1
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Aparna GM, Tetala KKR. Titanium particles incorporated polymer monolith microcolumn for phosphoprotein enrichment from biological samples. J Pharm Biomed Anal 2023; 233:115453. [PMID: 37224729 DOI: 10.1016/j.jpba.2023.115453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/28/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023]
Abstract
In proteomic studies, selective enrichment of target phosphoproteins from biological samples is of importance. Of various enrichment methods, affinity chromatography is widely preferred method. Development of micro-affinity columns with simple strategies are in constant demand. Here in this report, for the first time, we have embedded TiO2 particles within the monolith structure in a single step. Fourier transform infrared spectroscopy and scanning electron microscope analysis has confirmed the successful incorporation of TiO2 particles within the polymer monolith. Incorporation of 3-(trimethoxy silyl) propyl methacrylate within the poly(hydroxyethyl methacrylate) based monolith composition has enhanced its rigidity and one fold phosphoprotein (α-casein) adsorption capacity. Presence of only 66.6 µg of TiO2 particles within the monolith has displayed a four-fold higher affinity to α-casein over the non-phosphoprotein i.e. bovine serum albumin. Under optimized conditions (TiO2 particle and acrylate silane), the affinity monolith has a maximum adsorption capacity of ∼ 72 mg per gram monolith. Translation of TiO2 particles-monolith into a microcolumn of 3 cm long and 19 µL volume was successful. α-casein was selectively separated from an artificial protein mixture of α-casein and BSA, α-casein spiked human plasma, and cow milk within 7 min.
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Affiliation(s)
- G M Aparna
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamilnadu 632014, India
| | - Kishore K R Tetala
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamilnadu 632014, India.
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2
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Zhou X, Zhang H, Wang L, Wu R. An alkali-resistant zirconium-biligand organic framework with dual-metal centers for highly selective capture of phosphopeptides. Analyst 2022; 148:85-94. [PMID: 36444932 DOI: 10.1039/d2an01604d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The stability of MOFs plays one of the most important roles in material applications, while the delicate structure of MOFs suffers from the limitation of poor alkali tolerance. A new biligand Zr-MOF (biUIO-66-NH2NO2) with alkali-resistance performance and active functional groups has been synthesized in this study. The biUIO-66-NH2NO2 demonstrated a much better stability in 1% NH3·H2O solution than its parent material, UIO-66-NH2. Following further immobilization of Zr4+ ions, the biDZMOF consisting of dual-zirconium centers was prepared and was further applied in global enrichment of phosphopeptides by avoiding the instability of enrichment materials in the essential alkali elution procedure for the phosphopeptide enrichment workflow. The alkali-resistant elution of phosphopeptides from the biDZMOF can be directly coupled to a tandem mass spectrometry system for peptide analysis without desalting treatment. 425 phosphopeptides in total in 3 independent samples were identified from 10 μL human saliva after enrichment with biDZMOF. The improvement in alkali resistance and successful post-modification of biUIO-66-NH2NO2 suggest an efficient strategy to develop new types of MOF materials for application.
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Affiliation(s)
- Xiaoyu Zhou
- Laboratory of High-Resolution Mass Spectrometry Technologies, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China. .,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyan Zhang
- Laboratory of High-Resolution Mass Spectrometry Technologies, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China. .,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Li Wang
- Laboratory of High-Resolution Mass Spectrometry Technologies, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China. .,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Ren'an Wu
- Laboratory of High-Resolution Mass Spectrometry Technologies, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China. .,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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3
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Materials, workflows and applications of IMAC for phosphoproteome profiling in the recent decade: A review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Sahebi H, Massoud Bahrololoomi Fard S, Rahimi F, Jannat B, Sadeghi N. Ultrasound-assisted dispersive magnetic solid-phase extraction of cadmium, lead and copper ions from water and fruit juice samples using DABCO-based poly (ionic liquid) functionalized magnetic nanoparticles. Food Chem 2022; 396:133637. [PMID: 35853377 DOI: 10.1016/j.foodchem.2022.133637] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/05/2022] [Accepted: 07/03/2022] [Indexed: 11/04/2022]
Abstract
A poly (ionic liquid) (PIL) functionalized magnetic nanoparticles methodology was developed and utilized as an efficient adsorbent for the simultaneous extraction of cadmium, lead, and copper ions from water and fruit juice samples. The novel adsorbent was fabricated by grafting DABCO-based PIL onto silica-coated Fe3O4 nanoparticles via copper (0)-mediated reversible-deactivation radical polymerization. Different techniques properly characterized the developed nanoparticles. The central composite design was used to analyze the simultaneous effects of various parameters on the extraction efficiency. The detection limits for water samples ranged between 3.2 and 9.2 ng.L-1, and fruit juice samples varied from 0.0103 to 0.1082 μg.kg-1. The recovery ranged from 94.1 to 101.3% and 93.6 to 105.1% for water and fruit juice samples, respectively. The relive measurement uncertainty ranged from 7.7 to 13.6%. The proposed method is rapid, sensitive, environmentally friendly, and useful for monitoring the residues of heavy metal ions in water and fruit juice samples.
