1
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Batool R, Fatima B, Jabeen F, Hussain D, Imran M, Najam-ul-Haq M. Profiling of phosphorylated metabolites from lung cancer by zeolite loaded Mg-Al-Ce ternary hydroxide (Zeolite@MAC) composite. Heliyon 2023; 9:e16098. [PMID: 37215921 PMCID: PMC10196856 DOI: 10.1016/j.heliyon.2023.e16098] [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: 03/06/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
Phosphorylated metabolites are linked to metabolism, and the dysregulation of metabolic reactions brings cancer. Dysregulated levels lead to hyperactivation of glycolytic and mitochondrial oxidative phosphorylation pathways. Abnormal concentrations are the indicators of energy-related disorders. In this work, Zeolite-loaded Mg-Al-Ce hydroxides (Zeolite@MAC) are prepared by co-precipitation and characterized through FTIR, XRD, SEM, BET, AFM, TEM, and DLS. Magnesium-Aluminum-Cerium-Zeolite particles enrich phosphate-containing small molecules. These ternary hydroxides carried out the main adsorption mechanism, which swapped the surface hydroxyl group ligands for phosphate and the inner-sphere complex of CePO4. XH2O. Cerium plays a significant role in the complexation of phosphate, and adding Mg and Al further helps disperse Ce and increase the surface charge on the adsorbent. ΑTP and AMP are the standard molecules for parameter optimization. Zeolite@MAC enriches phosphorylated metabolites followed by their desorption via UV-vis spectrophotometry. MS profiles for healthy and lung cancer serum samples are obtained for phosphorylated metabolites. Characteristic phosphorylated metabolites have been detected in lung cancer samples with high expression. The role of phosphorylated metabolites is explored for abnormal metabolic pathways in lung cancer. The fabricated material is sensitive, selective, and highly enriched for identifying phosphate-specific biomarkers.
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Affiliation(s)
- Rimsha Batool
- Department of Biochemistry, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Batool Fatima
- Department of Biochemistry, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Fahmida Jabeen
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Dilshad Hussain
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Muhammad Imran
- Biochemistry Section, Institute of Chemical Sciences, University of Peshawar, 25120, Pakistan
| | - Muhammad Najam-ul-Haq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
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2
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Chen C, Wiorek A, Gomis-Berenguer A, Crespo GA, Cuartero M. Portable All-in-One Electrochemical Actuator-Sensor System for the Detection of Dissolved Inorganic Phosphorus in Seawater. Anal Chem 2023; 95:4180-4189. [PMID: 36724079 PMCID: PMC9979141 DOI: 10.1021/acs.analchem.2c05307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We present a methodology for the detection of dissolved inorganic phosphorous (DIP) in seawater using an electrochemically driven actuator-sensor system. The motivation for this work stems from the lack of tangible solutions for the in situ monitoring of nutrients in water systems. It does not require the addition of any reagents to the sample and works under mild polarization conditions, with the sample confined to a thin-layer compartment. Subsequent steps include the oxidation of polyaniline to lower the pH, the delivery of molybdate via a molybdenum electrode, and the formation of an electroactive phosphomolybdate complex from DIP species. The phosphomolybdate complex is ultimately detected by either cyclic voltammetry (CV) or square wave voltammetry (SWV). The combined release of protons and molybdate consistently results in a sample pH < 2 as well as a sufficient excess of molybdate, fulfilling the conditions required for the stoichiometric detection of DIP. The current of the voltammetric peak was found to be linearly related to DIP concentrations between 1 and 20 μM for CV and 0.1 and 20 μM for SWV, while also being selective against common silicate interference. The analytical application of the system was demonstrated by the validated characterization of five seawater samples, revealing an acceptable degree of difference compared to chromatography measurements. This work paves the way for the future DIP digitalization in environmental waters by in situ electrochemical probes with unprecedented spatial and temporal resolution. It is expected to provide real-time data on anthropogenic nutrient discharges as well as the improved monitoring of seawater restoration actions.
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Affiliation(s)
- Chen Chen
- Department
of Chemistry, School of Engineering Science in Chemistry, Biochemistry
and Health, KTH Royal Institute of Technology, SE-100 44Stockholm, Sweden
| | - Alexander Wiorek
- Department
of Chemistry, School of Engineering Science in Chemistry, Biochemistry
and Health, KTH Royal Institute of Technology, SE-100 44Stockholm, Sweden
| | - Alicia Gomis-Berenguer
- Department
of Chemistry, School of Engineering Science in Chemistry, Biochemistry
and Health, KTH Royal Institute of Technology, SE-100 44Stockholm, Sweden
| | - Gaston A. Crespo
- Department
of Chemistry, School of Engineering Science in Chemistry, Biochemistry
and Health, KTH Royal Institute of Technology, SE-100 44Stockholm, Sweden,UCAM-SENS,
Universidad Católica San Antonio de Murcia, UCAM HiTech, Avda. Andres Hernandez Ros 1, 30107Murcia, Spain
| | - Maria Cuartero
- Department
of Chemistry, School of Engineering Science in Chemistry, Biochemistry
and Health, KTH Royal Institute of Technology, SE-100 44Stockholm, Sweden,UCAM-SENS,
Universidad Católica San Antonio de Murcia, UCAM HiTech, Avda. Andres Hernandez Ros 1, 30107Murcia, Spain,
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3
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Guiot F, Praud C, Quillard S, Humbert B, Ropers MH, Paris M, Terrisse H. Surface reactivity of anatase particles towards phosphated species. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.130232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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4
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Xu H, Guo J, Li C, Zhao J, Gao Z, Song YY. Nanoarchitectonics of a MOF-in-Nanochannel (HKUST-1/TiO 2) Membrane for Multitarget Selective Enrichment and Staged Recovery. ACS APPLIED MATERIALS & INTERFACES 2022; 14:22006-22015. [PMID: 35533013 DOI: 10.1021/acsami.2c05296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enrichment and separation of specific endogenous molecules are essential for disease diagnosis and the pharmaceutical industry. Although many solid sorbents have been developed for target molecule enrichment, simultaneous separation of multitargets is still a challenge for adsorbents. In this study, we develop a multitarget selective sorbent based on a nanochannel membrane prepared by the anodization of a Ti-Cu alloy. The in situ growth of a metal-organic framework (MOF, herein using Cu-based HKUST-1) in the nanochannels enables the resulting MOF-in-nanochannel membrane to act as a nanofilter. Benefitting from the size-exclusion effect of MOFs and the distinct surface characteristics of each component in the HKUST-1/TiO2 nanochannels, the as-proposed membranes can be simply operated as a filter and exhibit satisfactory selectivities and enrichment capacities in the separation of aromatic amino acids, histidine-rich proteins, and phosphoproteins. More importantly, the adsorbed multitargets can be further controllably released from the membrane in a sequence via a staged recovery process. The use of this system is envisioned to provide an innovative and potential design for efficient sorption media for the selective enrichment and staged separation of specific biomolecules.
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Affiliation(s)
- Huijie Xu
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Junli Guo
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Chaowei Li
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Junjian Zhao
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Zhida Gao
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Yan-Yan Song
- College of Sciences, Northeastern University, Shenyang 110004, China
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5
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Abstract
Protein post-translational modifications (PTMs) enable cells to rapidly change in response to biological stimuli. With hundreds of different PTMs, understanding these control mechanisms is complex. To date, efforts have focused on investigating the effect of a single PTM on protein function. Yet, many proteins contain multiple PTMs. Moreover, one PTM can alter the prevalence of another, a phenomenon termed PTM crosstalk. Understanding PTM crosstalk is critical; however, its detection is challenging since PTMs occur substoichiometrically. Here, we develop an enrichment-free, label-free proteomics method that utilizes high-field asymmetric ion mobility spectrometry (FAIMS) to enhance the detection of PTM crosstalk. We show that by searching for multiple combinations of dynamic PTMs on peptide sequences, a 6-fold increase in candidate PTM crosstalk sites is identified compared with that of standard liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflows. Additionally, by cycling through FAIMS compensation voltages within a single LC-FAIMS-MS/MS run, we show that our LC-FAIMS-MS/MS workflow can increase multi-PTM-containing peptide identifications without additional increases in run times. With 159 novel candidate crosstalk sites identified, we envisage LC-FAIMS-MS/MS to play an important role in expanding the repertoire of multi-PTM identifications. Moreover, it is only by detecting PTM crosstalk that we can "see" the full picture of how proteins are regulated.
