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Huang P, Zhang H, Liu Y, Li L. Rapid Characterization of Phospholipids from Biological Matrix Enabled by Indium Tin Oxide (ITO) Coated Slide Assisted Enrichment MALDI Mass Spectrometry. ANALYSIS & SENSING 2024; 4:e202300097. [PMID: 39309316 PMCID: PMC11415247 DOI: 10.1002/anse.202300097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Indexed: 09/25/2024]
Abstract
Lipidomic analysis of human serum is essential to monitor the individual's health status. Herein, we develop a facile strategy for rapid characterization of phospholipids in human serum via indium tin oxide (ITO) coated glass slide solid phase extraction MALDI mass spectrometry (ITO-SPE-MALDI-MS). Phospholipid species are retained on ITO slide via solid phase extraction owing to the unique property of the ITO material; the measurement of phospholipid species from 1 μl human serum within 2 min is achievable. A comparison of ITO-SPE strategy with conventional extraction methods was further carried out using liquid chromatography-mass spectrometry (LC-MS) and ion-mobility mass spectrometry (IM-MS), resulting in a comparable enrichment performance for the phospholipid analysis. Furthermore, rapid lipidomic profiling of serum samples from human colorectal cancer patients and cell lines was demonstrated. Our results indicate that ITO-SPE-MALDI-MS provides a higher throughput strategy for the analysis of phospholipid species in complex biological mixtures, showcasing its potential for applications in the analysis of clinical biofluids.
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Affiliation(s)
- Penghsuan Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 (USA)
| | - Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI 53705 (USA)
| | - Yuan Liu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI 53705 (USA)
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 (USA)
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI 53705 (USA)
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2
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Cheng S, Altmeppen G, So C, Welp LM, Penir S, Ruhwedel T, Menelaou K, Harasimov K, Stützer A, Blayney M, Elder K, Möbius W, Urlaub H, Schuh M. Mammalian oocytes store mRNAs in a mitochondria-associated membraneless compartment. Science 2022; 378:eabq4835. [PMID: 36264786 DOI: 10.1126/science.abq4835] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Full-grown oocytes are transcriptionally silent and must stably maintain the messenger RNAs (mRNAs) needed for oocyte meiotic maturation and early embryonic development. However, where and how mammalian oocytes store maternal mRNAs is unclear. Here, we report that mammalian oocytes accumulate mRNAs in a mitochondria-associated ribonucleoprotein domain (MARDO). MARDO assembly around mitochondria was promoted by the RNA-binding protein ZAR1 and directed by an increase in mitochondrial membrane potential during oocyte growth. MARDO foci coalesced into hydrogel-like matrices that clustered mitochondria. Maternal mRNAs stored in the MARDO were translationally repressed. Loss of ZAR1 disrupted the MARDO, dispersed mitochondria, and caused a premature loss of MARDO-localized mRNAs. Thus, a mitochondria-associated membraneless compartment controls mitochondrial distribution and regulates maternal mRNA storage, translation, and decay to ensure fertility in mammals.
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Affiliation(s)
- Shiya Cheng
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Gerrit Altmeppen
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Chun So
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sarah Penir
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Torben Ruhwedel
- Electron Microscopy City Campus, Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Katerina Menelaou
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Bourn Hall Clinic, Cambridge, UK
| | - Katarina Harasimov
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Alexandra Stützer
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | | | | | - Wiebke Möbius
- Electron Microscopy City Campus, Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Melina Schuh
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
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3
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Bijttebier S, Theunis C, Jahouh F, Martins DR, Verhemeldonck M, Grauwen K, Dillen L, Mercken M. Development of immunoprecipitation - two-dimensional liquid chromatography - mass spectrometry methodology as biomarker read-out to quantify phosphorylated tau in cerebrospinal fluid from Alzheimer disease patients. J Chromatogr A 2021; 1651:462299. [PMID: 34107398 DOI: 10.1016/j.chroma.2021.462299] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/17/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
