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MALDI Profiling and Applications in Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:27-43. [DOI: 10.1007/978-3-030-15950-4_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kachuk C, Faulkner M, Liu F, Doucette AA. Automated SDS Depletion for Mass Spectrometry of Intact Membrane Proteins though Transmembrane Electrophoresis. J Proteome Res 2016; 15:2634-42. [DOI: 10.1021/acs.jproteome.6b00199] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Carolyn Kachuk
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Melissa Faulkner
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Fang Liu
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alan A. Doucette
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
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Gianazza E, Miller I, Palazzolo L, Parravicini C, Eberini I. With or without you — Proteomics with or without major plasma/serum proteins. J Proteomics 2016; 140:62-80. [DOI: 10.1016/j.jprot.2016.04.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 12/26/2022]
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Maijaroen S, Anwised P, Klaynongsruang S, Daduang S, Boonmee A. Comparison of recombinant α-hemoglobin from Crocodylus siamensis expressed in different cloning vectors and their biological properties. Protein Expr Purif 2016; 118:55-63. [DOI: 10.1016/j.pep.2015.09.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 09/26/2015] [Accepted: 09/29/2015] [Indexed: 10/23/2022]
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Monari E, Cuoghi A, Bellei E, Bergamini S, Lucchi A, Tomasi A, Cortellini P, Zaffe D, Bertoldi C. Analysis of protein expression in periodontal pocket tissue: a preliminary study. Proteome Sci 2015; 13:33. [PMID: 26719749 PMCID: PMC4696085 DOI: 10.1186/s12953-015-0089-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/18/2015] [Indexed: 02/08/2023] Open
Abstract
Background The periodontal disease is caused by a set of inflammatory disorders characterized by periodontal pocket formation that lead to tooth loss if untreated. The proteomic profile and related molecular conditions of pocket tissue in periodontally-affected patients are not reported in literature. To characterize the proteomic profile of periodontally-affected patients, their interproximal periodontal pocket tissue was compared with that of periodontally-healthy patients. Pocket-associated and healthy tissue samples, harvested during surgical therapy, were treated to extract the protein content. Tissues were always collected at sites where no periodontal-pathogenic bacteria were detectable. Proteins were separated using two-dimensional gel electrophoresis and identified by liquid chromatography/mass spectrometry. After identification, four proteins were selected for subsequent Western Blot quantitation both in pathological and healty tissues. Results A significant unbalance in protein expression between healthy and pathological sites was recorded. Thirty-two protein spots were overall identified, and four proteins (S100A9, HSPB1, LEG7 and 14-3-3) were selected for Western blot analysis of both periodontally-affected and healthy patients. The four selected proteins resulted over-expressed in periodontal pocket tissue when compared with the corresponding tissue of periodontally-healthy patients. The results of Western blot analysis are congruent with the defensive and the regenerative reaction of injured periodontal tissues. Conclusions The proteomic analysis was performed for the first time directly on periodontal pocket tissue. The proteomic network highlighted in this study enhances the understanding of periodontal disease pathogenesis necessary for specific therapeutic strategies setting.
