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Funke S, Perumal N, Bell K, Pfeiffer N, Grus FH. The potential impact of recent insights into proteomic changes associated with glaucoma. Expert Rev Proteomics 2017; 14:311-334. [PMID: 28271721 DOI: 10.1080/14789450.2017.1298448] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
INTRODUCTION Glaucoma, a major ocular neuropathy, is still far from being understood on a molecular scale. Proteomic workflows revealed glaucoma associated alterations in different eye components. By using state-of-the-art mass spectrometric (MS) based discovery approaches large proteome datasets providing important information about glaucoma related proteins and pathways could be generated. Corresponding proteomic information could be retrieved from various ocular sample species derived from glaucoma experimental models or from original human material (e.g. optic nerve head or aqueous humor). However, particular eye tissues with the potential for understanding the disease's molecular pathomechanism remains underrepresented. Areas covered: The present review provides an overview of the analysis depth achieved for the glaucomatous eye proteome. With respect to different eye regions and biofluids, proteomics related literature was found using PubMed, Scholar and UniProtKB. Thereby, the review explores the potential of clinical proteomics for glaucoma research. Expert commentary: Proteomics will provide important contributions to understanding the molecular processes associated with glaucoma. Sensitive discovery and targeted MS approaches will assist understanding of the molecular interplay of different eye components and biofluids in glaucoma. Proteomic results will drive the comprehension of glaucoma, allowing a more stringent disease hypothesis within the coming years.
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Affiliation(s)
- Sebastian Funke
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
| | - Natarajan Perumal
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
| | - Katharina Bell
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
| | - Norbert Pfeiffer
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
| | - Franz H Grus
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
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Funke S, Markowitsch S, Schmelter C, Perumal N, Mwiiri FK, Gabel-Scheurich S, Pfeiffer N, Grus FH. In-Depth Proteomic Analysis of the Porcine Retina by Use of a four Step Differential Extraction Bottom up LC MS Platform. Mol Neurobiol 2016; 54:7262-7275. [PMID: 27796761 DOI: 10.1007/s12035-016-0172-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 09/27/2016] [Indexed: 01/09/2023]
Abstract
The eye of the house swine (Sus scrofa domestica Linnaeus, 1758) represents a promising model for the study of human eye diseases encircling neurodegenerative retina disorders that go along with proteomic changes. To provide an in-depth view into the "normal" (untreated & healthy) porcine retina proteome as an important reference, a proteomic strategy has been developed encircling stepwise/differential extraction, LC MS and peptide de novo sequencing. Accordingly, pooled porcine retina homogenates were processed by stepwise DDM, CHAPS, ASB14 and ACN/TFA extraction. Retinal proteins were fractionated by 1D-SDS PAGE and further analyzed by LC ESI MS following database and de novo sequencing related protein identification and functional analyses. In summary, >2000 retinal proteins (FDR < 1 %) could be identified by use of the highly reproducible and selective extraction procedure. Moreover, an identification surplus of 36 % comparing initial one step extraction to the four step method could be documented. Despite most proteins were identified in the DDM and CHAPS fraction, all extraction steps contributed exclusive proteins with nucleus proteins enriched in the final ACN/TFA fraction. Additionally, for the first time new non-annotated de novo peptides could be documented for the porcine retina. The generated porcine retina proteome reference map contributes importantly to the understanding of the pig eye proteome and the developed workflow has strong translational potential considering retina studies of various species.
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Affiliation(s)
- Sebastian Funke
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Sascha Markowitsch
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Carsten Schmelter
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Natarajan Perumal
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Francis Kamau Mwiiri
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Silke Gabel-Scheurich
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Norbert Pfeiffer
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Franz H Grus
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany.
- Department of Experimental Ophthalmology, University Medical Center (Universitätsmedizin), Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany.