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Affiliation(s)
- Kish R. Adoni
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Debbie L. Cunningham
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - John K. Heath
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Aneika C. Leney
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
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6
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Ino Y, Nishi M, Yamaoka Y, Miyakawa K, Jeremiah SS, Osada M, Kimura Y, Ryo A. Phosphopeptide enrichment using Phos-tag technology reveals functional phosphorylation of the nucleocapsid protein of SARS-CoV-2. J Proteomics 2022; 255:104501. [PMID: 35093569 PMCID: PMC8800104 DOI: 10.1016/j.jprot.2022.104501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 11/28/2022]
Abstract
Phosphorylation of viral proteins serves as a regulatory mechanism during the intracellular life cycle of infected viruses. There is therefore a pressing need to develop a method to efficiently purify and enrich phosphopeptides derived from viral particles in biological samples. In this study, we utilized Phos-tag technology to analyze the functional phosphorylation of the nucleocapsid protein (N protein; NP) of severe respiratory syndrome coronavirus 2 (SARS-CoV-2). Viral particles were collected from culture supernatants of SARS-CoV-2-infected VeroE6/TMPRSS2 cells by ultracentrifugation, and phosphopeptides were purified by Phos-tag magnetic beads for LC-MS/MS analysis. Analysis revealed that NP was reproducibly phosphorylated at serine 79 (Ser79). Multiple sequence alignment and phylogenetic analysis showed that the Ser79 was a distinct phospho-acceptor site in SARS-CoV-2 but not in other beta-coronaviruses. We also found that the prolyl-isomerase Pin1 bound to the phosphorylated Ser79 in NP and positively regulated the production of viral particles. These results suggest that SARS-CoV-2 may have acquired the potent virus-host interaction during its evolution mediated by viral protein phosphorylation. Moreover, Phos-tag technology can provide a useful means for analyzing the functional phosphorylation of viral proteins. Significance In this study, we aimed to investigate the functional phosphorylation of SARS-CoV-2 NP. For this purpose, we used Phos-tag technology to purify and enrich virus-derived phosphopeptides with high selectivity and reproducibility. This method can be particularly useful in analyzing viral phosphopeptides from cell culture supernatants that often contain high concentrations of fetal bovine serum and supplements. We newly identified an NP phosphorylation site at Ser79, which is important for Pin1 binding. Furthermore, we showed that the interaction between Pin1 and phosphorylated NP could enhance viral replication in a cell culture model.
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Affiliation(s)
- Yoko Ino
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Graduate School of Health Sciences, Gunma Paz University, Tonyamachi 1-7-1, Takasaki-shi, Gunma 370-0006, Japan
| | - Mayuko Nishi
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yutaro Yamaoka
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Life Science Laboratory, Technology and Development Division, Kanto Chemical Co., Inc., Suzukawa 21, Isehara-shi, Kanagawa 259-1146, Japan
| | - Kei Miyakawa
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Sundararaj Stanleyraj Jeremiah
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Makoto Osada
- Graduate School of Health Sciences, Gunma Paz University, Tonyamachi 1-7-1, Takasaki-shi, Gunma 370-0006, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Akihide Ryo
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan.
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7
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Zhu C, Wu J, Jin X, Yan Y, Ding CF, Tang K, Zhang D. Post-synthesis of biomimetic chitosan with honeycomb-like structure for sensitive recognition of phosphorylated peptides. J Chromatogr A 2021; 1643:462072. [PMID: 33789194 DOI: 10.1016/j.chroma.2021.462072] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022]
Abstract
Chemical modification of biological materials is indispensable for enrichment of phosphorylated peptides. In this work, we synthesized a biomimetic honeycombed affinity chromatography (IMAC) adsorbent by preparing Crosslinked Chitosan, chelating aminomethyl phosphate decorated with Ti (IV) cation. The as-prepared CTSM@AMPA-Ti4+ composites with stable structure, low steric hindrance, and high Ti4+ loading amount were used as a promising adsorbent for enrichment of phosphopeptides. CTSM@AMPA-Ti4+ showed extremely high sensitivity (0.4 fmol) and selectivity at a low composition molar ratio of β-casein/BSA (1:1000). What's more, it can keep its performance in the case that used to capture phosphorylated peptides from standard protein ten times or soaking in the acid/base solution for a long time. In addition, CTSM@AMPA-Ti4+ successfully captured 35 phosphorylated peptides from human saliva. This study offers a way about diversiform functionalization of CTSM in phosphoproteome analysis and disease research.
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Affiliation(s)
- Canhong Zhu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Jiani Wu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Xueting Jin
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China.
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China.
| | - Keqi Tang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China
| | - Di Zhang
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China
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8
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Label-Free Quantitative Phosphoproteomics of the Fission Yeast Schizosaccharomyces pombe Using Strong Anion Exchange- and Porous Graphitic Carbon-Based Fractionation Strategies. Int J Mol Sci 2021; 22:ijms22041747. [PMID: 33572424 PMCID: PMC7916215 DOI: 10.3390/ijms22041747] [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] [Received: 01/18/2021] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/26/2022] Open
Abstract
The phosphorylation of proteins modulates various functions of proteins and plays an important role in the regulation of cell signaling. In recent years, label-free quantitative (LFQ) phosphoproteomics has become a powerful tool to analyze the phosphorylation of proteins within complex samples. Despite the great progress, the studies of protein phosphorylation are still limited in throughput, robustness, and reproducibility, hampering analyses that involve multiple perturbations, such as those needed to follow the dynamics of phosphoproteomes. To address these challenges, we introduce here the LFQ phosphoproteomics workflow that is based on Fe-IMAC phosphopeptide enrichment followed by strong anion exchange (SAX) and porous graphitic carbon (PGC) fractionation strategies. We applied this workflow to analyze the whole-cell phosphoproteome of the fission yeast Schizosaccharomyces pombe. Using this strategy, we identified 8353 phosphosites from which 1274 were newly identified. This provides a significant addition to the S. pombe phosphoproteome. The results of our study highlight that combining of PGC and SAX fractionation strategies substantially increases the robustness and specificity of LFQ phosphoproteomics. Overall, the presented LFQ phosphoproteomics workflow opens the door for studies that would get better insight into the complexity of the protein kinase functions of the fission yeast S. pombe.
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9
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Liu B, Wang B, Yan Y, Tang K, Ding CF. Efficient separation of phosphopeptides employing a Ti/Nb-functionalized core-shell structure solid-phase extraction nanosphere. Mikrochim Acta 2021; 188:32. [PMID: 33415462 DOI: 10.1007/s00604-020-04652-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/17/2020] [Indexed: 01/04/2023]
Abstract
A strategy for effectively enriching global phosphopeptides was successfully developed by using ammonia methyl phosphate (APA) as a novel chelating ligand and Ti4+ and Nb5+ as double functional ions (referred to as Fe3O4@mSiO2@APA@Ti4+/Nb5+). With the advantage of large specific surface area (151.1 m2/g), preeminent immobilized ability for metal ions (about 8% of total atoms), and unbiased enrichment towards phosphopeptides, Fe3O4@mSiO2@APA@Ti4+/Nb5+ displays high selectivity (maximum mass ratio β-casein to BSA is 1:1500), low limit of detection (LOD, as low as 0.05 fmol), good relative standard deviation (RSD, lower than 7%), recovery rate of 87% (18O isotope labeling method), outstanding phosphopeptide loading capacity (330 μg/mg), and at least five times re-use abilities. In the examination of the actual sample, 24 phosphopeptides were successfully detected in saliva and 4 phosphopeptides were also selectively extracted from human serum. All experiments have shown that Fe3O4@mSiO2@APA@Ti4+/Nb5+ exhibits exciting potential in view of the challenge of low abundance of phosphopeptides. Graphical abstract.
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Affiliation(s)
- Bin Liu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Baichun Wang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yinghua Yan
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Keqi Tang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Chuan-Fan Ding
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China
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Chen SH, Lin YC, Shih MK, Wang LF, Liu SS, Hsu JL. LC-MS Quantification of Site-Specific Phosphorylation Degree by Stable-Isotope Dimethyl Labeling Coupled with Phosphatase Dephosphorylation. Molecules 2020; 25:molecules25225316. [PMID: 33202651 PMCID: PMC7697701 DOI: 10.3390/molecules25225316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/03/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022] Open
Abstract
Protein phosphorylation is a crucial post-translational modification that plays an important role in the regulation of cellular signaling processes. Site-specific quantitation of phosphorylation levels can help decipher the physiological functions of phosphorylation modifications under diverse physiological statuses. However, quantitative analysis of protein phosphorylation degrees is still a challenging task due to its dynamic nature and the lack of an internal standard simultaneously available for the samples differently prepared for various phosphorylation extents. In this study, stable-isotope dimethyl labeling coupled with phosphatase dephosphorylation (DM + deP) was tried to determine the site-specific degrees of phosphorylation in proteins. Firstly, quantitation accuracy of the (DM + deP) approach was confirmed using synthetic peptides of various simulated phosphorylation degrees. Afterwards, it was applied to evaluate the phosphorylation stoichiometry of milk caseins. The phosphorylation degree of Ser130 on α-S1-casein was also validated by absolute quantification with the corresponding synthetic phosphorylated and nonphosphorylated peptides under a selected reaction monitoring (SRM) mode. Moreover, this (DM + deP) method was used to detect the phosphorylation degree change of Ser82 on the Hsp27 protein of HepG2 cells caused by tert-butyl hydroperoxide (t-BHP) treatment. The results showed that the absolute phosphorylation degree obtained from the (DM + deP) approach was comparable with the relative quantitation resulting from stable-isotope dimethyl labeling coupled with TiO2 enrichment. This study suggested that the (DM + deP) approach is promising for absolute quantification of site-specific degrees of phosphorylation in proteins, and it may provide more convincing information than the relative quantification method.