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Affiliation(s)
- Emanuela Monari
- Department of Diagnostic, Clinical and Public Health Medicine, University of Modena and Reggio Emilia, Largo del Pozzo, 71-41124 Modena, Italy
| | - Aurora Cuoghi
- Department of Diagnostic, Clinical and Public Health Medicine, University of Modena and Reggio Emilia, Largo del Pozzo, 71-41124 Modena, Italy
| | - Elisa Bellei
- Department of Diagnostic, Clinical and Public Health Medicine, University of Modena and Reggio Emilia, Largo del Pozzo, 71-41124 Modena, Italy
| | - Stefania Bergamini
- Department of Diagnostic, Clinical and Public Health Medicine, University of Modena and Reggio Emilia, Largo del Pozzo, 71-41124 Modena, Italy
| | | | - Aldo Tomasi
- Department of Diagnostic, Clinical and Public Health Medicine, University of Modena and Reggio Emilia, Largo del Pozzo, 71-41124 Modena, Italy
| | | | - Davide Zaffe
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Carlo Bertoldi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences with Transplant Surgery, Oncology and Regenerative Medicine Relevance, University of Modena and Reggio Emilia, Modena, Italy
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Sapan CV, Lundblad RL. Review of methods for determination of total protein and peptide concentration in biological samples. Proteomics Clin Appl 2015; 9:268-76. [DOI: 10.1002/prca.201400088] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 01/08/2015] [Accepted: 01/27/2015] [Indexed: 11/06/2022]
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Doucette AA, Vieira DB, Orton DJ, Wall MJ. Resolubilization of precipitated intact membrane proteins with cold formic acid for analysis by mass spectrometry. J Proteome Res 2014; 13:6001-12. [PMID: 25384094 DOI: 10.1021/pr500864a] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein precipitation in organic solvent is an effective strategy to deplete sodium dodecyl sulfate (SDS) ahead of MS analysis. Here we evaluate the recovery of membrane and water-soluble proteins through precipitation with chloroform/methanol/water or with acetone (80%). With each solvent system, membrane protein recovery was greater than 90%, which was generally higher than that of cytosolic proteins. With few exceptions, residual supernatant proteins detected by MS were also detected in the precipitation pellet, having higher MS signal intensity in the pellet fraction. Following precipitation, we present a novel strategy for the quantitative resolubilization of proteins in an MS-compatible solvent system. The pellet is incubated at -20 °C in 80% formic acid/water and then diluted 10-fold with water. Membrane protein recovery matches that of sonication of the pellet in 1% SDS. The resolubilized proteins are stable at room temperature, with no observed formylation as is typical of proteins suspended in formic acid at room temperature. The protocol is applied to the molecular weight determination of membrane proteins from a GELFrEE-fractionated sample of Escherichia coli proteins.
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Affiliation(s)
- Alan A Doucette
- Department of Chemistry and ‡Department of Pathology, Dalhousie University , Halifax, Nova Scotia, Canada
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Lichtenauer AM, Herzog R, Tarantino S, Aufricht C, Kratochwill K. Equalizer technology followed by DIGE-based proteomics for detection of cellular proteins in artificial peritoneal dialysis effluents. Electrophoresis 2014; 35:1387-94. [DOI: 10.1002/elps.201300499] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/17/2014] [Accepted: 02/21/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Anton Michael Lichtenauer
- Department of Pediatrics and Adolescent Medicine; Medical University of Vienna; Austria
- Zytoprotec GmbH; Vienna Austria
| | - Rebecca Herzog
- Department of Pediatrics and Adolescent Medicine; Medical University of Vienna; Austria
- Zytoprotec GmbH; Vienna Austria
| | - Silvia Tarantino
- Department of Pediatrics and Adolescent Medicine; Medical University of Vienna; Austria
| | - Christoph Aufricht
- Department of Pediatrics and Adolescent Medicine; Medical University of Vienna; Austria
| | - Klaus Kratochwill
- Department of Pediatrics and Adolescent Medicine; Medical University of Vienna; Austria
- Zytoprotec GmbH; Vienna Austria
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Dudley E. MALDI Profiling and Applications in Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:33-58. [DOI: 10.1007/978-3-319-06068-2_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Henning AK, Groschup MH, Mettenleiter TC, Karger A. Analysis of the bovine plasma proteome by matrix-assisted laser desorption/ionisation time-of-flight tandem mass spectrometry. Vet J 2013; 199:175-80. [PMID: 24268478 DOI: 10.1016/j.tvjl.2013.10.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 10/15/2013] [Accepted: 10/18/2013] [Indexed: 01/03/2023]
Abstract
In this study, the bovine plasma proteome was analysed using a three step protocol: (1) plasma was treated with a combinatorial peptide ligand library (CPLL) to assimilate the differences in concentrations of different proteins in raw plasma; (2) CPLL-treated material was fractionated by three standard electrophoretic separation techniques, and (3) samples were analysed by nano-liquid chromatography (nLC) matrix-assisted laser desorption/ionisation (MALDI) time-of-flight tandem (TOF/TOF) mass spectrometry. The efficiencies of three fractionation protocols for plasma proteome analysis were compared. After size fractionation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), resolution of proteins was better and yields of identified proteins were higher than after charge-based fractionation by preparative gel-free isoelectric focussing. For proteins with isoelectric points >6 and molecular weights ⩾ 63 kDa, the best results were obtained with a 'shotgun' approach, in which the CPLL-treated plasma was digested and the peptides, rather than the proteins, were fractionated by gel-free isoelectric focussing. However, the three fractionation techniques were largely complementary, since only about one-third of the proteome was identified by each approach.
