)-immobilized enzymes (trypsin or PNGase F) for ultrafast and highly efficient proteome digestion and deglycosylation. Unlike other magnetic material-immobilized enzymes, TMF-immobilized enzymes display a unique temperature-triggered magnetic response behavior. At room temperature, a TMF-immobilized enzyme completely dissolves in an aqueous solution and forms a homogeneous system with a protein/peptide sample for efficient digestion but cannot be separated by magnetic force because of its excellent water dispersity. Above its lower critical solution temperature (LCST), thermoflocculation of a TMF-immobilized enzyme allows it to be easily recovered by increasing the temperature and magnetic force. Taking advantage of the unique homogeneous reaction of a TMF-immobilized enzyme, both protein digestion and glycopeptide deglycosylation can be finished within 3 min, and the whole sample processing time can be reduced by more than 20 times. The application of a TMF-immobilized enzyme in large-scale profiling of protein N-glycosylation in urine samples led to the successful identification of 2,197 N-glycopeptides and further demonstrated the potential of this strategy for fast and high-throughput analysis of N-glycoproteome in clinical samples.
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Affiliation(s)
- Zhiya Fan
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing, China
| | - Tong Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing, China
| | - Fei Zheng
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing, China
| | - Weijie Qin
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing, China.,College of Basic Medicine, Anhui Medical University, Hefei, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing, China
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27
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Chen Z, Yu Q, Yu Q, Johnson J, Shipman R, Zhong X, Huang J, Asthana S, Carlsson C, Okonkwo O, Li L. In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease. Mol Cell Proteomics 2021; 20:100081. [PMID: 33862227 PMCID: PMC8724636 DOI: 10.1016/j.mcpro.2021.100081] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 01/22/2023] Open
Abstract
As the body fluid that directly interchanges with the extracellular fluid of the central nervous system (CNS), cerebrospinal fluid (CSF) serves as a rich source for CNS-related disease biomarker discovery. Extensive proteome profiling has been conducted for CSF, but studies aimed at unraveling site-specific CSF N-glycoproteome are lacking. Initial efforts into site-specific N-glycoproteomics study in CSF yield limited coverage, hindering further experimental design of glycosylation-based disease biomarker discovery in CSF. In the present study, we have developed an N-glycoproteomic approach that combines enhanced N-glycopeptide sequential enrichment by hydrophilic interaction chromatography (HILIC) and boronic acid enrichment with electron transfer and higher-energy collision dissociation (EThcD) for large-scale intact N-glycopeptide analysis. The application of the developed approach to the analyses of human CSF samples enabled identifications of a total of 2893 intact N-glycopeptides from 511 N-glycosites and 285 N-glycoproteins. To our knowledge, this is the largest site-specific N-glycoproteome dataset reported for CSF to date. Such dataset provides molecular basis for a better understanding of the structure-function relationships of glycoproteins and their roles in CNS-related physiological and pathological processes. As accumulating evidence suggests that defects in glycosylation are involved in Alzheimer's disease (AD) pathogenesis, in the present study, a comparative in-depth N-glycoproteomic analysis was conducted for CSF samples from healthy control and AD patients, which yielded a comparable N-glycoproteome coverage but a distinct expression pattern for different categories of glycoforms, such as decreased fucosylation in AD CSF samples. Altered glycosylation patterns were detected for a number of N-glycoproteins including alpha-1-antichymotrypsin, ephrin-A3 and carnosinase CN1 etc., which serve as potentially interesting targets for further glycosylation-based AD study and may eventually lead to molecular elucidation of the role of glycosylation in AD progression.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Jillian Johnson
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Richard Shipman
- Department of Applied Science, University of Wisconsin-Stout, Menomonie, Wisconsin, USA
| | - Xiaofang Zhong
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Sanjay Asthana
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Cynthia Carlsson
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Ozioma Okonkwo
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA; School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA.