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Affiliation(s)
- Sin-Hong Chen
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Ya-Chi Lin
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Ming-Kuei Shih
- Graduate Institute of Food Culture and Innovation, National Kaohsiung University of Hospitality and Tourism, Kaohsiung 81271, Taiwan;
| | - Li-Fei Wang
- Hospitality and Tourism Research Center, National Kaohsiung University of Hospitality and Tourism, Kaohsiung 81271, Taiwan;
| | - Shyh-Shyan Liu
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
- Correspondence: (S.-S.L.); (J.-L.H.); Tel.: +886-8-7703202 (ext. 5075) (S.-S.L.); +886-8-7703202 (ext. 5197) (J.-L.H.); Fax: +886-8-7740178 (S.-S.L.); +886-8-7740550 (J.-L.H.)
| | - Jue-Liang Hsu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
- Research Center for Tropic Agriculture, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
- Correspondence: (S.-S.L.); (J.-L.H.); Tel.: +886-8-7703202 (ext. 5075) (S.-S.L.); +886-8-7703202 (ext. 5197) (J.-L.H.); Fax: +886-8-7740178 (S.-S.L.); +886-8-7740550 (J.-L.H.)
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11
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Yi L, Yan Y, Tang K, Ding CF. Facile preparation of polymer-grafted ZIF-8-modified magnetic nanospheres for effective identification and capture of phosphorylated and glycosylated peptides. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4657-4664. [PMID: 32909572 DOI: 10.1039/d0ay01412e] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As a member of MOFs, Zn-MOFs (ZIF-8) are seldom used in phosphopeptide enrichment because ZIF-8 is soluble in acid solutions. Therefore, properly designing a novel strategy to overcome the defect of ZIF-8 is necessary. In this study, a novel multifunctional nanoprobe was designed by uniting magnetic core, titania shell and hydrophilic metal-organic frameworks (named as Fe3O4@PDA@mTiO2@PEI-g-ZIF-8). Integrating the strategies of hydrophilic interaction affinity chromatography (HILIC), immobilized metal ion affinity chromatography (IMAC) and metal oxide affinity chromatography (MOAC), the Fe3O4@PDA@mTiO2@PEI-g-ZIF-8 mesoporous microspheres can enrich phosphorylated peptides and glycosylated peptides simultaneously. Fe3O4@PDA@mTiO2@PEI-g-ZIF-8 has high selectivity (maximum molar ratio β-casein/HRP : BSA = 1 : 1000), low detection limit (2 fmol) towards phosphopeptides and glycopeptides. Besides, the Fe3O4@PDA@mTiO2@PEI-g-ZIF-8 also exhibited a fine performance in the actual sample detection. In the experiment, taking saliva as a sample, 16 phosphorylated peptides were identified, and from a human serum sample, 4 phosphorylated peptides were selectively identified. All in all, the materials show great potential in the future study of phosphoproteomics and glycoproteomics.
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Affiliation(s)
- Linhua Yi
- School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo 315211, China.
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12
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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Trang HK, Marcus RK. Application of polydopamine‐coated nylon capillary‐channeled polymer fibers as a stationary phase for mass spectrometric phosphopeptide analysis. Electrophoresis 2019; 41:215-224. [DOI: 10.1002/elps.201900392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/21/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Hung K. Trang
- Clemson University Department of Chemistry Biosystems Research Complex Clemson SC USA
| | - R. Kenneth Marcus
- Clemson University Department of Chemistry Biosystems Research Complex Clemson SC USA
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Influence of the production technology on kefir characteristics: Evaluation of microbiological aspects and profiling of phosphopeptides by LC-ESI-QTOF-MS/MS. Food Res Int 2019; 129:108853. [PMID: 32036889 DOI: 10.1016/j.foodres.2019.108853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 12/24/2022]
Abstract
The influence of production technology, namely, temperature, pH and 2-step fermentation (back-slopping approach), on the microbiological characteristics and on the phosphopeptide profile of kefir obtained with kefir grains was investigated. The growth of yeasts, lactic acid bacteria (LAB) and acetic acetic bacteria (AAB) in both grains and kefir was affected by the incubation temperature and by the use of back-slopping. In particular, at 25 °C the microbiota of kefir grains was mainly composed by LAB and yeasts, while at 18 °C yeasts represented the dominant group in kefir. Back-slopping at 25 °C determined a significant increase of AAB. A comprehensive characterization of potentially bioactive peptides, including caseino-phosphopeptides (CPPs), was performed, for the first time, in kefir obtained with kefir grains, using preliminary enrichment on hydroxyapatite followed by dephosphorylation and analysis by Liquid Chromatography-ElectroSpray Ionization-Quadrupole-Time of Flight-tandem mass spectrometry (LC-ESI-QTOF-MS/MS). As a result, seventy-three phosphopeptides, mostly arising from caseins (79% β-casein, 8% αs1-casein and 9% αs2-casein) and all including from three to five serine residues in their sequences, were identified. Seventy-one of them showed the typical motif "SerP-SerP-SerP-Glu-Glu", which is crucial for the ability of caseins to bind to minerals. Several peptides were observed, for the first time, from the 1-40 region of β-casein. As for the effect of production technology, phosphopeptide profiles of kefirs obtained at 25 °C and 18 °C were very similar, whereas kefir produced under acidic conditions showed a predominance of smaller peptides, suggesting a higher level of proteolysis. Conversely, kefir obtained through back-slopping at 25 °C contained longer peptides, thus indicating a lower proteolytic activity and a poor reproducibility in the kefir phosphopeptide profile occurring when grains are reused.
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Si-Hung L, Troyer C, Causon T, Hann S. Sensitive quantitative analysis of phosphorylated primary metabolites using selective metal oxide enrichment and GC- and IC- MS/MS. Talanta 2019; 205:120147. [PMID: 31450417 DOI: 10.1016/j.talanta.2019.120147] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/20/2022]
Abstract
In this study, we present a novel selective cleanup/enrichment method based on metal oxide solid phase extraction combined with quantitative gas chromatography-tandem mass spectrometry and ion exchange chromatography-tandem mass spectrometry for the analysis of phosphorylated metabolites in yeast cell extracts relevant to biotechnological processes. Following screening of several commercially available metal oxide-based enrichment materials, all steps of the enrichment process (loading, washing and elution) were optimized for both the selective enrichment of 12 phosphorylated compounds from the glycolysis and pentose phosphate pathways, and the simultaneous removal of highly abundant matrix components such as organic acids and sugars. The full analytical workflow was then validated to meet the demands of accurate quantification of phosphorylated metabolites in yeast (Pichia pastoris) cell extracts using the best performing material and cleanup/enrichment method combined with quantification strategies based on internal standardization with isotopically labeled internal standards and external calibration. A good recovery (>70%) for 5 of the 12 targeted phosphorylated compounds with RSDs of less than 6.0% was obtained while many sugars, organic acids and amino acids were removed (>99% of glucose, and >95% of aspartate, succinate, glutamate, alanine, glycine, serine, threonine, proline, and valine). The use of isotopically labeled internal standards added to the samples prior to SPE, enables accurate quantification of the metabolites as it compensates for errors introduced during sample pretreatment and GC-MS or LC-MS analysis. To the best of our knowledge, this is the first time an effective and selective metal oxide-based affinity chromatography cleanup/enrichment method was designed and applied successfully for intracellular phosphorylated metabolites.
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Affiliation(s)
- Le Si-Hung
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christina Troyer
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Tim Causon
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stephan Hann
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria.