In Alzheimer's disease (AD) brain, one of the histopathological hallmarks is the neurofibrillary tangles consisting of aggregated and hyperphosphorylated tau. Currently many tau binding antibodies are under development to target the extracellular species responsible for the spreading of the disease in the brain. As such, an in-house developed antibody JNJ-63733657 with picomolar affinity towards tau phosphorylated at both T212 and T217 (further named p217+tau) was recently tested in phase I clinical trial NCT03375697. Following multiple dose administration in healthy subjects and subjects with AD, there were dose dependant reductions in free p217+tau fragments in cerebrospinal fluid (CSF) following antibody administration, as measured with a novel single molecule ELISA assay (Simoa PT3 x PT82 assay), demonstrating epitope engagement of the therapeutic antibody [Galpern, Haeverans, Janssens, Triana-Baltzer, Kolb, Li, Nandy, Mercken, Van Kolen, Sun, Van Nueten, 2020]. Total p217+tau levels also were reduced in CSF as measured with the Simoa PT3 x PT82 assay. In this study we developed an orthogonal immunoprecipitation - liquid chromatography - triple quadrupole mass spectrometry (IP-LC-TQMS) assay to verify the observed reductions in total p217+ tau levels. In this assay, an excess of JNJ-63733657 is added to the clinical CSF to ensure all p217+tau is bound by the antibody instead of having a pool of bound and unbound antigen and to immunoprecipitate all p217+tau, which is followed by on-bead digestion with trypsin to release surrogate peptides. Tryptic peptides with missed cleavages were monitored when phosphorylation occurred close to the cleavage site as this induced miscleavages. Compared with acidified mobile phases typically used for peptide analysis, reversed phase LC with mobile phase at basic pH resulted in sharper peaks and improved selectivity and sensitivity for the target peptides. With this setup a diphospho-tau tryptic peptide SRTPSLPTPPTREPK*2 could be measured with pT217 accounting for at least one of the phospho-sites. This is the first time that the presence of a diphopsho-tau peptide is reported to be present in human CSF. A two-dimensional LC-TQMS method was developed to remove matrix interferences. Selective trapping of diphospho-peptides via a metal oxide chromatography mechanism was achieved in a first dimension with a conventional reversed phase stationary phase and acidified mobile phase. Subsequent elution at basic pH enabled detection of low picomolar p217+tau levels in human CSF (lower limit of quantification: 2 pM), resulting in an approximate 5-fold increase in sensitivity. This enabled the quantification of total p217+tau in CSF leading to the confirmation that in addition to reductions in free p217+tau levels total p217+tau levels were also reduced following administration of the tau mAb JNJ-63733657, correlating with the previous measurement with the PT3 x PT82 Simoa assay. An orthogonal sample clean-up using offline TiO2/ZrO2 combined with 1DLC-TQMS was developed to confirm the presence of mono-ptau (pT217) tryptic peptides in CSF.
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Affiliation(s)
| | - Clara Theunis
- R&D Neurosciences, Janssen Pharmaceutica, Turnhoutseweg 30, Beerse, Belgium.
| | - Farid Jahouh
- DMPK, Janssen Pharmaceutica, Turnhoutseweg 30, Beerse, Belgium.
| | | | | | - Karolien Grauwen
- R&D Neurosciences, Janssen Pharmaceutica, Turnhoutseweg 30, Beerse, Belgium.
| | - Lieve Dillen
- DMPK, Janssen Pharmaceutica, Turnhoutseweg 30, Beerse, Belgium.
| | - Marc Mercken
- R&D Neurosciences, Janssen Pharmaceutica, Turnhoutseweg 30, Beerse, Belgium.
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Li J, Zhan X. Mass spectrometry-based proteomics analyses of post-translational modifications and proteoforms in human pituitary adenomas. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140584. [PMID: 33321259 DOI: 10.1016/j.bbapap.2020.140584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022]
Abstract
Pituitary adenoma (PA) is a common intracranial neoplasm, which affects the hypothalamus-pituitary-target organ axis systems, and is hazardous to human health. Post-translational modifications (PTMs), including phosphorylation, ubiquitination, nitration, and sumoylation, are vitally important in the PA pathogenesis. The large-scale analysis of PTMs could provide a global view of molecular mechanisms for PA. Proteoforms, which are used to define various protein structural and functional forms originated from the same gene, are the future direction of proteomics research. The global studies of different proteoforms and PTMs of hypophyseal hormones such as growth hormone (GH) and prolactin (PRL) and the proportion change of different GH proteoforms or PRL proteoforms in human pituitary tissue could provide new insights into the clinical value of pituitary hormones in PAs. Multiple quantitative proteomics methods, including mass spectrometry (MS)-based label-free and stable isotope-labeled strategies in combination with different PTM-peptide enrichment methods such as TiO2 enrichment of tryptic phosphopeptides and antibody enrichment of other PTM-peptides increase the feasibility for researchers to study PA proteomes. This article reviews the research status of PTMs and proteoforms in PAs, including the enrichment method, technical limitation, quantitative proteomics strategies, and the future perspectives, to achieve the goals of in-depth understanding its molecular pathogenesis, and discovering effective biomarkers and clinical therapeutic targets for predictive, preventive, and personalized treatment of PA patients.
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Affiliation(s)
- Jiajia Li
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, Shandong 250117, P. R. China; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 P. R. China; State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Xianquan Zhan
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, Shandong 250117, P. R. China; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 P. R. China; State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China; Department of Oncology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China.