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28
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Application of Molecular Imprinting Technology in Post-translational Modified Protein Enrichment. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2021. [DOI: 10.1016/s1872-2040(20)60071-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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29
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Hydrophilic polydopamine-derived mesoporous channels for loading Ti(IV) ions for salivary phosphoproteome research. Anal Chim Acta 2020; 1146:53-60. [PMID: 33461719 DOI: 10.1016/j.aca.2020.12.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/21/2020] [Accepted: 12/18/2020] [Indexed: 11/20/2022]
Abstract
Salivary phosphoproteome holds great promise in clinic diagnosis. For profiling of salivary phosphoproteome, it is essential to develop efficient enrichment methods prior to mass spectrum (MS). Among developed enrichment strategies, immobilized metal ions affinity chromatography (IMAC) has exhibited outstanding performance. In this work, we report a coherent approach where polydopamine (PDA) is first utilized to form mesoporous structure through soft templating method, then chelated with Ti4+ to construct hydrophilic polydopamine-derived magnetic mesoporous nanocomposite (denoted Fe3O4@mPDA@Ti4+). In virtue of the merits including ordered mesoporous channels, appropriate superparamagnetism, and abundant Ti4+, the enrichment strategy based on Fe3O4@mPDA@Ti4+ combined with MS is employed for accurate identification of phosphopeptides in β-casein digest and human saliva. As expected, Fe3O4@mPDA@Ti4+ revealed a great selectivity (1:200) and a low detection limit (0.1 fmol μL-1) toward phosphopeptides. More importantly, the further successful capture of phosphopeptides from human saliva indicated the prominent potential of this method for seeking phosphopeptide biomarkers in further analysis.
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30
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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31
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Tang R, Yu Y, Dong J, Yao Y, Ma S, Ou J, Ye M. Facile preparation of bifunctional adsorbents for efficiently enriching N-glycopeptides and phosphopeptides. Anal Chim Acta 2020; 1144:111-120. [PMID: 33453787 DOI: 10.1016/j.aca.2020.12.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 01/23/2023]
Abstract
In bottom-up strategy, specific enrichment of glycopeptides and phosphopeptides from complicated biological samples is a prerequisite for efficient identifying glycosylation and phosphorylation by mass spectrometry. Although there were a plethora of materials used as either hydrophilic interaction liquid chromatography (HILIC) or immobilized metal affinity chromatography (IMAC) adsorbents, even several bifunctional materials for simultaneous enrichment of glycopeptides and phosphopeptides, most of them are not easily commercialized as many other well-performing adsorbents due to the complicated preparation process. In our case, a one-step modification strategy was developed to prepare bifunctional adsorbents for HILIC and IMAC, employing O-phospho-l-serine as the modifier and poly(GMA-co-EDMA) microspheres, a kind of macroporous adsorption resin (MAR) with epoxy groups, as the matrix. The MARs were directly modified with O-phospho-l-serine under facile condition for HILIC strategy and further chelated with Ti4+ for IMAC strategy. A total of 522 unique N-glycopeptides and 442 unique N-glycosylation sites mapped to 275 N-glycoproteins was identified from HeLa cell proteins, showing excellent enrichment efficiency in HILIC. Additionally, 3141 unique phosphopeptides were unambiguously identified from 200 μg of digest of HeLa cell proteins, demonstrating great enrichment efficiency in IMAC. Moreover, these materials have been successfully applied in the analysis of multiple biological samples including human serum and milk, demonstrating their feasibility for real sample applications and potential business value.
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Affiliation(s)
- Ruizhi Tang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yang Yu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Dong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yating Yao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Shujuan Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Junjie Ou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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32
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Arribas Diez I, Govender I, Naicker P, Stoychev S, Jordaan J, Jensen ON. Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment. J Proteome Res 2020; 20:453-462. [PMID: 33226818 DOI: 10.1021/acs.jproteome.0c00508] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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.
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Affiliation(s)
- Ignacio Arribas Diez
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Ireshyn Govender
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa
| | - Previn Naicker
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa
| | - Stoyan Stoychev
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa.,ReSyn Biosciences, Pretoria 1610, Gauteng, South Africa
| | - Justin Jordaan
- ReSyn Biosciences, Pretoria 1610, Gauteng, South Africa.,Rhodes University, Grahamstown 6139, South Africa
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M DK-5230, Denmark
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