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Affiliation(s)
- Hamed Sahebi
- Halal Research Center of IRI, Food and Drug Administration, Ministry of Health and Medical Education, Tehran, Iran
| | | | - Farnaz Rahimi
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Behrooz Jannat
- Halal Research Center of IRI, Food and Drug Administration, Ministry of Health and Medical Education, Tehran, Iran.
| | - Nafiseh Sadeghi
- Department of Food and Drug Control, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
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5
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Identification, production and bioactivity of casein phosphopeptides – A review. Food Res Int 2022; 157:111360. [DOI: 10.1016/j.foodres.2022.111360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 01/23/2023]
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6
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Du Z, Yang Q, Liu Y, Chen S, Zhao H, Bai H, Shao W, Zhang Y, Qin W. A New Strategy for High-Efficient Tandem Enrichment and Simultaneous Profiling of N-Glycopeptides and Phosphopeptides in Lung Cancer Tissue. Front Mol Biosci 2022; 9:923363. [PMID: 35685241 PMCID: PMC9171396 DOI: 10.3389/fmolb.2022.923363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
N-glycosylation and phosphorylation, two common posttranslational modifications, play important roles in various biological processes and are extensively studied for biomarker and drug target screening. Because of their low abundance, enrichment of N-glycopeptides and phosphopeptides prior to LC–MS/MS analysis is essential. However, simultaneous characterization of these two types of posttranslational modifications in complex biological samples is still challenging, especially for tiny amount of samples obtained in tissue biopsy. Here, we introduced a new strategy for the highly efficient tandem enrichment of N-glycopeptides and phosphopeptides using HILIC and TiO2 microparticles. The N-glycopeptides and phosphosites obtained by tandem enrichment were 21%–377% and 22%–263% higher than those obtained by enriching the two PTM peptides separately, respectively, using 160–20 μg tryptic digested peptides as the starting material. Under the optimized conditions, 2798 N-glycopeptides from 434 N-glycoproteins and 5130 phosphosites from 1986 phosphoproteins were confidently identified from three technical replicates of HeLa cells by mass spectrometry analysis. Application of this tandem enrichment strategy in a lung cancer study led to simultaneous characterization of the two PTM peptides and discovery of hundreds of differentially expressed N-glycosylated and phosphorylated proteins between cancer and normal tissues, demonstrating the high sensitivity of this strategy for investigation of dysregulated PTMs using very limited clinical samples.
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Affiliation(s)
- Zhuokun Du
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Qianying Yang
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Yuanyuan Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Sijie Chen
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Hongxian Zhao
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
| | - Haihong Bai
- Phase I Clinical Trial Center, Beijing Shijitan Hospital of Capital Medical University, Beijing, China
| | - Wei Shao
- School of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Yangjun Zhang
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
- *Correspondence: Yangjun Zhang, ; Weijie Qin,
| | - Weijie Qin
- School of Basic Medical Science, Anhui Medical University, Hefei, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, China
- *Correspondence: Yangjun Zhang, ; Weijie Qin,
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Etier A, Dumetz F, Chéreau S, Ponts N. Post-Translational Modifications of Histones Are Versatile Regulators of Fungal Development and Secondary Metabolism. Toxins (Basel) 2022; 14:toxins14050317. [PMID: 35622565 PMCID: PMC9145779 DOI: 10.3390/toxins14050317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023] Open
Abstract
Chromatin structure is a major regulator of DNA-associated processes, such as transcription, DNA repair, and replication. Histone post-translational modifications, or PTMs, play a key role on chromatin dynamics. PTMs are involved in a wide range of biological processes in eukaryotes, including fungal species. Their deposition/removal and their underlying functions have been extensively investigated in yeasts but much less in other fungi. Nonetheless, the major role of histone PTMs in regulating primary and secondary metabolisms of filamentous fungi, including human and plant pathogens, has been pinpointed. In this review, an overview of major identified PTMs and their respective functions in fungi is provided, with a focus on filamentous fungi when knowledge is available. To date, most of these studies investigated histone acetylations and methylations, but the development of new methodologies and technologies increasingly allows the wider exploration of other PTMs, such as phosphorylation, ubiquitylation, sumoylation, and acylation. Considering the increasing number of known PTMs and the full range of their possible interactions, investigations of the subsequent Histone Code, i.e., the biological consequence of the combinatorial language of all histone PTMs, from a functional point of view, are exponentially complex. Better knowledge about histone PTMs would make it possible to efficiently fight plant or human contamination, avoid the production of toxic secondary metabolites, or optimize the industrial biosynthesis of certain beneficial compounds.