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16
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Lin H, Chen H, Shao X, Deng C. A capillary column packed with a zirconium(IV)-based organic framework for enrichment of endogenous phosphopeptides. Mikrochim Acta 2018; 185:562. [PMID: 30488348 DOI: 10.1007/s00604-018-3109-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/21/2018] [Indexed: 01/04/2023]
Abstract
A zirconium(IV)-based metal organic framework (Zr-MOF) was deposited on polydopamine-coated silica microspheres to form microspheres of type SiO2@PDA@Zr-MOF. These were packed into capillary columns for enrichment of phosphopeptides. The column was off-line coupled to both matrix-assisted laser desorption/ionization time of flight mass spectrometry and LC-ESI-MS/MS. The method has a detection limit as low as 4 fmol of β-casein digest and a selectivity as high as 1:1000 (molar ratio of β-casein and BSA digest). It was applied to the analysis of human saliva. In total, 240 endogenous phosphopeptides were identified in only 25 μL human saliva. Graphical abstract A zirconium-based metal organic framework (Zr-MOF) was modified outside of polydopamine-coated silica microspheres to form microspheres named SiO2@PDA@Zr-MOF. Then they were packed in capillary columns for selective enrichment of phosphopeptides via interaction between Zr-O clusters and phosphate groups. The pre-concentration resulted in a better detection of phosphopeptides by mass spectrometry. Tris: Tris(hydroxymethyl)aminomethane; DMF: Dimethyl Formamide; Zr-MOF: Zirconium(IV)-organic framework; MOAC: Metal oxide affinity chromatography.
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Affiliation(s)
- Haizhu Lin
- The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.,Department of Chemistry, and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China
| | - Hemei Chen
- The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.,Department of Chemistry, and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China
| | - Xi Shao
- The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.,Department of Chemistry, and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China
| | - Chunhui Deng
- The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China. .,Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China. .,Department of Chemistry, and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China.
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Cheng LC, Li Z, Graeber TG, Graham NA, Drake JM. Phosphopeptide Enrichment Coupled with Label-free Quantitative Mass Spectrometry to Investigate the Phosphoproteome in Prostate Cancer. J Vis Exp 2018. [PMID: 30124664 PMCID: PMC6126612 DOI: 10.3791/57996] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phosphoproteomics involves the large-scale study of phosphorylated proteins. Protein phosphorylation is a critical step in many signal transduction pathways and is tightly regulated by kinases and phosphatases. Therefore, characterizing the phosphoproteome may provide insights into identifying novel targets and biomarkers for oncologic therapy. Mass spectrometry provides a way to globally detect and quantify thousands of unique phosphorylation events. However, phosphopeptides are much less abundant than non-phosphopeptides, making biochemical analysis more challenging. To overcome this limitation, methods to enrich phosphopeptides prior to the mass spectrometry analysis are required. We describe a procedure to extract and digest proteins from tissue to yield peptides, followed by an enrichment for phosphotyrosine (pY) and phosphoserine/threonine (pST) peptides using an antibody-based and/or titanium dioxide (TiO2)-based enrichment method. After the sample preparation and mass spectrometry, we subsequently identify and quantify phosphopeptides using liquid chromatography-mass spectrometry and analysis software.
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Affiliation(s)
- Larry C Cheng
- Graduate Program in Cellular and Molecular Pharmacology, School of Graduate Studies, Rutgers University, The State University of New Jersey; Graduate Program in Quantitative Biomedicine, School of Graduate Studies, Rutgers University, The State University of New Jersey
| | - Zhen Li
- Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School
| | - Thomas G Graeber
- Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, Jonsson Comprehensive Cancer Center, UCLA Metabolomics Center, and California NanoSystems Institute, David Geffen School of Medicine, University of California, Los Angeles
| | - Nicholas A Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California
| | - Justin M Drake
- Graduate Program in Cellular and Molecular Pharmacology, School of Graduate Studies, Rutgers University, The State University of New Jersey; Graduate Program in Quantitative Biomedicine, School of Graduate Studies, Rutgers University, The State University of New Jersey; Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School; Pharmacology, Rutgers Robert Wood Johnson Medical School; Cancer Metabolism and Growth Program, Rutgers Cancer Institute of New Jersey;
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18
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Fan M, Wang F, Wang C. Reflux Precipitation Polymerization: A New Platform for the Preparation of Uniform Polymeric Nanogels for Biomedical Applications. Macromol Biosci 2018; 18:e1800077. [DOI: 10.1002/mabi.201800077] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 05/19/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Mingliang Fan
- State Key Laboratory of Molecular Engineering of Polymers; Department of Macromolecular Science; Fudan University; 220 Han Dan Road Shanghai 200433 China
| | - Fang Wang
- State Key Laboratory of Molecular Engineering of Polymers; Department of Macromolecular Science; Fudan University; 220 Han Dan Road Shanghai 200433 China
| | - Changchun Wang
- State Key Laboratory of Molecular Engineering of Polymers; Department of Macromolecular Science; Fudan University; 220 Han Dan Road Shanghai 200433 China
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Wagner S, Zapata C, Wan W, Gawlitza K, Weber M, Rurack K. Role of Counterions in Molecularly Imprinted Polymers for Anionic Species. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:6963-6975. [PMID: 29792030 DOI: 10.1021/acs.langmuir.8b00500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Small-molecule oxoanions are often imprinted noncovalently as carboxylates into molecularly imprinted polymers (MIPs), requiring the use of an organic counterion. Popular species are either pentamethylpiperidine (PMP) as a protonatable cation or tetraalkylammonium (TXA) ions as permanent cations. The present work explores the influence of the TXA as a function of their alkyl chain length, from methyl to octyl, using UV/vis absorption, fluorescence titrations, and HPLC as well as MD simulations. Protected phenylalanines (Z-l/d-Phe) served as templates/analytes. While the influence of the counterion on the complex stability constants and anion-induced spectral changes shows a monotonous trend with increasing alkyl chain length at the prepolymerization stage, the cross-imprinting/rebinding studies showed a unique pattern that suggested the presence of adaptive cavities in the MIP matrix, related to the concept of induced fit of enzyme-substrate interaction. Larger cavities formed in the presence of larger counterions can take up pairs of Z-x-Phe and smaller TXA, eventually escaping spectroscopic detection. Correlation of the experimental data with the MD simulations revealed that counterion mobility, the relative distances between the three partners, and the hydrogen bond lifetimes are more decisive for the response features observed than actual distances between interacting atoms in a complex or the orientation of binding moieties. TBA has been found to yield the highest imprinting factor, also showing a unique dual behavior regarding the interaction with template and fluorescent monomer. Finally, interesting differences between both enantiomers have been observed in both theory and experiment, suggesting true control of enantioselectivity. The contribution concludes with suggestions for translating the findings into actual MIP development.
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Affiliation(s)
- Sabine Wagner
- Chemical and Optical Sensing Division (1.9) , Bundesanstalt für Materialforschung und-prüfung (BAM) , Richard-Willstätter-Str. 11 , D-12489 Berlin , Germany
| | - Carlos Zapata
- Chemical and Optical Sensing Division (1.9) , Bundesanstalt für Materialforschung und-prüfung (BAM) , Richard-Willstätter-Str. 11 , D-12489 Berlin , Germany
- Computational Molecular Design Group, Department of Numerical Mathematics , Zuse Institute Berlin , Takustrasse 7 , D-14195 Berlin , Germany
- School of Analytical Sciences Adlershof (SALSA) , Humboldt-Universität zu Berlin , Unter den Linden 6 , D-10099 Berlin , Germany
| | - Wei Wan
- Chemical and Optical Sensing Division (1.9) , Bundesanstalt für Materialforschung und-prüfung (BAM) , Richard-Willstätter-Str. 11 , D-12489 Berlin , Germany
| | - Kornelia Gawlitza
- Chemical and Optical Sensing Division (1.9) , Bundesanstalt für Materialforschung und-prüfung (BAM) , Richard-Willstätter-Str. 11 , D-12489 Berlin , Germany
| | - Marcus Weber
- Computational Molecular Design Group, Department of Numerical Mathematics , Zuse Institute Berlin , Takustrasse 7 , D-14195 Berlin , Germany
| | - Knut Rurack
- Chemical and Optical Sensing Division (1.9) , Bundesanstalt für Materialforschung und-prüfung (BAM) , Richard-Willstätter-Str. 11 , D-12489 Berlin , Germany
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20
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Jiang J, Sun X, She X, Li J, Li Y, Deng C, Duan G. Magnetic microspheres modified with Ti(IV) and Nb(V) for enrichment of phosphopeptides. Mikrochim Acta 2018; 185:309. [PMID: 29802452 DOI: 10.1007/s00604-018-2837-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 05/06/2018] [Indexed: 01/04/2023]
Abstract
Magnetic microspheres (Fe3O4) were coated with polydopamine (PDA) and loaded with the metal ions Ti(IV) and Nb(V) to give a material of type Fe3O4@PDA-Ti/Nb. It is shown to be useful for affinity chromatography and for enrichment of phosphopeptides from both standard protein solutions and real samples. For comparison, such microspheres loaded with single metal ions only (Fe3O4@PDA-Ti and Fe3O4@PDA-Nb) and their physical mixtures were also investigated under identical conditions. The binary metal ion-loaded magnetic microspheres display better enrichment efficiency than the single metal ion-loaded microspheres and their physical mixture. Both multiphosphopeptides and monophosphopeptides can be extracted. The Fe3O4@PDA-Ti/Nb microspheres exhibit ultra-high sensitivity (the lowest detection amount being 2 fmol) and selectivity at a low mass ratio such as in case of β-casein/BSA (1:1000). Graphical abstract Magnetic microspheres (Fe3O4) were coated with polydopamine (PDA) and loaded with the metal ions Ti(IV) and Nb(V) to give a material of type Fe3O4@PDA-Ti/Nb. Results showed its great potential as an affinity probe in phosphoproteome research due to rapid magnetic separation of phosphopeptides, ultrahigh sensitivity and selectivity, and remarkable reusability.