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Percy AJ, Hardie DB, Jardim A, Yang J, Elliott MH, Zhang S, Mohammed Y, Borchers CH. Multiplexed panel of precisely quantified salivary proteins for biomarker assessment. Proteomics 2016; 17. [PMID: 27538354 DOI: 10.1002/pmic.201600230] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/21/2016] [Accepted: 08/15/2016] [Indexed: 12/31/2022]
Abstract
An increasingly popular "absolute" quantitative technique involves the SRM or MRM approach with stable isotope-labeled standards (SIS). Using this approach, many proteins in human plasma/serum have been quantified for biomarker assessment and disease stratification. Due to the complexity of plasma and the invasive nature of its collection, alternative biosamples are currently being explored. Here, we present the broadest panel of multiplexed MRM assays with SIS peptides for saliva proteins developed to date. The validated panel consists of 158 candidate human saliva protein biomarkers, inferred from 244 interference-free peptides. The resulting concentrations were reproducibly quantified over a 6 order-of-magnitude concentration range (from 218 μg/mL to 88 pg/mL; average CVs of 12% over analytical triplicates). All concentrations were determined from reverse standard curves, which were generated using a constant concentration of endogenous material with varying concentrations of spiked-in SIS peptides. The large-scale screening of the soluble and membrane-associated proteins contained within the 158-plex assay could present new opportunities for biomarker assessment and clinical diagnostics.
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Affiliation(s)
- Andrew J Percy
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada
| | - Armando Jardim
- Institute of Parasitology, McGill University, Montreal, QC, Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada
| | - Monica H Elliott
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada
| | - Suping Zhang
- MRM Proteomics, Vancouver Island Technology Park, Victoria, BC, Canada
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada.,Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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Van Eyk JE, Corrales FJ, Aebersold R, Cerciello F, Deutsch EW, Roncada P, Sanchez JC, Yamamoto T, Yang P, Zhang H, Omenn GS. Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016. J Proteome Res 2016; 15:3979-3987. [PMID: 27573249 DOI: 10.1021/acs.jproteome.6b00444] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Biology and Disease-driven Human Proteome Project (B/D-HPP) is aimed at supporting and enhancing the broad use of state-of-the-art proteomic methods to characterize and quantify proteins for in-depth understanding of the molecular mechanisms of biological processes and human disease. Based on a foundation of the pre-existing HUPO initiatives begun in 2002, the B/D-HPP is designed to provide standardized methods and resources for mass spectrometry and specific protein affinity reagents and facilitate accessibility of these resources to the broader life sciences research and clinical communities. Currently there are 22 B/D-HPP initiatives and 3 closely related HPP resource pillars. The B/D-HPP groups are working to define sets of protein targets that are highly relevant to each particular field to deliver relevant assays for the measurement of these selected targets and to disseminate and make publicly accessible the information and tools generated. Major developments are the 2016 publications of the Human SRM Atlas and of "popular protein sets" for six organ systems. Here we present the current activities and plans of the BD-HPP initiatives as highlighted in numerous B/D-HPP workshops at the 14th annual HUPO 2015 World Congress of Proteomics in Vancouver, Canada.
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Affiliation(s)
- Jennifer E Van Eyk
- Advanced Clinical BioSystems Research Institute, Department of Medicine, Cedars-Sinai Medical Centre , Los Angeles, California 90038, United States
| | - Fernando J Corrales
- Department of Hepatology, Proteomics Laboratory, CIMA, University of Navarra; Ciberhed; PRB2, ProteoRed-ISCIII, 31008 Pamplona, Spain
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich , 8093 Zürich, Switzerland
| | - Ferdinando Cerciello
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich , 8093 Zürich, Switzerland
| | - Eric W Deutsch
- Institute for Systems Biology , Seattle, Washington 98109, United States
| | - Paola Roncada
- Istituto Sperimentale Italiano L. Spallanzani , 20133 Milano, Italy
| | - Jean-Charles Sanchez
- Centre Medicale Universitaire , Human Protein Sciences Department, CH-1211 Geneva, Switzerland
| | - Tadashi Yamamoto
- Niigata University , Department of Structural Pathology, Institute of Nephrology, Medical and Dental School, Asachimachi-dori Niigata 951-8510, Japan
| | - Pengyuan Yang
- Fudan University , Department of Chemistry, Shanghai 200433, P.R. China
| | - Hui Zhang
- Johns Hopkins University , Department of Pathology, Baltimore, Maryland 21287, United States
| | - Gilbert S Omenn
- Center for Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan 48109, United States
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