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Li J, Fan C, Yao Y, Liu Z, Li F, Jiang B. Highly efficient enrichment of intact phosphoproteins by a cadmium ion‐based co‐precipitation strategy. J Sep Sci 2022; 45:1336-1344. [DOI: 10.1002/jssc.202100892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Jiangfeng Li
- School of Basic Medical Sciences, Academy of Medical Science Zhengzhou University Zhengzhou China
| | - Chongyuan Fan
- School of Basic Medical Sciences, Academy of Medical Science Zhengzhou University Zhengzhou China
| | - Yating Yao
- School of Basic Medical Sciences, Academy of Medical Science Zhengzhou University Zhengzhou China
| | - Zhaochen Liu
- The First Affiliated Hospital of Zhengzhou University Zhengzhou University Zhengzhou China
| | - Fangfang Li
- School of Basic Medical Sciences, Academy of Medical Science Zhengzhou University Zhengzhou China
| | - Binghua Jiang
- School of Basic Medical Sciences, Academy of Medical Science Zhengzhou University Zhengzhou China
- Department of Pathology, Anatomy and Cell Biology Thomas Jefferson University Philadelphia PA19107 USA
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Analysis of Proteomic Characteristics of Peripheral Blood in Preeclampsia and Study of Changes in Fetal Arterial Doppler Parameters Based on Magnetic Nanoparticles. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:7145487. [PMID: 34765014 PMCID: PMC8577888 DOI: 10.1155/2021/7145487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022]
Abstract
Background Traditional mass spectrometry detection methods have low detection efficiency for low-abundance proteins, thus limiting the application of proteomic analysis in the diagnosis of preeclampsia. Magnetic nanomaterials have good superparamagnetism and have obvious advantages in the field of biological separation and enrichment. Aim The objective of this study is to explore the value of superparamagnetic iron oxide nanoparticles in the proteomic analysis of preeclampsia. Materials and Methods 42 patients and 40 normal pregnant women were selected in this study for analysis. Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed to evaluate the function of these differential proteins. Proteomic analysis was used to analyze the differential proteins. Color Doppler ultrasound technology was used to detect changes in the blood flow of the fetal umbilical artery and cerebral artery. Results 16 differential proteins in the serum of pregnant women with preeclampsia and normal pregnant women were detected. The 16 proteins are mainly related to angiogenesis and endothelial function proteins, coagulation cascade proteins, placental growth factor, and so on. Biological function analysis revealed that these proteins are mainly enriched in the nuclear factor kB (NF-κB) signaling pathway. Moreover, our data suggested that compared with the fetus in the uterus of normal pregnant women, the umbilical artery S/D, PI, and RI of the fetus in preeclampsia were greatly increased, and the cerebral artery S/D, PI, and RI were greatly decreased. Conclusion Biological function analysis revealed that 16 proteins are mainly enriched in the NF-κB signaling pathway. Compared with the normal group, the umbilical artery S/D, PI, and RI of the preeclampsia group were greatly increased, and the cerebral artery S/D, PI, and RI were all greatly reduced. Our findings provided a more comprehensive reference for us to study the mechanism of preeclampsia at the molecular level and also provide data support for the screening of relevant markers for early diagnosis of preeclampsia.
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Partial-, Double-Enzymatic Dephosphorylation and EndoGluC Hydrolysis as an Original Approach to Enhancing Identification of Casein Phosphopeptides (CPPs) by Mass Spectrometry. Foods 2021; 10:foods10092134. [PMID: 34574245 PMCID: PMC8471704 DOI: 10.3390/foods10092134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 01/07/2023] Open
Abstract
The identification of phosphopeptides is currently a challenge when they are part of a complex matrix of peptides, such as a milk protein enzymatic hydrolysate. This challenge increases with both the number of phosphorylation sites on the phosphopeptides and their amino acid length. Here, this paper reports a four-phase strategy from an enzymatic casein hydrolysate before a mass spectrometry analysis in order to enhance the identification of phosphopeptides and phosphosites: (i) the control protein hydrolysate, (ii) a two-step enzymatic dephosphorylation of the latter, allowing for the almost total dephosphorylation of peptides, (iii) a one-step enzymatic dephosphorylation, allowing for the partial dephosphorylation of the peptides and (iv) an additional endoGluC enzymatic hydrolysis, allowing for the cleavage of long-size peptides into shorter ones. The reverse-phase high-pressure liquid chromatography–tandem mass spectrometry (RP-HPLC-MS/MS) analyses of hydrolysates that underwent this four-phase strategy allowed for the identification of 28 phosphorylation sites (90%) out of the 31 referenced in UniprotKB/Swiss-Prot (1 June 2021), compared to 17 sites (54%) without the latter. The alpha-S2 casein phosphosites, referenced by their similarity in the UniProt database, were experimentally identified, whereas pSer148, pThr166 and pSer187 from a multiphosphorylated long-size kappa-casein were not. Data are available via ProteomeXchange with identifier PXD027132.