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5
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Qiu W, Evans CA, Landels A, Pham TK, Wright PC. Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials. Anal Chim Acta 2020; 1129:158-180. [PMID: 32891386 DOI: 10.1016/j.aca.2020.04.053] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022]
Abstract
Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.
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Affiliation(s)
- Wen Qiu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China
| | - Caroline A Evans
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Andrew Landels
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Trong Khoa Pham
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom.
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6
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Dziomba S, Pawelec A, Ciura K, Dolegowska M, Klimowska A, Rodzaj W, Guerrouache M, Carbonnier B, Wielgomas B. Low-cost and green dispersive solid phase extraction of hydrophilic compounds using titanium dioxide nanoparticles. Microchem J 2019. [DOI: 10.1016/j.microc.2018.11.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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7
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Dunn J, Ferluga S, Sharma V, Futschik M, Hilton DA, Adams CL, Lasonder E, Hanemann CO. Proteomic analysis discovers the differential expression of novel proteins and phosphoproteins in meningioma including NEK9, HK2 and SET and deregulation of RNA metabolism. EBioMedicine 2018; 40:77-91. [PMID: 30594554 PMCID: PMC6412084 DOI: 10.1016/j.ebiom.2018.12.048] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 12/26/2022] Open
Abstract
Background Meningioma is the most frequent primary intracranial tumour. Surgical resection remains the main therapeutic option as pharmacological intervention is hampered by poor knowledge of their proteomic signature. There is an urgent need to identify new therapeutic targets and biomarkers of meningioma. Methods We performed proteomic profiling of grade I, II and III frozen meningioma specimens and three normal healthy human meninges using LC-MS/MS to analyse global proteins, enriched phosphoproteins and phosphopeptides. Differential expression and functional annotation of proteins was completed using Perseus, IPA® and DAVID. We validated differential expression of proteins and phosphoproteins by Western blot on a meningioma validation set and by immunohistochemistry. Findings We quantified 3888 proteins and 3074 phosphoproteins across all meningioma grades and normal meninges. Bioinformatics analysis revealed commonly upregulated proteins and phosphoproteins to be enriched in Gene Ontology terms associated with RNA metabolism. Validation studies confirmed significant overexpression of proteins such as EGFR and CKAP4 across all grades, as well as the aberrant activation of the downstream PI3K/AKT pathway, which seems differential between grades. Further, we validated upregulation of the total and activated phosphorylated form of the NIMA-related kinase, NEK9, involved in mitotic progression. Novel proteins identified and validated in meningioma included the nuclear proto-oncogene SET, the splicing factor SF2/ASF and the higher-grade specific protein, HK2, involved in cellular metabolism. Interpretation Overall, we generated a proteomic thesaurus of meningiomas for the identification of potential biomarkers and therapeutic targets. Fund This study was supported by Brain Tumour Research.
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Affiliation(s)
- Jemma Dunn
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry, John Bull Building, Plymouth Science Park, Research Way, Derriford, Plymouth PL6 8BU, UK
| | - Sara Ferluga
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry, John Bull Building, Plymouth Science Park, Research Way, Derriford, Plymouth PL6 8BU, UK
| | - Vikram Sharma
- School of Biomedical Science, Faculty of Medicine and Dentistry, University of Plymouth, Derriford Research Facility, Research Way, Derriford, Plymouth PL6 8BU, UK
| | - Matthias Futschik
- School of Biomedical Science, Faculty of Medicine and Dentistry, University of Plymouth, Derriford Research Facility, Research Way, Derriford, Plymouth PL6 8BU, UK
| | - David A Hilton
- Cellular and Anatomical Pathology, Plymouth Hospitals NHS Trust, Derriford Road, Plymouth PL6 8DH, UK
| | - Claire L Adams
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry, John Bull Building, Plymouth Science Park, Research Way, Derriford, Plymouth PL6 8BU, UK
| | - Edwin Lasonder
- School of Biomedical Science, Faculty of Medicine and Dentistry, University of Plymouth, Derriford Research Facility, Research Way, Derriford, Plymouth PL6 8BU, UK
| | - C Oliver Hanemann
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry, John Bull Building, Plymouth Science Park, Research Way, Derriford, Plymouth PL6 8BU, UK.