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Affiliation(s)
- Jiebing Jiang
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Xueni Sun
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany
| | - Xiaojian She
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Jiajia Li
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yan Li
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China.
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Gengli Duan
- Fudan University Affiliated Pudong Medical Center & Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201203, China
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Development of Gd3+-immobilized glutathione-coated magnetic nanoparticles for highly selective enrichment of phosphopeptides. Talanta 2018; 180:368-375. [DOI: 10.1016/j.talanta.2017.12.048] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/01/2017] [Accepted: 12/14/2017] [Indexed: 01/19/2023]
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22
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Berard A, Kroeker A, McQueen P, Coombs KM. Methods and approaches to disease mechanisms using systems kinomics. Synth Syst Biotechnol 2018; 3:34-43. [PMID: 29911197 PMCID: PMC5884222 DOI: 10.1016/j.synbio.2017.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Accepted: 12/13/2017] [Indexed: 02/06/2023] Open
Abstract
All cellular functions, ranging from regular cell maintenance and homeostasis, specialized functions specific to cellular types, or generating responses due to external stimulus, are mediated by proteins within the cell. Regulation of these proteins allows the cell to alter its behavior under different circumstances. A major mechanism of protein regulation is utilizing protein kinases and phosphatases; enzymes that catalyze the transfer of phosphates between substrates [1]. Proteins involved in phosphate signaling are well studied and include kinases and phosphatases that catalyze opposing reactions regulating both structure and function of the cell. Kinomics is the study of kinases, phosphatases and their targets, and has been used to study the functional changes in numerous diseases and infectious diseases with aims to delineate the cellular functions affected. Identifying the phosphate signaling pathways changed by certain diseases or infections can lead to novel therapeutic targets. However, a daunting 518 putative protein kinase genes have been identified [2], indicating that this protein family is very large and complex. Identifying which enzymes are specific to a particular disease can be a laborious task. In this review, we will provide information on large-scale systems biology methodologies that allow global screening of the kinome to more efficiently identify which kinase pathways are pertinent for further study.
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Affiliation(s)
- Alicia Berard
- Department of Medical Microbiology, University of Manitoba, Winnipeg, R3E 0J9, Canada
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | | | - Peter McQueen
- Department of Medical Microbiology, University of Manitoba, Winnipeg, R3E 0J9, Canada
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Kevin M. Coombs
- Department of Medical Microbiology, University of Manitoba, Winnipeg, R3E 0J9, Canada
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Lin H, Deng C. Development of immobilized Sn 4+ affinity chromatography material for highly selective enrichment of phosphopeptides. Proteomics 2017; 16:2733-2741. [PMID: 27650410 DOI: 10.1002/pmic.201600187] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 09/01/2016] [Accepted: 09/16/2016] [Indexed: 01/24/2023]
Abstract
In this work, we first immobilized tin(IV) ion on polydopamine-coated magnetic graphene (magG@PDA) to synthesize Sn4+ -immobilized magG@PDA (magG@PDA-Sn4+ ) and successfully applied the material to highly selective enrichment of phosphopeptides. The material gathered the advantages of large surface area of graphene, superparamagnetism of Fe3 O4 , good hydrophilicity and biocompatibility of polydopamine, and strong interaction between Sn4+ and phosphopeptides. The enrichment performance of magG@PDA-Sn4+ toward phosphopeptides from digested β-casein at different concentrations, with and without added digested BSA was investigated and compared with magG@PDA-Ti4+ . The results showed high selectivity and sensitivity of the Sn4+ -IMAC material toward phosphopeptides, as good as the Ti4+ -IMAC material. Finally, magG@PDA-Sn4+ was applied to the analysis of endogenous phosphopeptides from a real sample, human saliva, with both MALDI-TOF MS and nano-LC-ESI-MS/MS. The results indicated that the as-synthesized Sn4+ -IMAC material not only has good enrichment performance, but also could serve as a supplement to the Ti4+ -IMAC material and expand the phosphopeptide coverage enriched by the single Ti4+ -IMAC material, demonstrating the broad application prospects of magG@PDA-Sn4+ in phosphoproteome research.
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Affiliation(s)
- Haizhu Lin
- Department of Chemistry and Institutes of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, P. R. China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, P. R. China.
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Schumacher FR, Delamarre L, Jhunjhunwala S, Modrusan Z, Phung QT, Elias JE, Lill JR. Building proteomic tool boxes to monitor MHC class I and class II peptides. Proteomics 2017; 17. [PMID: 27928884 DOI: 10.1002/pmic.201600061] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/13/2016] [Accepted: 11/25/2016] [Indexed: 01/22/2023]
Abstract
Major histocompatibility complex Class I (MHCI) and Class II (MHCII) presented peptides powerfully modulate T cell immunity and play a vital role in generating effective anti-tumor and anti-viral immune responses in mammals. Characterizing these MHCI or MHCII presented peptides can help generate therapeutic treatments, afford information on T cell mediated biomarkers, provide insight into disease progression, and reduce adverse anti-drug side effects from engineered biotherapeutics. Here, we explore the tools and techniques commonly employed to discover both MHCI- and MHCII-presented peptides. We describe complementary strategies that enhance the characterization of these peptides and the informatics tools employed for both predicting and characterizing MHCI- and MHCII-presented epitopes. The evolution of methodologies for isolating MHC-presented peptides is discussed, as are the mass spectrometric workflows that can be employed for their characterization. We provide a perspective on where this field is headed, and how these tools may be applicable to the discovery and monitoring of epitopes in a variety of scenarios.
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Affiliation(s)
| | - Lélia Delamarre
- Department of Cancer Immunology, Genentech Inc., San Francisco, CA, USA
| | - Suchit Jhunjhunwala
- Department of Bioinformatics & Computational Biology, Genentech Inc., San Francisco, CA, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech Inc., San Francisco, CA, USA
| | - Qui T Phung
- Department of Proteomics and Biological Resources, Genentech Inc., San Francisco, CA, USA
| | - Joshua E Elias
- Department of Chemical & Systems Biology, School of Medicine, Stanford University, San Francisco, CA, USA
| | - Jennie R Lill
- Department of Proteomics & Biological Resources, Genentech Inc., San Francisco, CA, USA
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25
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Sun H, Zhang Q, Zhang L, Zhang W, Zhang L. Facile preparation of molybdenum (VI) oxide – Modified graphene oxide nanocomposite for specific enrichment of phosphopeptides. J Chromatogr A 2017; 1521:36-43. [DOI: 10.1016/j.chroma.2017.08.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/21/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
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26
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Jiang J, Sun X, Li Y, Deng C, Duan G. Facile synthesis of Fe 3O 4@PDA core-shell microspheres functionalized with various metal ions: A systematic comparison of commonly-used metal ions for IMAC enrichment. Talanta 2017; 178:600-607. [PMID: 29136869 DOI: 10.1016/j.talanta.2017.09.071] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 01/04/2023]
Abstract
Metal ions differed greatly in affinity towards phosphopeptides, and thus it is essential to systematically compare the phosphopeptides enrichment ability of different metal ions usually used in the IMAC techniques. In this work, for the first time, eight metal ions, including Nb5+, Ti4+, Zr4+, Ga3+, Y3+, In3+, Ce4+, Fe3+, were immobilized on the polydopamine (PDA)-coated Fe3O4 (denoted as Fe3O4@PDA-Mn+), and systematically compared by the real biosamples, in addition to standard phosphopeptides. Fe3O4 microspheres were synthesized via the solvothermal reaction, followed by self-polymerization of dopamine on the surface. Then through taking advantage of the hydroxyl and amino group of PDA, the eight metal ions were easily adhered to the surface of Fe3O4@PDA. After characterization, the resultant Fe3O4@PDA-Mn+ microspheres were applied to phosphopeptides enrichment based on the binding affinity between metal ions and phosphopeptides. According to the results, different metal ions presented diverse phosphopeptides enrichment efficiency in terms of selectivity, sensitivity and the enrichment ability from real complex samples, and Fe3O4@PDA-Nb5+ and Fe3O4@PDA-Ti4+ showed obvious advantages of the phosphopeptides enrichment effect after the comparison. This systematic comparison may provide certain reference for the use and development of IMAC materials in the future.
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Affiliation(s)
- Jiebing Jiang
- Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xueni Sun
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053 Regensburg, Germany
| | - Yan Li
- Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203, China.