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Hu W, Liu L, Fan Y, Huang M. Facile synthesis of mesoporous copper silicate aggregates for highly selective enrichment of hemoglobin. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Wang X, Yu J, Yang H, Shen J, Liu H, Zhou J. A new Ti-based IMAC nanohybrid with high hydrophilicity and enhanced absorption capacity for the selective enrichment of phosphopeptides. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1179:122851. [PMID: 34246169 DOI: 10.1016/j.jchromb.2021.122851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/24/2021] [Accepted: 06/27/2021] [Indexed: 11/17/2022]
Abstract
Ti-based immobilized metal affinity chromatography (IMAC) nanomaterial has shown high potential in phosphoproteome mass-spectrometric (MS) analysis. However, the limited surface area and poor solubility will greatly restrict its use in phosphoproteome research. To overcome these two key drawbacks, a novel Ti-based IMAC nanomaterial was prepared by Ti-bonded β-cyclodextrin (β-CD) anchored on the surface of carbon nanotubes (CNTs) (denoted as COOH-CNTs-CD-Ti) and successfully applied as a biofunctional adsorbent for selectively enriching trace phosphopeptides. In the selective enrichment process, CNTs provided greater surface area for the absorption of phosphopeptides, while β-CD also offered a greater opportunity for the interaction between phosphopeptides and Ti4+. COOH-CNTs-CD-Ti with the aforementioned properities exhibited higher selectivity for phosphopeptides from the standard protein digests, the tryptic digests of nonfat milk and human serum, showing a great selective enrichment capability towards complex biological samples.
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Affiliation(s)
- XinHui Wang
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China; College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - JiaLin Yu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - HaoDing Yang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jian Shen
- College of Chemistry and Materials Science, Jiangsu Key Laboratory of Biofunctional Materials, Nanjing Normal University, Nanjing 210023, China
| | - HaiLong Liu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - JiaHong Zhou
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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14
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Hydrophilic polydopamine-derived mesoporous channels for loading Ti(IV) ions for salivary phosphoproteome research. Anal Chim Acta 2020; 1146:53-60. [PMID: 33461719 DOI: 10.1016/j.aca.2020.12.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/21/2020] [Accepted: 12/18/2020] [Indexed: 11/20/2022]
Abstract
Salivary phosphoproteome holds great promise in clinic diagnosis. For profiling of salivary phosphoproteome, it is essential to develop efficient enrichment methods prior to mass spectrum (MS). Among developed enrichment strategies, immobilized metal ions affinity chromatography (IMAC) has exhibited outstanding performance. In this work, we report a coherent approach where polydopamine (PDA) is first utilized to form mesoporous structure through soft templating method, then chelated with Ti4+ to construct hydrophilic polydopamine-derived magnetic mesoporous nanocomposite (denoted Fe3O4@mPDA@Ti4+). In virtue of the merits including ordered mesoporous channels, appropriate superparamagnetism, and abundant Ti4+, the enrichment strategy based on Fe3O4@mPDA@Ti4+ combined with MS is employed for accurate identification of phosphopeptides in β-casein digest and human saliva. As expected, Fe3O4@mPDA@Ti4+ revealed a great selectivity (1:200) and a low detection limit (0.1 fmol μL-1) toward phosphopeptides. More importantly, the further successful capture of phosphopeptides from human saliva indicated the prominent potential of this method for seeking phosphopeptide biomarkers in further analysis.
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Capriotti AL, Aita SE, Cavaliere C, Cerrato A, Montone CM, Piovesana S, Laganà A. A rapid and innovative extraction and enrichment method for the metaproteomic characterization of dissolved organic matter in groundwater samples. J Sep Sci 2020; 44:1612-1620. [PMID: 33236487 DOI: 10.1002/jssc.202001025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/13/2020] [Accepted: 11/20/2020] [Indexed: 11/08/2022]
Abstract
Metaproteomic analysis of aquifer systems provides valuable information on the microbial populations, their influence on drinking water quality, and the effect on human health. In the present paper, an extraction and enrichment method by C18 extra-wide pore cartridge was developed, optimized, and applied for the first time to the metaproteomic characterization of dissolved organic matter in groundwater samples. In particular, three elution procedures were tested and compared on water spiked with a yeast protein extract to maximize the recovery of proteins from a complex matrix. The maximum protein recovery was obtained by the use of two sequential elution buffers, one employing a denaturing agent and the other one containing an acidified organic solvent. A comprehensive metaproteomic analysis of the dissolved organic matter of groundwater was then performed by nano-high performance liquid chromatography coupled to high-resolution mass spectrometry. A total of 239 proteins was identified; in agreement with the current knowledge on proteins in aquifer systems, most identified sequences derived from bacteria, protobacteria, and ciliates. The paper is the first metaproteomic study applied to groundwater samples with particular emphasis on the need for sample pretreatment to obtain comprehensive information on the proteome in dissolved organic matter.