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8
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Arrington JV, Hsu CC, Elder SG, Andy Tao W. Recent advances in phosphoproteomics and application to neurological diseases. Analyst 2018; 142:4373-4387. [PMID: 29094114 DOI: 10.1039/c7an00985b] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphorylation has an incredible impact on the biological behavior of proteins, altering everything from intrinsic activity to cellular localization and complex formation. It is no surprise then that this post-translational modification has been the subject of intense study and that, with the advent of faster, more accurate instrumentation, the number of large-scale mass spectrometry-based phosphoproteomic studies has swelled over the past decade. Recent developments in sample preparation, phosphorylation enrichment, quantification, and data analysis strategies permit both targeted and ultra-deep phosphoproteome profiling, but challenges remain in pinpointing biologically relevant phosphorylation events. We describe here technological advances that have facilitated phosphoproteomic analysis of cells, tissues, and biofluids and note applications to neuropathologies in which the phosphorylation machinery may be dysregulated, much as it is in cancer.
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9
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Ahmed A, Raja VJ, Cavaliere P, Dephoure N. Robust, Reproducible, and Economical Phosphopeptide Enrichment Using Calcium Titanate. J Proteome Res 2018; 18:1411-1417. [DOI: 10.1021/acs.jproteome.8b00883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adnan Ahmed
- Department of Biochemistry, Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, New York 10021, United States
| | - Vijay J. Raja
- Department of Biochemistry, Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, New York 10021, United States
| | - Paola Cavaliere
- Department of Biochemistry, Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, New York 10021, United States
| | - Noah Dephoure
- Department of Biochemistry, Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, New York 10021, United States
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10
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Inomata T, Baslam M, Masui T, Koshu T, Takamatsu T, Kaneko K, Pozueta-Romero J, Mitsui T. Proteomics Analysis Reveals Non-Controlled Activation of Photosynthesis and Protein Synthesis in a Rice npp1 Mutant under High Temperature and Elevated CO₂ Conditions. Int J Mol Sci 2018; 19:ijms19092655. [PMID: 30205448 PMCID: PMC6165220 DOI: 10.3390/ijms19092655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 11/26/2022] Open
Abstract
Rice nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) catalyzes the hydrolytic breakdown of the pyrophosphate and phosphodiester bonds of a number of nucleotides including ADP-glucose and ATP. Under high temperature and elevated CO2 conditions (HT + ECO2), the npp1 knockout rice mutant displayed rapid growth and high starch content phenotypes, indicating that NPP1 exerts a negative effect on starch accumulation and growth. To gain further insight into the mechanisms involved in the NPP1 downregulation induced starch overaccumulation, in this study we conducted photosynthesis, leaf proteomic, and chloroplast phosphoproteomic analyses of wild-type (WT) and npp1 plants cultured under HT + ECO2. Photosynthesis in npp1 leaves was significantly higher than in WT. Additionally, npp1 leaves accumulated higher levels of sucrose than WT. The proteomic analyses revealed upregulation of proteins related to carbohydrate metabolism and the protein synthesis system in npp1 plants. Further, our data indicate the induction of 14-3-3 proteins in npp1 plants. Our finding demonstrates a higher level of protein phosphorylation in npp1 chloroplasts, which may play an important role in carbohydrate accumulation. Together, these results offer novel targets and provide additional insights into carbohydrate metabolism regulation under ambient and adverse conditions.
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Affiliation(s)
- Takuya Inomata
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
| | - Marouane Baslam
- Department of Biochemistry, Niigata University, Niigata 950-218, Japan.
| | - Takahiro Masui
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
| | - Tsutomu Koshu
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
| | - Takeshi Takamatsu
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
- Department of Biochemistry, Niigata University, Niigata 950-218, Japan.
| | - Kentaro Kaneko
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
| | - Javier Pozueta-Romero
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Mutiloako Etorbidea Zenbaki Gabe, 31192 Mutiloabeti, Nafarroa, Spain.
| | - Toshiaki Mitsui
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
- Department of Biochemistry, Niigata University, Niigata 950-218, Japan.
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11
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Dekker LJM, Zeneyedpour L, Snoeijers S, Joore J, Leenstra S, Luider TM. Determination of Site-Specific Phosphorylation Ratios in Proteins with Targeted Mass Spectrometry. J Proteome Res 2018; 17:1654-1663. [PMID: 29457462 DOI: 10.1021/acs.jproteome.7b00911] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We show that parallel reaction monitoring (PRM) can be used for exact quantification of phosphorylation ratios of proteins using stable-isotope-labeled peptides. We have compared two different PRM approaches on a digest of a U87 cell culture, namely, direct-PRM (tryptic digest measured by PRM without any further sample preparation) and TiO2-PRM (tryptic digest enriched with TiO2 cartridges, followed by PRM measurement); these approaches are compared for the following phosphorylation sites: neuroblast differentiation-associated protein (AHNAK S5480-p), calcium/calmodulin-dependent protein kinase type II subunit delta (CAMK2D T337-p), and epidermal growth factor receptor (EGFR S1166-p). A reproducible percentage of phosphorylation could be determined (CV 6-13%) using direct-PRM or TiO2-PRM. In addition, we tested the approaches in a cell culture experiment in which U87 cells were deprived of serum. As a "gold standard" we included immune precipitation of EGFR followed by PRM (IP-PRM). For EGFR (S1166) and AHNAK (S5480) a statistical significant change in the percentage of phosphorylation could be observed as a result of serum deprivation; for EGFR (S1166) this change was observed for both TiO2-PRM and IP-PRM. The presented approach has the potential to multiplex and to quantify the ratio of phosphorylation in a single analysis.