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Gengli Duan
- Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203, China
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Long XY, Zhang ZJ, Li JY, Sheng D, Lian HZ. Controllable Preparation of CuFeMnO4 Nanospheres as a Novel Multifunctional Affinity Probe for Efficient Adsorption and Selective Enrichment of Low-Abundance Peptides and Phosphopeptides. Anal Chem 2017; 89:10446-10453. [DOI: 10.1021/acs.analchem.7b02476] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Xing-Yu Long
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing 210023, China
- Editorial
Department of Journal, Guizhou Normal University, Guiyang 550001, China
| | - Zi-Jin Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing 210023, China
| | - Jia-Yuan Li
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing 210023, China
| | - Dong Sheng
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing 210023, China
| | - Hong-Zhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, Nanjing 210023, China
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28
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Lin H, Yuan K, Deng C. Preparation of a TiO 2-NH 2 modified MALDI plate for on-plate simultaneous enrichment of phosphopeptides and glycopeptides. Talanta 2017; 175:427-434. [PMID: 28842012 DOI: 10.1016/j.talanta.2017.07.078] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/18/2017] [Accepted: 07/25/2017] [Indexed: 01/21/2023]
Abstract
In this work, a TiO2 film was prepared on a MALDI plate by atomic layer deposition (ALD) technique and then modified with -NH2. The obtained TiO2-NH2 modified plate was applied for on-plate simultaneous enrichment of phosphopeptides and glycopeptides. The ALD TiO2 film displayed quite uniform morphology, and attached firmly to the MALDI plate with rather stable physical and chemical properties, which resulted in fine stability of the plate in performance. The -NH2 groups offered the film better hydrophilicity and affinity toward glycopeptides. The on-plate simultaneous enrichment performance of the TiO2-NH2 modified plate was investigated by β-casein digests, HRP digests and human serum.
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Affiliation(s)
- Haizhu Lin
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Kaiping Yuan
- State Key Laboratory of ASIC and System, Fudan University, Shanghai 200433, China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200433, China.
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29
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Design and synthesis of an immobilized metal affinity chromatography and metal oxide affinity chromatography hybrid material for improved phosphopeptide enrichment. J Chromatogr A 2017; 1505:56-62. [DOI: 10.1016/j.chroma.2017.05.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 01/12/2023]
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30
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Casado P, Hijazi M, Britton D, Cutillas PR. Impact of phosphoproteomics in the translation of kinase-targeted therapies. Proteomics 2016; 17. [DOI: 10.1002/pmic.201600235] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/29/2016] [Accepted: 10/20/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Pedro Casado
- Cell Signalling and Proteomics Group; Centre for Haemato-Oncology; Barts Cancer Institute; Queen Mary University of London; UK
| | - Maruan Hijazi
- Cell Signalling and Proteomics Group; Centre for Haemato-Oncology; Barts Cancer Institute; Queen Mary University of London; UK
| | - David Britton
- Cell Signalling and Proteomics Group; Centre for Haemato-Oncology; Barts Cancer Institute; Queen Mary University of London; UK
| | - Pedro R. Cutillas
- Cell Signalling and Proteomics Group; Centre for Haemato-Oncology; Barts Cancer Institute; Queen Mary University of London; UK
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31
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Carrier M, Joint M, Lutzing R, Page A, Rochette-Egly C. Phosphoproteome and Transcriptome of RA-Responsive and RA-Resistant Breast Cancer Cell Lines. PLoS One 2016; 11:e0157290. [PMID: 27362937 PMCID: PMC4928811 DOI: 10.1371/journal.pone.0157290] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 05/26/2016] [Indexed: 01/21/2023] Open
Abstract
Retinoic acid (RA), the main active vitamin A metabolite, controls multiple biological processes such as cell proliferation and differentiation through genomic programs and kinase cascades activation. Due to these properties, RA has proven anti-cancer capacity. Several breast cancer cells respond to the antiproliferative effects of RA, while others are RA-resistant. However, the overall signaling and transcriptional pathways that are altered in such cells have not been elucidated. Here, in a large-scale analysis of the phosphoproteins and in a genome-wide analysis of the RA-regulated genes, we compared two human breast cancer cell lines, a RA-responsive one, the MCF7 cell line, and a RA-resistant one, the BT474 cell line, which depicts several alterations of the “kinome”. Using high-resolution nano-LC-LTQ-Orbitrap mass spectrometry associated to phosphopeptide enrichment, we found that several proteins involved in signaling and in transcription, are differentially phosphorylated before and after RA addition. The paradigm of these proteins is the RA receptor α (RARα), which was phosphorylated in MCF7 cells but not in BT474 cells after RA addition. The panel of the RA-regulated genes was also different. Overall our results indicate that RA resistance might correlate with the deregulation of the phosphoproteome with consequences on gene expression.
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Affiliation(s)
- Marilyn Carrier
- Department of Functional Genomics and Cancer, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964, CNRS, UMR7104, Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, Strasbourg, France
| | - Mathilde Joint
- Proteomics Platform, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964, CNRS, UMR7104, Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, Strasbourg, France
| | - Régis Lutzing
- Department of Functional Genomics and Cancer, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964, CNRS, UMR7104, Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, Strasbourg, France
| | - Adeline Page
- Proteomics Platform, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964, CNRS, UMR7104, Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, Strasbourg, France
| | - Cécile Rochette-Egly
- Department of Functional Genomics and Cancer, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964, CNRS, UMR7104, Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, Strasbourg, France
- * E-mail:
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Maes E, Tirez K, Baggerman G, Valkenborg D, Schoofs L, Encinar JR, Mertens I. The use of elemental mass spectrometry in phosphoproteomic applications. MASS SPECTROMETRY REVIEWS 2016; 35:350-360. [PMID: 25139451 DOI: 10.1002/mas.21440] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 05/14/2014] [Accepted: 05/14/2014] [Indexed: 06/03/2023]
Abstract
Reversible phosphorylation is one of the most important post-translational modifications in mammalian cells. Because this molecular switch is an important mechanism that diversifies and regulates proteins in cellular processes, knowledge about the extent and quantity of phosphorylation is very important to understand the complex cellular interplay. Although phosphoproteomics strategies are applied worldwide, they mainly include only molecular mass spectrometry (like MALDI or ESI)-based experiments. Although identification and relative quantification of phosphopeptides is straightforward with these techniques, absolute quantification is more complex and usually requires for specific isotopically phosphopeptide standards. However, the use of elemental mass spectrometry, and in particular inductively coupled plasma mass spectrometry (ICP-MS), in phosphoproteomics-based experiments, allow one to absolutely quantify phosphopeptides. Here, these phosphoproteomic applications with ICP-MS as elemental detector are reviewed. Pioneering work and recent developments in the field are both described. Additionally, the advantage of the parallel use of molecular and elemental mass spectrometry is stressed.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- KU Leuven, Research Group of Functional Genomics and Proteomics, Leuven, Belgium
| | - Kristof Tirez
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Geert Baggerman
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Liliane Schoofs
- KU Leuven, Research Group of Functional Genomics and Proteomics, Leuven, Belgium
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
| | - Inge Mertens
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
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Lin H, Deng C. Development of Hf 4+ -immobilized polydopamine-coated magnetic graphene for highly selective enrichment of phosphopeptides. Talanta 2016; 149:91-97. [DOI: 10.1016/j.talanta.2015.11.037] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 11/26/2022]
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Development of diamond-lanthanide metal oxide affinity composites for the selective capture of endogenous serum phosphopeptides. Anal Bioanal Chem 2016; 408:1633-41. [DOI: 10.1007/s00216-015-9272-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/04/2015] [Accepted: 12/11/2015] [Indexed: 01/28/2023]
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Lee J, Park IS, Park G, Cho K, Park HS, Min DH. A robust and quantitative assay platform for multiplexed, high throughput screening of protein kinase inhibitors. Chem Commun (Camb) 2016; 52:12112-12115. [DOI: 10.1039/c6cc05834e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a new platform for multiplexed protein kinase activity assay using TiO2decorated graphene oxide (GO), which is applicable to high throughput inhibitor screening.