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Affiliation(s)
| | - Sara Elsa Aita
- Department of Chemistry, Università di Roma "La Sapienza,", Rome, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Università di Roma "La Sapienza,", Rome, Italy
| | - Andrea Cerrato
- Department of Chemistry, Università di Roma "La Sapienza,", Rome, Italy
| | | | - Susy Piovesana
- Department of Chemistry, Università di Roma "La Sapienza,", Rome, Italy
| | - Aldo Laganà
- Department of Chemistry, Università di Roma "La Sapienza,", Rome, Italy.,CNR NANOTEC, Campus Ecotekne, University of Salento, Lecce, Italy
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Sürmen MG, Sürmen S, Ali A, Musharraf SG, Emekli N. Phosphoproteomic strategies in cancer research: a minireview. Analyst 2020; 145:7125-7149. [PMID: 32996481 DOI: 10.1039/d0an00915f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Understanding the cellular processes is central to comprehend disease conditions and is also true for cancer research. Proteomic studies provide significant insight into cancer mechanisms and aid in the diagnosis and prognosis of the disease. Phosphoproteome is one of the most studied complements of the whole proteome given its importance in the understanding of cellular processes such as signaling and regulations. Over the last decade, several new methods have been developed for phosphoproteome analysis. A significant amount of these efforts pertains to cancer research. The current use of powerful analytical instruments in phosphoproteomic approaches has paved the way for deeper and sensitive investigations. However, these methods and techniques need further improvements to deal with challenges posed by the complexity of samples and scarcity of phosphoproteins in the whole proteome, throughput and reproducibility. This review aims to provide a comprehensive summary of the variety of steps used in phosphoproteomic methods applied in cancer research including the enrichment and fractionation strategies. This will allow researchers to evaluate and choose a better combination of steps for their phosphoproteome studies.
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Affiliation(s)
- Mustafa Gani Sürmen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Saime Sürmen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Arslan Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Syed Ghulam Musharraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Nesrin Emekli
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Medipol University, Istanbul, Turkey
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Sahebi H, Konoz E, Ezabadi A, Niazi A, Ahmadi SH. Sensitive Determination of Imatinib Mesylate in Human Plasma Using DABCO-Based Ionic Liquid-Modified Magnetic Nanoparticles. Chromatographia 2020. [DOI: 10.1007/s10337-020-03923-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Liu W, Tang H, Abuzeid AMI, Tan L, Wang A, Wan X, Zhang H, Liu Y, Li G. Protein phosphorylation networks in spargana of Spirometra erinaceieuropaei revealed by phosphoproteomic analysis. Parasit Vectors 2020; 13:248. [PMID: 32404185 PMCID: PMC7218563 DOI: 10.1186/s13071-020-04119-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 05/06/2020] [Indexed: 01/07/2023] Open
Abstract
Background Sparganosis caused by Spirometra erinaceieuropaei spargana is a zoonotic parasitic infection that has been reported in many countries, including China, Japan, Thailand and Korea, as well as European countries and the USA. The biological and clinical significance of the parasite have previously been reported. Although the genomic and transcriptomic analysis of S. erinaceieuropaei provided insightful views about the development and pathogenesis of this species, little knowledge has been acquired in terms of post-translational regulation that is essential for parasite growth, development and reproduction. Here, we performed site-specific phosphoproteomic profiling, with an aim to obtain primary information about the global phosphorylation status of spargana. Results A total of 3228 phosphopeptides and 3461 phosphorylation sites were identified in 1758 spargana proteins. The annotated phosphoproteins were involved in a variety of biological pathways, including cellular (28%), metabolic (20%) and single-organism (17%) processes. The functional enrichment of phosphopeptides by Gene Ontology analysis indicated that most spargana phosphoproteins were related to the cytoskeleton cellular compartment, signaling molecular function, and a variety of biological processes, including a molecular function regulator, guanyl-nucleotide exchange factor activity, protein kinase activities, and calcium ion binding. The highly enriched pathways of phosphorylation proteins include the phosphatidylinositol signaling system, phagosome, endocytosis, inositol phosphate metabolism, terpenoid backbone biosynthesis, and peroxisome. Domain analysis identified an EF-hand domain and pleckstrin homology domain among the key domains. Conclusions To our knowledge, this study performed the first global phosphoproteomic analysis of S. erinaceieuropaei. The dataset reported herein provides a valuable resource for future studies on the signaling pathways of this important zoonotic parasite.![]()
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Affiliation(s)
- Wei Liu
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China.,The Key Laboratory of Animal Vaccine & Protein Engineering, Changsha, 410128, Hunan, People's Republic of China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong Province, People's Republic of China
| | - Asmaa M I Abuzeid
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Lei Tan
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China.,The Key Laboratory of Animal Vaccine & Protein Engineering, Changsha, 410128, Hunan, People's Republic of China
| | - Aibing Wang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China.,The Key Laboratory of Animal Vaccine & Protein Engineering, Changsha, 410128, Hunan, People's Republic of China
| | - Xueping Wan
- Department of Physiology, Medical College of Georgia at Augusta University, Augusta, GA, 30912, USA
| | - Haoji Zhang
- College of Life Science and Engineering, Foshan University, Foshan, 528225, Guangdong Province, People's Republic of China
| | - Yisong Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, People's Republic of China. .,Department of Physiology, Medical College of Georgia at Augusta University, Augusta, GA, 30912, USA.