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Affiliation(s)
- Lennard J M Dekker
- Erasmus MC , Department of Neurology , Wytemaweg 80 , 3015 CN Rotterdam , The Netherlands
| | - Lona Zeneyedpour
- Erasmus MC , Department of Neurology , Wytemaweg 80 , 3015 CN Rotterdam , The Netherlands
| | | | - Jos Joore
- Pepscope , Dantelaan 83 , 3533 VB Utrecht , The Netherlands
| | - Sieger Leenstra
- Erasmus MC , Department of Neurosurgery , 3015 CN Rotterdam , The Netherlands
| | - Theo M Luider
- Erasmus MC , Department of Neurology , Wytemaweg 80 , 3015 CN Rotterdam , The Netherlands
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12
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Ren L, Li C, Shao W, Lin W, He F, Jiang Y. TiO2 with Tandem Fractionation (TAFT): An Approach for Rapid, Deep, Reproducible, and High-Throughput Phosphoproteome Analysis. J Proteome Res 2017; 17:710-721. [DOI: 10.1021/acs.jproteome.7b00520] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Liangliang Ren
- State
Key Laboratory of Proteomics, National Center for Protein Sciences
(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Beijing Proteome Research Center, Beijing 102206, China
| | - Chaoying Li
- State
Key Laboratory of Proteomics, National Center for Protein Sciences
(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Beijing Proteome Research Center, Beijing 102206, China
| | - Wenli Shao
- State
Key Laboratory of Proteomics, National Center for Protein Sciences
(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Beijing Proteome Research Center, Beijing 102206, China
- Graduate
School, Anhui Medical University, Hefei 230032, China
| | - Weiran Lin
- State
Key Laboratory of Proteomics, National Center for Protein Sciences
(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Beijing Proteome Research Center, Beijing 102206, China
| | - Fuchu He
- State
Key Laboratory of Proteomics, National Center for Protein Sciences
(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Beijing Proteome Research Center, Beijing 102206, China
| | - Ying Jiang
- State
Key Laboratory of Proteomics, National Center for Protein Sciences
(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Beijing Proteome Research Center, Beijing 102206, China
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BAE SW, KIM JI, CHOI I, SUNG J, HONG JI, YEO WS. Zinc Ion-immobilized Magnetic Microspheres for Enrichment and Identification of Multi-phosphorylated Peptides by Mass Spectrometry. ANAL SCI 2017; 33:1381-1386. [DOI: 10.2116/analsci.33.1381] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Se Won BAE
- Green Chemistry and Materials Group, Korea Institute of Industrial Technology (KITECH)
| | - Jae Il KIM
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University
| | - Inseong CHOI
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University
| | - Jiha SUNG
- Department of Applied Chemistry, Dongduk Women’s University
| | - Jong-In HONG
- Department of Chemistry, Seoul National University
| | - Woon-Seok YEO
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University
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Improving Proteome Coverage by Reducing Sample Complexity via Chromatography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:83-143. [DOI: 10.1007/978-3-319-41448-5_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Jabeen F, Najam-ul-Haq M, Ashiq MN, Rainer M, Huck CW, Bonn GK. Gadolinium oxide: Exclusive selectivity and sensitivity in the enrichment of phosphorylated biomolecules. J Sep Sci 2016; 39:4175-4182. [DOI: 10.1002/jssc.201600651] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/20/2016] [Accepted: 08/20/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Fahmida Jabeen
- Division of Analytical Chemistry, Institute of Chemical Sciences; Bahauddin Zakariya University; Multan Pakistan
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University; Innsbruck Austria
| | - Muhammad Najam-ul-Haq
- Division of Analytical Chemistry, Institute of Chemical Sciences; Bahauddin Zakariya University; Multan Pakistan
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University; Innsbruck Austria
| | - Muhammad Naeem Ashiq
- Division of Analytical Chemistry, Institute of Chemical Sciences; Bahauddin Zakariya University; Multan Pakistan
| | - Matthias Rainer
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University; Innsbruck Austria
| | - Christian W. Huck
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University; Innsbruck Austria
| | - Guenther K. Bonn
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University; Innsbruck Austria
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Zhang W, Yuan Z, Huang L, Kang J, Jiang R, Zhong H. Titanium Dioxide Photocatalytic Polymerization of Acrylamide for Gel Electrophoresis (TIPPAGE) of Proteins and Structural Identification by Mass Spectrometry. Sci Rep 2016; 6:20981. [PMID: 26865351 PMCID: PMC4750088 DOI: 10.1038/srep20981] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/14/2016] [Indexed: 11/09/2022] Open
Abstract