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Affiliation(s)
- Jieon Lee
- Center for RNA Research
- Institute for Basic Science
- Department of Chemistry
- Seoul National University
- Seoul
| | - Il-Soo Park
- Center for RNA Research
- Institute for Basic Science
- Department of Chemistry
- Seoul National University
- Seoul
| | - Ginam Park
- Center for RNA Research
- Institute for Basic Science
- Department of Chemistry
- Seoul National University
- Seoul
| | - Kyukwang Cho
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon
- Korea
| | - Hee-Sung Park
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon
- Korea
| | - Dal-Hee Min
- Center for RNA Research
- Institute for Basic Science
- Department of Chemistry
- Seoul National University
- Seoul
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36
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Semba RD, Lam M, Sun K, Zhang P, Schaumberg DA, Ferrucci L, Ping P, Van Eyk JE. Priorities and trends in the study of proteins in eye research, 1924-2014. Proteomics Clin Appl 2015; 9:1105-22. [PMID: 26123431 PMCID: PMC4695326 DOI: 10.1002/prca.201500006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/26/2015] [Accepted: 06/25/2015] [Indexed: 11/12/2022]
Abstract
PURPOSE To identify the proteins that are relevant to eye research and develop assays for the study of a set of these proteins. EXPERIMENTAL DESIGN We conducted a bibliometric analysis by merging gene lists for human and mouse from the National Center for Biotechnology Information FTP site and combining them with PubMed references that were retrieved with the search terms "eye" [MeSH Terms] OR "eye" [All Fields] OR "eyes" [All Fields]. RESULTS For human and mouse eye studies, respectively, the total number of publications was 13,525 and 23,895 and the total number of proteins was 4050 and 4717. For proteins in human and mouse eye studies, respectively, 88.7 and 81.7% had five or fewer citations. The top 50 most intensively studied proteins for human and mouse eye studies were generally in the areas of photoreceptors and phototransduction, inflammation, and angiogenesis, neurodevelopment, lens transparency, and cell-cycle and cellular processes. We proposed selected reaction monitoring assays that were developed in silico for the top fifty most intensively studied proteins in human and mouse eye research. CONCLUSIONS AND CLINICAL RELEVANCE We conclude that scientists engaged in eye research tend to focus on the same proteins. Newer resources and tools in proteomics can expand the investigations to lesser-known proteins of the eye.
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Affiliation(s)
- Richard D. Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Maggie Lam
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Kai Sun
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Pingbo Zhang
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Debra A. Schaumberg
- Center for Translational Medicine, Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, Baltimore, MD
| | - Peipei Ping
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Jennifer E. Van Eyk
- Advanced Clinical BioSystems Research Institute, The Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
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Maes E, Mertens I, Valkenborg D, Pauwels P, Rolfo C, Baggerman G. Proteomics in cancer research: Are we ready for clinical practice? Crit Rev Oncol Hematol 2015; 96:437-48. [PMID: 26277237 DOI: 10.1016/j.critrevonc.2015.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/20/2015] [Accepted: 07/14/2015] [Indexed: 12/13/2022] Open
Abstract
Although genomics has delivered major advances in cancer prognostics, treatment and diagnostics, it still only provides a static image of the situation. To study more dynamic molecular entities, proteomics has been introduced into the cancer research field more than a decade ago. Currently, however, the impact of clinical proteomics on patient management and clinical decision-making is low and the implementations of scientific results in the clinic appear to be scarce. The search for cancer-related biomarkers with proteomics however, has major potential to improve risk assessment, early detection, diagnosis, prognosis, treatment selection and monitoring. In this review, we provide an overview of the transition of oncoproteomics towards translational oncology. We describe which lessons are learned from currently approved protein biomarkers and previous proteomic studies, what the pitfalls and challenges are in clinical proteomics applications, and how proteomic research can be successfully translated into medical practice.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium; CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Inge Mertens
- Flemish Institute for Technological Research (VITO), Mol, Belgium; CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Mol, Belgium; CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Patrick Pauwels
- Molecular Pathology Unit, Pathology Department, Antwerp University Hospital, Edegem, Belgium
| | - Christian Rolfo
- Phase I - Early Clinical Trials Unit, Oncology Department, Antwerp University Hospital & Center for Oncological Research (CORE), Antwerp University, Edegem, Belgium.
| | - Geert Baggerman
- Flemish Institute for Technological Research (VITO), Mol, Belgium; CFP-CeProMa, University of Antwerp, Antwerp, Belgium
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38
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Sun X, Liu X, Feng J, Li Y, Deng C, Duan G. Hydrophilic Nb5+-immobilized magnetic core–shell microsphere – A novel immobilized metal ion affinity chromatography material for highly selective enrichment of phosphopeptides. Anal Chim Acta 2015; 880:67-76. [DOI: 10.1016/j.aca.2015.04.029] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 04/05/2015] [Accepted: 04/16/2015] [Indexed: 01/03/2023]
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Krásný L, Pompach P, Strnadová M, Hynek R, Vališ K, Havlíček V, Novák P, Volný M. High-throughput workflow for identification of phosphorylated peptides by LC-MALDI-TOF/TOF-MS coupled to in situ enrichment on MALDI plates functionalized by ion landing. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:802-811. [PMID: 26169134 DOI: 10.1002/jms.3586] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 06/04/2023]
Abstract
We report an MS-based workflow for identification of phosphorylated peptides from trypsinized protein mixtures and cell lysates that is suitable for high-throughput sample analysis. The workflow is based on an in situ enrichment on matrix-assisted laser desorption/ionization (MALDI) plates that were functionalized by TiO2 using automated ion landing apparatus that can operate unsupervised. The MALDI plate can be functionalized by TiO2 into any array of predefined geometry (here, 96 positions for samples and 24 for mass calibration standards) made compatible with a standard MALDI spotter and coupled with high-performance liquid chromatography. The in situ MALDI plate enrichment was compared with a standard precolumn-based separation and achieved comparable or better results than the standard method. The performance of this new workflow was demonstrated on a model mixture of proteins as well as on Jurkat cells lysates. The method showed improved signal-to-noise ratio in a single MS spectrum, which resulted in better identification by MS/MS and a subsequent database search. Using the workflow, we also found specific phosphorylations in Jurkat cells that were nonspecifically activated by phorbol 12-myristate 13-acetate. These phosphorylations concerned the mitogen-activated protein kinase/extracellular signal-regulated kinase signaling pathway and its targets and were in agreement with the current knowledge of this signaling cascade. Control sample of non-activated cells was devoid of these phosphorylations. Overall, the presented analytical workflow is able to detect dynamic phosphorylation events in minimally processed mammalian cells while using only a short high-performance liquid chromatography gradient.
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Affiliation(s)
- Lukáš Krásný
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Institute of Chemical Technology, Technická 5, Prague, 16628, Czech Republic
| | - Petr Pompach
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague, 128 40, Czech Republic
| | - Marcela Strnadová
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
| | - Radovan Hynek
- Institute of Chemical Technology, Technická 5, Prague, 16628, Czech Republic
| | - Karel Vališ
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague, 128 40, Czech Republic
| | - Vladimír Havlíček
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, 17.listopadu 12, Olomouc, 771 46, Czech Republic
| | - Petr Novák
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague, 128 40, Czech Republic
| | - Michael Volný
- Applied Physics Laboratory, University of Washington, 1013 NE 40th St, Seattle, WA, 98105, USA
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Comparative Study of Three Methods of Sample Preparation for Proteomics Research. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1016/s1872-2040(15)60828-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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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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Abstract
Antibody-free approaches for quantitative LC–MS/MS-based protein bioanalysis are reviewed and critically evaluated, and compared with the more widely used immunoaffinity-based approaches. Antibody-free workflows will be divided into four groups and discussed in the following order: direct analysis of signature peptides after proteolytic digestion; enrichment of target proteins and signature peptides by fractionated protein precipitation; enrichment of target proteins and signature peptides by reversed-phase and ion-exchange solid-phase extraction; and enrichment of target proteins and signature peptides by (antibody-free) affinity-solid-phase extraction.
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Silva-Sanchez C, Li H, Chen S. Recent advances and challenges in plant phosphoproteomics. Proteomics 2015; 15:1127-41. [PMID: 25429768 DOI: 10.1002/pmic.201400410] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/29/2014] [Accepted: 11/24/2014] [Indexed: 12/13/2022]
Abstract
Plants are sessile organisms that need to respond to environmental changes quickly and efficiently. They can accomplish this by triggering specialized signaling pathways often mediated by protein phosphorylation and dephosphorylation. Phosphorylation is a fast response that can switch on or off a myriad of biological pathways and processes. Proteomics and MS are the main tools employed in the study of protein phosphorylation. Advances in the technologies allow simultaneous identification and quantification of thousands of phosphopeptides and proteins that are essential to understanding the sophisticated biological systems and regulations. In this review, we summarize the advances in phosphopeptide enrichment and quantitation, MS for phosphorylation site mapping and new data acquisition methods, databases and informatics, interpretation of biological insights and crosstalk with other PTMs, as well as future directions and challenges in the field of phosphoproteomics.