| | - Guoqing Li
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
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Sahebi H, Konoz E, Ezabadi A, Niazi A, Ahmadi SH. Simultaneous determination of five penicillins in milk using a new ionic liquid-modified magnetic nanoparticle based dispersive micro-solid phase extraction followed by ultra-performance liquid chromatography-tandem mass spectrometry. Microchem J 2020. [DOI: 10.1016/j.microc.2020.104605] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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20
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Qiu W, Evans CA, Landels A, Pham TK, Wright PC. Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials. Anal Chim Acta 2020; 1129:158-180. [PMID: 32891386 DOI: 10.1016/j.aca.2020.04.053] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022]
Abstract
Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.
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Affiliation(s)
- Wen Qiu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China
| | - Caroline A Evans
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Andrew Landels
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Trong Khoa Pham
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom.
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21
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Yıldırım D, Kip Ç, Tsogtbaatar K, Koçer İ, Çelik E, Tuncel A. Microfluidic immobilized metal affinity chromatography based on Ti(IV)-decorated silica microspheres for purification of phosphoproteins. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1140:122010. [DOI: 10.1016/j.jchromb.2020.122010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 12/20/2019] [Accepted: 01/30/2020] [Indexed: 02/09/2023]
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22
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Piovesana S, Capriotti AL, Cavaliere C, Sparnacci K, Gianotti V, Laus M, Antonioli D, Laganà A. Magnetic molecularly imprinted multishell particles for zearalenone recognition. POLYMER 2020. [DOI: 10.1016/j.polymer.2019.122102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Chaowamalee S, Ngamcharussrivichai C. Facile fabrication of mesostructured natural rubber/silica nanocomposites with enhanced thermal stability and hydrophobicity. NANOSCALE RESEARCH LETTERS 2019; 14:382. [PMID: 31848825 PMCID: PMC6917676 DOI: 10.1186/s11671-019-3197-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
Natural rubber (NR)/hexagonal mesoporous silica (HMS) nanocomposites (NRHMS) with enhanced thermal and hydrophobic properties were facilely prepared via in situ sol-gel formation with pH adjustment using a low sulphuric acid (H2SO4) acid concentration. The effect of the amount of 0.5 M H2SO4 (2.5-10 g) added into the pre-synthesis mixture on the physicochemical properties of the obtained NRHMS nanocomposites was investigated. With a small addition of H2SO4 solution, the fabricated NRHMS nanocomposite possessed an improved wormhole-like mesostructure arrangement with a thicker silica wall, which retarded the thermal decomposition of the NR phase, as deduced from the auto-oxidation of NR by thermogravimetric analysis. The H2O adsorption-desorption measurement revealed an increased hydrophobicity of the NRHMS composites, explained by the acid-catalyzed bridging of free silanol groups to siloxane bonds, which was supported by the X-ray photoelectron spectroscopy analysis. Scanning transmission electron microscopy with energy dispersive X-ray spectroscopy elemental mapping revealed a good dispersion of the NR phase within the mesostructured silica. However, a high amount of added H2SO4 solution led to silica-NR phase separation due to the decreased hydrophobic interaction between the silica precursor and rubber chain, as well as an agglomeration of the NR phase itself. The mechanism of NRHMS nanocomposite formation under pH-controlled conditions was proposed to proceed via a cooperative self-assembly route.
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Affiliation(s)
- Supphathee Chaowamalee
- Department of Chemical Technology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
- Center of Excellence on Petrochemical and Materials Technology (PETROMAT), Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Chawalit Ngamcharussrivichai
- Department of Chemical Technology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.
- Center of Excellence on Petrochemical and Materials Technology (PETROMAT), Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.