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Affiliation(s)
- Ann-Kristin Henning
- Institute of Molecular Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany; Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Thomas C Mettenleiter
- Institute of Molecular Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Axel Karger
- Institute of Molecular Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany.
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Tomatis VM, Papadopulos A, Malintan NT, Martin S, Wallis T, Gormal RS, Kendrick-Jones J, Buss F, Meunier FA. Myosin VI small insert isoform maintains exocytosis by tethering secretory granules to the cortical actin. ACTA ACUST UNITED AC 2013; 200:301-20. [PMID: 23382463 PMCID: PMC3563687 DOI: 10.1083/jcb.201204092] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Before undergoing neuroexocytosis, secretory granules (SGs) are mobilized and tethered to the cortical actin network by an unknown mechanism. Using an SG pull-down assay and mass spectrometry, we found that myosin VI was recruited to SGs in a Ca(2+)-dependent manner. Interfering with myosin VI function in PC12 cells reduced the density of SGs near the plasma membrane without affecting their biogenesis. Myosin VI knockdown selectively impaired a late phase of exocytosis, consistent with a replenishment defect. This exocytic defect was selectively rescued by expression of the myosin VI small insert (SI) isoform, which efficiently tethered SGs to the cortical actin network. These myosin VI SI-specific effects were prevented by deletion of a c-Src kinase phosphorylation DYD motif, identified in silico. Myosin VI SI thus recruits SGs to the cortical actin network, potentially via c-Src phosphorylation, thereby maintaining an active pool of SGs near the plasma membrane.
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Affiliation(s)
- Vanesa M Tomatis
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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Bellei E, Monari E, Cuoghi A, Bergamini S, Guerzoni S, Ciccarese M, Ozben T, Tomasi A, Pini LA. Discovery by a proteomic approach of possible early biomarkers of drug-induced nephrotoxicity in medication-overuse headache. J Headache Pain 2013; 14:6. [PMID: 23565828 PMCID: PMC3606963 DOI: 10.1186/1129-2377-14-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 01/14/2013] [Indexed: 01/19/2023] Open
Abstract
Background Medication-overuse headache (MOH) is a chronic headache condition that results from the overuse of analgesics drugs, triptans, or other antimigraine compounds. The epidemiology of drug-induced disorders suggests that medication overuse could lead to nephrotoxicity, particularly in chronic patients. The aim of this work was to confirm and extend the results obtained from a previous study, in which we analyzed the urinary proteome of 3 MOH patients groups: non-steroidal anti-inflammatory drugs (NSAIDs), triptans and mixtures abusers, in comparison with non-abusers individuals (controls). Methods In the present work we employed specialized proteomic techniques, namely two-dimensional gel electrophoresis (2-DE) coupled with mass spectrometry (MS), and the innovative Surface-Enhanced Laser Desorption/Ionization Time-of-Flight mass spectrometry (SELDI-TOF-MS), to discover characteristic proteomic profiles associated with MOH condition. Results By 2-DE and MS analysis we identified 21 over-excreted proteins in MOH patients, particularly in NSAIDs abusers, and the majority of these proteins were involved in a variety of renal impairments, as resulted from a literature search. Urine protein profiles generated by SELDI-TOF-MS analysis showed different spectra among groups. Moreover, significantly higher number of total protein spots and protein peaks were detected in NSAIDs and mixtures abusers. Conclusions These findings confirm the presence of alterations in proteins excretion in MOH patients. Analysis of urinary proteins by powerful proteomic technologies could lead to the discovery of early candidate biomarkers, that might allow to identify MOH patients prone to develop potential drug overuse-induced nephrotoxicity.
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Affiliation(s)
- Elisa Bellei
- Department of Diagnostic Medicine, Clinic and Public Health, University of Modena and Reggio Emilia, Via del Pozzo 71, 41100, Modena, Italy.
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