Polyacrylamide gel electrophoresis (PAGE) coupled with mass spectrometry has been well established for separating, identifying and quantifying protein mixtures from cell lines, tissues or other biological samples. The copolymerization process of acrylamide and bis-acrylamide is the key to mastering this powerful technique. In general, this is a vinyl addition reaction initiated by free radical-generating reagents such as ammonium persulfate (APS) and tetramethylethylenediamine (TEMED) under basic pH and degassing experimental condition. We report herein a photocatalytic polymerization approach that is based on photo-generated hydroxyl radicals with nanoparticles of titanium dioxide. It was shown that the polymerization process is greatly accelerated in acidic condition when ultraviolet light shots on the gel solution containing TiO2 nanoparticles without degassing. This feature makes it very useful in preparing Triton X-100 acid urea (TAU) gel that has been developed for separating basic proteins such as histones and variants in acidic experimental condition. Additionally, the presence of titanium dioxide in the gel not only improves mechanistic property of gels but also changes the migration pattern of different proteins that have different affinities to titanium dioxide.
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Affiliation(s)
- Wenyang Zhang
- Mass Spectrometry Center for Structural Identification of Biological Molecules and Precision Medicine, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Zhiwei Yuan
- Mass Spectrometry Center for Structural Identification of Biological Molecules and Precision Medicine, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Lulu Huang
- Mass Spectrometry Center for Structural Identification of Biological Molecules and Precision Medicine, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Jie Kang
- Mass Spectrometry Center for Structural Identification of Biological Molecules and Precision Medicine, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Ruowei Jiang
- Mass Spectrometry Center for Structural Identification of Biological Molecules and Precision Medicine, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Hongying Zhong
- Mass Spectrometry Center for Structural Identification of Biological Molecules and Precision Medicine, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
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18
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Affiliation(s)
- Nicholas M. Riley
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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Abstract
The comprehensive study of the phosphoproteome is heavily dependent on appropriate enrichment strategies that are most often, but not exclusively, carried out on the peptide level. In this chapter, I give an overview of the most widely used techniques. In addition to dedicated antibodies, phosphopeptides are enriched by their selective interaction with metals in the form of chelated metal ions or metal oxides. The negative charge of the phosphate group is also exploited in a variety of chromatographic fractionation methods that include different types of ion exchange chromatography, hydrophilic interaction chromatography (HILIC), and electrostatic repulsion HILIC (ERLIC) chromatography. Selected examples from the literature will demonstrate how a combination of these techniques with current high-performance mass spectrometry enables the identification of thousands of phosphorylation sites from various sample types.
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Affiliation(s)
- Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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20
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Zhao H, Cunningham DL, Creese AJ, Heath JK, Cooper HJ. FAIMS and Phosphoproteomics of Fibroblast Growth Factor Signaling: Enhanced Identification of Multiply Phosphorylated Peptides. J Proteome Res 2015; 14:5077-87. [PMID: 26503514 DOI: 10.1021/acs.jproteome.5b00713] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We have applied liquid chromatography high-field asymmetric waveform ion mobility spectrometry tandem mass spectrometry (LC-FAIMS-MS/MS) and liquid chromatography tandem mass spectrometry (LC-MS/MS) to the investigation of site-specific phosphorylation in fibroblast growth factor (FGF) signaling. We have combined a SILAC approach with chemical inhibition by SU5402 (an FGF receptor tyrosine kinase inhibitor) and dasatinib (a Src family kinase inhibitor). The results show that incorporation of FAIMS within the workflow results in (a) an increase in the relative proportion of phosphothreonine and phosphotyrosine sites identified, (b) an increase in phosphopeptide identifications from precursors with charge states ≥ +3 (with an associated increase in peptide length), and (c) an increase in the identification of multiply phosphorylated peptides. Approximately 20% of the phosphorylation sites identified via the FAIMS workflow had not been reported previously, and over 80% of those were from multiply phosphorylated peptides. Moreover, FAIMS provided access to a distinct set of phosphorylation sites regulated in response to SU5402 and dasatinib. The enhanced identification of multiply phosphorylated peptides was particularly striking in the case of sites regulated by SU5402. In addition to providing a compelling example of the complementarity of FAIMS in phosphoproteomics, the results provide a valuable resource of phosphorylation sites for further investigation of FGF signaling and trafficking.