- Center of Excellence in Catalysis for Bioenergy and Renewable Chemicals (CBRC), Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.
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Capriotti AL, Antonelli M, Antonioli D, Cavaliere C, Chiarcos R, Gianotti V, Piovesana S, Sparnacci K, Laus M, Laganà A. Effect of shell structure of Ti-immobilized metal ion affinity chromatography core-shell magnetic particles for phosphopeptide enrichment. Sci Rep 2019; 9:15782. [PMID: 31673007 PMCID: PMC6823385 DOI: 10.1038/s41598-019-51995-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/28/2019] [Indexed: 11/09/2022] Open
Abstract
Magnetic materials in sample preparation for shotgun phosphoproteomics offer several advantages over conventional systems, as the enrichment can be achieved directly in solution, but they still suffer from some drawbacks, due to limited stability and selectivity, which is supposed to be affected by the hydrophilicity of the polymeric supports used for cation immobilization. The paper describes the development of an improved magnetic material with increased stability, thanks to a two-step covering of the magnetic core, for the enrichment of phosphopeptides in biological samples. Four materials were prepared featuring a polymeric shell with tunable hydrophilicity, obtained by "grafting from" polymerization of glycidyl methacrylate with 0-8.3% of polyethylene glycol methacrylate (PEGMA), the latter used to modulate the hydrophilicity of the material surface. Finally, the materials were functionalized with iminodiacetic acid for Ti4+ ion immobilization. The materials were analyzed for their composition by a combination of CHN elemental analysis and thermogravimetric analysis, also hyphenated to gas chromatography and mass spectrometric detection. Surface characteristics were evaluated by water contact angle measurements, scanning electron microscopy and energy dispersive X-ray spectrometry. These materials were applied to the enrichment of phosphopeptides from yeast protein digests. Peptides were identified by proteomics techniques using nano-high performance liquid chromatography coupled to mass spectrometry and bioinformatics. Qualitatively the peptides identified by the four systems were comparable, with 1606-1693 phosphopeptide identifications and a selectivity of 47-54% for all materials. The physico-chemical features of the identified peptides were also the same for the four materials. In particular, the grand average of hydropathy index values indicated that the enriched phosphopeptides were hydrophilic (ca. 90%), and only some co-enriched non-phosphorylated peptides were hydrophobic (21-28%), regardless of the material used for enrichment. Peptides had a pI ≤ 7, which indicated a well-known bias for acidic peptides binding, attributed to the interaction with the metal center itself. The results indicated that the enrichment of phosphopeptides and the co-enrichment of non-phosphorylated peptides is mainly driven by interactions with Ti4+ and does not depend on the amount of PEGMA chains in the polymer shell.
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Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Michela Antonelli
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Diego Antonioli
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
- INSTM, UdR Alessandria, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Riccardo Chiarcos
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
| | - Valentina Gianotti
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
- INSTM, UdR Alessandria, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Susy Piovesana
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Katia Sparnacci
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
- INSTM, UdR Alessandria, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Michele Laus
- Department of Science and Technological Innovation, Università degli Studi del Piemonte Orientale, Alessandria, Italy
- INSTM, UdR Alessandria, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Aldo Laganà
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
- CNR NANOTEC, Campus Ecotekne, University of Salento, Via Monteroni, 73100, Lecce, Italy
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Layer-by-layer assembled magnetic bimetallic metal-organic framework composite for global phosphopeptide enrichment. J Chromatogr A 2019; 1601:45-52. [DOI: 10.1016/j.chroma.2019.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/22/2022]
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26
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Wang S, Zhang J, Cai W, Shao X. Titanium dioxide as an adsorbent to enhance the detection ability of near-infrared diffuse reflectance spectroscopy. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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27
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Capriotti AL, Cavaliere C, La Barbera G, Montone CM, Piovesana S, Laganà A. Recent Applications of Magnetic Solid-phase Extraction for Sample Preparation. Chromatographia 2019. [DOI: 10.1007/s10337-019-03721-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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28
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Yu Y, Qi Y, Jin Y. Milk digestion peptidomics: Tracking caseinophosphopeptides in simulated gastrointestinal digestion. FOOD BIOSCI 2019. [DOI: 10.1016/j.fbio.2019.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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29
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Sahebi H, Konoz E, Ezabadi A. Synthesis of DABCO-based ionic liquid functionalized magnetic nanoparticles as a novel sorbent for the determination of cephalosporins in milk samples by dispersive solid-phase extraction followed by ultra-performance liquid chromatography-tandem mass spectrometry. NEW J CHEM 2019. [DOI: 10.1039/c9nj02200g] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this study, DABCO-based ionic liquid-functionalized magnetic iron oxide nanoparticles were synthesized for the first time by the quaternization reaction with 1-(2,3-dihydroxypropyl)-1,4-diazabicyclo[2.2.2]octanylium chloride and chloro-functionalized Fe3O4 nanoparticles.