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Affiliation(s)
- Cecilia Silva-Sanchez
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
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Li J, Silva-Sanchez C, Zhang T, Chen S, Li H. Phosphoproteomics technologies and applications in plant biology research. FRONTIERS IN PLANT SCIENCE 2015; 6:430. [PMID: 26136758 PMCID: PMC4468387 DOI: 10.3389/fpls.2015.00430] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/27/2015] [Indexed: 05/20/2023]
Abstract
Protein phosphorylation has long been recognized as an essential mechanism to regulate many important processes of plant life. However, studies on phosphorylation mediated signaling events in plants are challenged with low stoichiometry and dynamic nature of phosphorylated proteins. Significant advances in mass spectrometry based phosphoproteomics have taken place in recent decade, including phosphoprotein/phosphopeptide enrichment, detection and quantification, and phosphorylation site localization. This review describes a variety of separation and enrichment methods for phosphoproteins and phosphopeptides, the applications of technological innovations in plant phosphoproteomics, and highlights significant achievement of phosphoproteomics in the areas of plant signal transduction, growth and development.
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Affiliation(s)
- Jinna Li
- College of Life Sciences, Heilongjiang UniversityHarbin, China
| | - Cecilia Silva-Sanchez
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
| | - Tong Zhang
- Plant Molecular and Cellular Biology Program, Department of Biology, UF Genetics Institute, University of FloridaGainesville, FL, USA
| | - Sixue Chen
- College of Life Sciences, Heilongjiang UniversityHarbin, China
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
- Plant Molecular and Cellular Biology Program, Department of Biology, UF Genetics Institute, University of FloridaGainesville, FL, USA
| | - Haiying Li
- College of Life Sciences, Heilongjiang UniversityHarbin, China
- *Correspondence: Haiying Li, College of Life Sciences, Heilongjiang University, 74 Xuefu Rd, Harbin 150080, China
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Fatima B, Jabeen F, Padashbarmchi Z, Najam-ul-Haq M. Enhanced enrichment performance of nickel oxide nanoparticles via fabrication of a nanocomposite with a graphene template. RSC Adv 2015. [DOI: 10.1039/c4ra17299j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Using graphene as a template after modification with nickel oxide, a nanocomposite with an increased surface area is fabricated and applied to phosphopeptides.
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Affiliation(s)
- Batool Fatima
- Division of Analytical Chemistry
- Institute of Chemical Sciences
- Bahauddin Zakariya University
- Multan 60800
- Pakistan
| | - Fahmida Jabeen
- Division of Analytical Chemistry
- Institute of Chemical Sciences
- Bahauddin Zakariya University
- Multan 60800
- Pakistan
| | - Zahra Padashbarmchi
- Department of Environmental Sciences
- Faculty of Natural Resources
- University of Tehran
- Karaj
- Iran
| | - Muhammad Najam-ul-Haq
- Division of Analytical Chemistry
- Institute of Chemical Sciences
- Bahauddin Zakariya University
- Multan 60800
- Pakistan
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Xu L, Zhu W, Sun R, Ding Y. A Ti4+-immobilized phosphate polymer-patterned silicon substrate for on-plate selective enrichment and self-desalting of phosphopeptides. Analyst 2015; 140:3216-24. [DOI: 10.1039/c5an00102a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A circular hydrophobic–hydrophilic-Ti4+ immobilized phosphate polymer is patterned as the sample support for selective enrichment, wash-free self-desalting and mass spectroscopy (MS) analysis of phosphopeptides.
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Affiliation(s)
- Lei Xu
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Wei Zhu
- Department of Oncology
- First Affiliated Hospital of Nanjing Medical University
- Nanjing 210029
- PR China
| | - Rui Sun
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Yin Ding
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
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Huang X, Wang J, Wang J, Liu C, Wang S. Preparation of graphene–hafnium oxide composite for selective enrichment and analysis of phosphopeptides. RSC Adv 2015. [DOI: 10.1039/c5ra17471f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A novel graphene–hafnium oxide composite was prepared and applied to selective enrichment phosphopeptides from biosamples.
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Affiliation(s)
- Xuan Huang
- Key Laboratory of Food Nutrition and Safety
- Ministry of Education
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Junping Wang
- Key Laboratory of Food Nutrition and Safety
- Ministry of Education
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Junying Wang
- Biotechnology Research Institute
- Chinese Academy of Agricultural Sciences
- Beijing 10081
- China
| | - Cuicui Liu
- Key Laboratory of Food Nutrition and Safety
- Ministry of Education
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety
- Ministry of Education
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin 300457
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Zhu X, Gu J, Yang J, Wang Z, Li Y, Zhao L, Zhao W, Shi J. Zr-based metal–organic frameworks for specific and size-selective enrichment of phosphopeptides with simultaneous exclusion of proteins. J Mater Chem B 2015; 3:4242-4248. [DOI: 10.1039/c5tb00113g] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Zr-based MOFs were successfully developed as affinity adsorbents for sensitive and specific enrichment of phosphopeptides with an interesting molecule-sieving effect.
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Affiliation(s)
- Xiangyang Zhu
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Jinlou Gu
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Jian Yang
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Zhe Wang
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Yongsheng Li
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Liming Zhao
- State Key Laboratory of Bioreactor Engineering
- R&D Center of Separation and Extraction Technology in Fermentation Industry
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Wenru Zhao
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Jianlin Shi
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
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Romero-Rodríguez MC, Abril N, Sánchez-Lucas R, Jorrín-Novo JV. Multiplex staining of 2-DE gels for an initial phosphoproteome analysis of germinating seeds and early grown seedlings from a non-orthodox specie: Quercus ilex L. subsp. ballota [Desf.] Samp. FRONTIERS IN PLANT SCIENCE 2015; 6:620. [PMID: 26322061 PMCID: PMC4531236 DOI: 10.3389/fpls.2015.00620] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/27/2015] [Indexed: 05/08/2023]
Abstract
As a preliminary step in the phosphoproteome analysis of germinating seeds (0 and 24 h after seed imbibition) and early grown seedlings (216 h after seed imbibition) from a non-orthodox sp. Quercus ilex, a multiplex (SYPRO-Ruby and Pro-Q DPS) staining of high-resolution 2-DE gels was used. By using this protocol it was possible to detect changes in protein-abundance and/or phosphorylation status. This simple approach could be a good complementary alternative to the enrichment protocols used in the search for phosphoprotein candidates. While 482 spots were visualized with SYPRO-Ruby, 222 were with Pro-Q DPS. Statistically significant differences in spot intensity were observed among samples, these corresponding to 85 SYPRO-Ruby-, 20 Pro-Q-DPS-, and 35 SYPRO-Ruby and Pro-Q-DPS-stained spots. Fifty-five phosphoprotein candidates showing qualitative or quantitative differences between samples were subjected to MALDI-TOF-TOF MS analysis, with 20 of them being identified. Identified proteins belonged to five different functional categories, namely: carbohydrate and amino acid metabolism, defense, protein folding, and oxidation-reduction processes. With the exception of a putative cyclase, the other 19 proteins had at least one orthologous phosphoprotein in Arabidopsis thaliana, Medicago truncatula, N. tabacum, and Glycine max. Out of the 20 identified, seven showed differences in intensity in Pro-Q-DPS but not in SYPRO-Ruby-stained gels, including enzymes of the glycolysis and amino acid metabolism. This bears out that theory the regulation of these enzymes occurs at the post-translational level by phosphorylation with no changes at the transcriptional or translational level. This is different from the mechanism reported in orthodox seeds, in which concomitant changes in abundance and phosphorylation status have been observed for these enzymes.
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Affiliation(s)
- M. Cristina Romero-Rodríguez
- Department of Biochemistry and Molecular Biology, University of CordobaCordoba, Spain
- Agricultural and Plant Proteomics Research Group, Department of Biochemistry and Molecular Biology, Escuela Técnica Superior de Ingenieros Agrónomos y de Montes, University of CordobaCordoba, Spain
- Centro Multidisciplinario de Investigaciones Tecnológicas, Universidad Nacional de AsunciónSan Lorenzo, Paraguay
| | - Nieves Abril
- Department of Biochemistry and Molecular Biology, University of CordobaCordoba, Spain
| | - Rosa Sánchez-Lucas
- Department of Biochemistry and Molecular Biology, University of CordobaCordoba, Spain
- Agricultural and Plant Proteomics Research Group, Department of Biochemistry and Molecular Biology, Escuela Técnica Superior de Ingenieros Agrónomos y de Montes, University of CordobaCordoba, Spain
| | - Jesús V. Jorrín-Novo
- Department of Biochemistry and Molecular Biology, University of CordobaCordoba, Spain
- Agricultural and Plant Proteomics Research Group, Department of Biochemistry and Molecular Biology, Escuela Técnica Superior de Ingenieros Agrónomos y de Montes, University of CordobaCordoba, Spain
- *Correspondence: Jesús V. Jorrín-Novo, Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Rabanales, Ed. Severo Ochoa, Planta Baja, 14071 Cordoba, Spain
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Küster SK, Pabst M, Zenobi R, Dittrich PS. Automatisierte Detektion von Proteinphosphorylierung durch Nanoliter-Enzymreaktionen auf Mikroarrays. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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