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Affiliation(s)
- Hongyan Zhao
- School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Debbie L Cunningham
- School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Andrew J Creese
- School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - John K Heath
- School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Helen J Cooper
- School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
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21
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Wakabayashi M, Kyono Y, Sugiyama N, Ishihama Y. Extended Coverage of Singly and Multiply Phosphorylated Peptides from a Single Titanium Dioxide Microcolumn. Anal Chem 2015; 87:10213-21. [DOI: 10.1021/acs.analchem.5b01216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Masaki Wakabayashi
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29, Yoshida-Shimo-Adachi-Cho,
Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yutaka Kyono
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29, Yoshida-Shimo-Adachi-Cho,
Sakyo-ku, Kyoto, 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29, Yoshida-Shimo-Adachi-Cho,
Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29, Yoshida-Shimo-Adachi-Cho,
Sakyo-ku, Kyoto, 606-8501, Japan
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22
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Wang ZG, Lv N, Bi WZ, Zhang JL, Ni JZ. Development of the affinity materials for phosphorylated proteins/peptides enrichment in phosphoproteomics analysis. ACS APPLIED MATERIALS & INTERFACES 2015; 7:8377-92. [PMID: 25845677 DOI: 10.1021/acsami.5b01254] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Reversible protein phosphorylation is a key event in numerous biological processes. Mass spectrometry (MS) is the most powerful analysis tool in modern phosphoproteomics. However, the direct MS analysis of phosphorylated proteins/peptides is still a big challenge because of the low abundance and insufficient ionization of phosphorylated proteins/peptides as well as the suppression effects of nontargets. Enrichment of phosphorylated proteins/peptides by affinity materials from complex biosamples is the most widely used strategy to enhance the MS detection. The demand of efficiently enriching phosphorylated proteins/peptides has spawned diverse affinity materials based on different enrichment principles (e.g., electronic attraction, chelating). In this review, we summarize the recent development of various affinity materials for phosphorylated proteins/peptides enrichment. We will highlight the design and fabrication of these affinity materials, discuss the enrichment mechanisms involved in different affinity materials, and suggest the future challenges and research directions in this field.
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Affiliation(s)
- Zhi-Gang Wang
- †State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- ‡University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Nan Lv
- †State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- ‡University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wen-Zhi Bi
- †State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- ‡University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Ji-Lin Zhang
- †State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Jia-Zuan Ni
- †State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- §College of Life Science, Shenzhen University, Shenzhen 518060, P. R. China
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Wang MC, Lee YH, Liao PC. Optimization of titanium dioxide and immunoaffinity-based enrichment procedures for tyrosine phosphopeptide using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Bioanal Chem 2014; 407:1343-56. [PMID: 25486920 DOI: 10.1007/s00216-014-8352-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 11/06/2014] [Accepted: 11/17/2014] [Indexed: 01/25/2023]
Abstract
Tyrosine phosphorylation is an important regulator of signaling in cellular pathways, and dysregulated tyrosine phosphorylation causes several diseases. Mass spectrometry has revealed the importance of global phosphoproteomic characterization. Analysis of tyrosine phosphorylation by studying the mass-spectrometry (MS)-determined phosphoproteome remains difficult because of the relatively low abundance of tyrosine phosphoproteins. To effectively evaluate tyrosine-phosphopeptide enrichment and reduce ion suppression from non-phosphorylated peptides in MS analysis, three trypsin-digested BSA peptides and 14 standard phosphopeptides, including six tyrosine phosphopeptides, four serine phosphopeptides, and four threonine phosphopeptides, were subjected to titanium dioxide immunoaffinity-based enrichment and also to combined enrichment using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography-mass spectrometry (LC-MS) analyses. The enrichment factors were evaluated to determine the efficiency of each enrichment procedure. Comparison of five optimized enrichment methods, including TiO2-based immunoaffinity purification in Tris and MOPS buffer systems, TiO2-immunoaffinity enrichment, and immunoaffinity-TiO2 enrichment for total tyrosine, serine and threonine phosphopeptides, revealed that the order of the enrichment factors for total tyrosine phosphopeptides is: (i) immunoaffinity-TiO2 (enrichment factor = 38,244), (ii) TiO2-immunoaffinity (enrichment factor = 24,987), (iii) TiO2 micro-column (enrichment factor = 10,305), (iv) immunoaffinity in Tris buffer system (enrichment factor = 1450), and (v) immunoaffinity in the MOPS buffer system (enrichment factor = 32). These results reveal that an alternative enrichment scheme before use of a TiO2 micro-column, using immunoaffinity 4G10 and PY99 antibody enrichment under optimized conditions, can provide greater selectivity for tyrosine-phosphopeptide enrichment.