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Affiliation(s)
- Hamed Sahebi
- Department of Chemistry
- Faculty of Science
- Azad University Central Tehran Branch
- Tehran
- Iran
| | - Elaheh Konoz
- Department of Chemistry
- Faculty of Science
- Azad University Central Tehran Branch
- Tehran
- Iran
| | - Ali Ezabadi
- Department of Chemistry
- Faculty of Science
- Azad University Central Tehran Branch
- Tehran
- Iran
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Tan S, Wang J, Han Q, Liang Q, Ding M. A porous graphene sorbent coated with titanium(IV)-functionalized polydopamine for selective lab-in-syringe extraction of phosphoproteins and phosphopeptides. Mikrochim Acta 2018; 185:316. [PMID: 29876662 DOI: 10.1007/s00604-018-2846-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/22/2018] [Indexed: 11/26/2022]
Abstract
A novel polydopamine coated three-dimensional porous graphene aerogel sorbent carrying immobilized titanium(IV) ions (denoted as Ti4+@PDA@GA) was fabricated without using an organic solvent. The material is shown to be a viable carbon foam type of monolithic sorbent for selective lab-in-syringe enrichment of phosphoproteins and phosphopeptides. The phosphoproteins can be separated from a sample by aspiration and then bind to the sorbent. The analytes then can be dispensed within 5 min. The weight percent of titanium in the monolith typically is 14%, and the absorption capacities for the model proteins β-casein and κ-casein are 1300 and 1345 mg g-1, respectively. The absorption capacities for nonphosphoproteins are much smaller, typically 160 mg g-1 for β-lactoglobulin, 125 mg g-1 for bovine serum, and 4.8 mg g-1 for lysozyme. The results demonstrate that the selectivity for phosphoproteins was excellent on multiple biological samples including standard protein mixtures, spiked human blood serum, and drinking milk. The selective enrichment of phosphopeptides also makes the method a promising tool in phosphoproteomics. Graphical abstract Schematic of a polydopamine coated three-dimensional porous graphene aerogel for immobilization of titanium(IV) ions. The material served as a monolithic sorbent for selective enrichment of phosphopeptides and phosphoproteins from biological samples. The enrichment process can be carried out conveniently using a lab-in-syringe way.
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Affiliation(s)
- Siyuan Tan
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology;Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Jundong Wang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology;Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Qiang Han
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology;Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Qionglin Liang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology;Department of Chemistry, Tsinghua University, Beijing, 100084, China.
| | - Mingyu Ding
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology;Department of Chemistry, Tsinghua University, Beijing, 100084, China.
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Núñez C, Chantada-Vázquez MDP, Bravo SB, Vázquez-Estévez S. Novel functionalized nanomaterials for the effective enrichment of proteins and peptides with post-translational modifications. J Proteomics 2018; 181:170-189. [DOI: 10.1016/j.jprot.2018.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/02/2018] [Accepted: 04/09/2018] [Indexed: 02/07/2023]
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Peptidomic strategy for purification and identification of potential ACE-inhibitory and antioxidant peptides in Tetradesmus obliquus microalgae. Anal Bioanal Chem 2018; 410:3573-3586. [DOI: 10.1007/s00216-018-0925-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/15/2018] [Accepted: 01/29/2018] [Indexed: 01/10/2023]
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Saliva as a source of new phosphopeptide biomarkers: Development of a comprehensive analytical method based on shotgun peptidomics. Talanta 2018; 183:245-249. [PMID: 29567172 DOI: 10.1016/j.talanta.2018.02.085] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 12/15/2022]
Abstract
The paper describes the development of an enrichment method for the analysis of the endogenous phosphopeptides in saliva. The method was based on magnetic solid phase extraction by a magnetic graphitized carbon black-TiO2 composite material and was developed considering different saliva pre-treatments, namely C18 solid phase extraction for purification, direct dilution in loading buffer or acetonitrile precipitation. The method was based on a shotgun proteomics workflow and the enriched peptide mixture was analysed by nanoHPLC and high resolution tandem mass spectrometry. Acetonitrile precipitation provided the best results, with up to 165 endogenous phosphopeptides identified in saliva samples from healthy individuals. The physico-chemical features of the identified endogenous phosphopeptides indicated that such peptides were large, hydrophilic and basic.
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La Barbera G, Capriotti AL, Cavaliere C, Ferraris F, Laus M, Piovesana S, Sparnacci K, Laganà A. Development of an enrichment method for endogenous phosphopeptide characterization in human serum. Anal Bioanal Chem 2018; 410:1177-1185. [DOI: 10.1007/s00216-017-0822-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/05/2017] [Accepted: 12/08/2017] [Indexed: 12/15/2022]
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