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Affiliation(s)
- Ming-Chuan Wang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, 138 Sheng-Li Road, Tainan, 70428, Taiwan, Republic of China
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Yang C, Zhong X, Li L. Recent advances in enrichment and separation strategies for mass spectrometry-based phosphoproteomics. Electrophoresis 2014; 35:3418-29. [PMID: 24687451 PMCID: PMC4849134 DOI: 10.1002/elps.201400017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/21/2014] [Accepted: 03/21/2014] [Indexed: 12/29/2022]
Abstract
Due to the significance of protein phosphorylation in various biological processes and signaling events, new analytical techniques for enhanced phosphoproteomics have been rapidly introduced in the recent years. The combinatorial use of the phospho-specific enrichment techniques and prefractionation methods prior to MS analysis enable comprehensive profiling of the phosphoproteome and facilitate deciphering the critical roles that phosphorylation plays in signaling pathways in various biological systems. This review places special emphasis on the recent five-year (2009-2013) advances for enrichment and separation techniques that have been utilized for phosphopeptides prior to MS analysis.
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Affiliation(s)
- Chenxi Yang
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Xuefei Zhong
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705, United States
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25
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Huang J, Wang F, Ye M, Zou H. Enrichment and separation techniques for large-scale proteomics analysis of the protein post-translational modifications. J Chromatogr A 2014; 1372C:1-17. [DOI: 10.1016/j.chroma.2014.10.107] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 12/16/2022]
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26
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Wang ST, Huang W, Deng YF, Gao Q, Yuan BF, Feng YQ. “Old” metal oxide affinity chromatography as “novel” strategy for specific capture of cis-diol-containing compounds. J Chromatogr A 2014; 1361:100-7. [DOI: 10.1016/j.chroma.2014.07.091] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 07/24/2014] [Accepted: 07/29/2014] [Indexed: 11/30/2022]
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27
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Slade WO, Werth EG, Chao A, Hicks LM. Phosphoproteomics in photosynthetic organisms. Electrophoresis 2014; 35:3441-51. [PMID: 24825726 DOI: 10.1002/elps.201400154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 04/18/2014] [Accepted: 04/29/2014] [Indexed: 02/04/2023]
Abstract
As primarily sessile organisms, photosynthetic species survive in dynamic environments by using elegant signaling pathways to manifest molecular responses to extracellular cues. These pathways exploit phosphorylation of specific amino acids (e.g. serine, threonine, tyrosine), which impact protein structure, function, and localization. Despite substantial progress in implementation of phosphoproteomics to understand photosynthetic organisms, researchers still struggle to translate a biological question into an experimental strategy and vice versa. This review evaluates the current status of phosphoproteomics in photosynthetic organisms and concludes with recommendations based on current knowledge.
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Affiliation(s)
- William O Slade
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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28
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Huang BY, Yang CK, Liu CP, Liu CY. Stationary phases for the enrichment of glycoproteins and glycopeptides. Electrophoresis 2014; 35:2091-107. [PMID: 24729282 DOI: 10.1002/elps.201400034] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 03/25/2014] [Accepted: 04/04/2014] [Indexed: 12/20/2022]
Abstract
The analysis of protein glycosylation is important for biomedical and biopharmaceutical research. Recent advances in LC-MS analysis have enabled the identification of glycosylation sites, the characterisation of glycan structures and the identification and quantification of glycoproteins and glycopeptides. However, this type of analysis remains challenging due to the low abundance of glycopeptides in complex protein digests, the microheterogeneity at glycosylation sites, ion suppression effects and the competition for ionisation by co-eluting peptides. Specific sample preparation is necessary for comprehensive and site-specific glycosylation analyses using MS. Therefore, researchers continue to pursue new columns to broaden their applications. The current manuscript covers recent literature published from 2008 to 2013. The stationary phases containing various chemical bonding methods or ligands immobilisation strategies on solid supports that selectively enrich N-linked or sialylated N-glycopeptides are categorised with either physical or chemical modes of binding. These categories include lectin affinity, hydrophilic interactions, boronate affinity, titanium dioxide affinity, hydrazide chemistry and other separation techniques. This review should aid in better understanding the syntheses and physicochemical properties of each type of stationary phases for enriching glycoproteins and glycopeptides.
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Affiliation(s)
- Bao-Yu Huang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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