1
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Sun X, Xie Y, Qu J, Yuan D. Systematic characterization of components of Makyo-kanseki-to granule and serum metabolomics for exploring its protective mechanism against acute lung injury in lipopolysaccharide-induced rats. J Sep Sci 2023; 46:e2200705. [PMID: 36385590 DOI: 10.1002/jssc.202200705] [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: 08/29/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022]
Abstract
Makyo-kanseki-to has been used for the treatment of pneumonia, becoming a basic formula for coronavirus disease 2019. However, the chemical profile of Makyo-kanseki-to granule and its possible mechanism against acute lung injury from terminal metabolic regulation have been unclear. The aim of this study was to characterize the constituents in Makyo-kanseki-to granule and reveal the potential related mechanism of Makyo-kanseki-to granule treatment for acute lung injury using a rat model of lipopolysaccharide-induced acute lung injury. Totally, 78 constituents were characterized based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Makyo-kanseki-to granule could alleviate acute lung injury through modulating rectal temperature, pulmonary edema, histopathology, and processes of inflammatory and oxidative stress. Twenty-two potential biomarkers in acute lung injury rats were identified by metabolomics based on ultra-performance liquid chromatography coupled with quadrupole exactive high-field mass spectrometry. They were mainly involved in amino acids and glycerophospholipid metabolism, which were regulated by Makyo-kanseki-to granule. The present results not only increase the understanding of the chemical profile and molecular mechanism of Makyo-kanseki-to granule mediated protection against acute lung injury but also provide an experimental basis and new ideas for further development and clinical application of Makyo-kanseki-to granule.
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Affiliation(s)
- Xin Sun
- Department of Traditional Chinese Medicine, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Yuanyuan Xie
- Key Laboratory of Digitalized Quality Evaluation Technology of Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Jialing Qu
- Clinical Laboratory of Integrative Medicine, The first affiliated hospital of Dalian Medical University, Dalian, P. R. China
| | - Dan Yuan
- Department of Traditional Chinese Medicine, Shenyang Pharmaceutical University, Shenyang, P. R. China
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2
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Bu F, Cheng Q, Zhang Y, Zhang X, Yan K, Liu F, Li Z, Lu X, Ren Y, Liu S. Discovery of Missing Proteins from an Aneuploidy Cell Line Using a Proteogenomic Approach. J Proteome Res 2021; 20:5329-5339. [PMID: 34748338 DOI: 10.1021/acs.jproteome.1c00772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With the steadfast development of proteomic technology, the number of missing proteins (MPs) has been continuously shrinking, with approximately 1470 MPs that have not been explored yet. Due to this phenomenon, the discovery of MPs has been increasingly more difficult and elusive. In order to face this challenge, we have hypothesized that a stable aneuploid cell line with increased chromosomes serves as a useful material for assisting MP exploration. Ker-CT cell line with trisomy at chromosome 5 and 20 was selected for this purpose. With a combination strategy of RNA-Seq and LC-MS/MS, a total of 22 178 transcripts and 8846 proteins were identified in Ker-CT. Although the transcripts corresponding to 15 and 15 MP genes located at chromosome 5 and 20 were detected, none of the MPs were found in Ker-CT. Surprisingly, 3 MPs containing at least two unique non-nest peptides of length ≥9 amino acids were identified in Ker-CT, whose genes are located on chromosome 3 and 10, respectively. Furthermore, the 3 MPs were verified using the method of parallel reaction monitoring (PRM). These results suggest that the abnormal status of chromosomes may not only impact the expression of the corresponding genes in trisomy chromosomes, but also influence that of other chromosomes, which benefits MP discovery. The data obtained in this study are available via ProteomeXchange (PXD028647) and PeptideAtlas (PASS01700), respectively.
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Affiliation(s)
- Fanyu Bu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Qingqiu Cheng
- Clinical Laboratory Center of Dongguan Eighth People's Hospital, Dongguan 523325, China
| | - Yuxing Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Xia Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Keqiang Yan
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Frank Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Zelong Li
- Biological Resource Center of Plants, Animals and Microorganisms, China National Gene Bank, BGI-Shenzhen, Guangdong 518120, China
| | - Xiaomei Lu
- Clinical Laboratory Center of Dongguan Eighth People's Hospital, Dongguan 523325, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
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3
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Liu L, Cui ZX, Zhang YB, Xu W, Yang XW, Zhong LJ, Zhang P, Gong Y. Identification and quantification analysis of the chemical constituents from Mahonia fortune using Q‑Exactive HF Mass Spectrometer and UPLC-ESI-MS/MS. J Pharm Biomed Anal 2021; 196:113903. [PMID: 33493743 DOI: 10.1016/j.jpba.2021.113903] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/26/2020] [Accepted: 12/27/2020] [Indexed: 01/06/2023]
Abstract
In this research, a comprehensive and innovative method was established for the qualitative and quantitative analysis of the main components in Mahonia fortune (MF). On the one hand, comprehensive insight of the constituents in MF extracts was achieved with a Q‑Exactive HF Mass Spectrometer using data-independent acquisition method. The identification of 17 compounds was based on comparison with authentic reference standards and the deduction of 119 additional compounds both in positive and negative modes was using the MS-dial strategy and comparison with literature data. The proportion of alkaloids and phenols were the most in MF. On the other hand, an ultra-performance liquid chromatographic-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) method for the quantification of 25 components in MF extract were developed and validated. The method established provided satisfactory precision and accuracy; acceptable recovery and stability; a good linearity and a reasonable limit of detection. The MF samples from 11 different sources were detected, and relative principal component analysis were applied to discriminate these samples. The variations of Columbamine, Jatrorrhizine, Palmatine and Berberine were suggested as important indicators of MF quality. This study supplies a novel and comprehensive method for the quality evaluation of MF. This research presents a MS based analytical strategy which shows an application potential in the analysis of the chemical constituents in Traditional Chinese Medicine (TCM).
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Affiliation(s)
- Lu Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Xueyuan Road 38, Haidian District, Beijing, 100191, China
| | - Ze-Xu Cui
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Xueyuan Road 38, Haidian District, Beijing, 100191, China
| | - You-Bo Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Xueyuan Road 38, Haidian District, Beijing, 100191, China
| | - Wei Xu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Xueyuan Road 38, Haidian District, Beijing, 100191, China
| | - Xiu-Wei Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Xueyuan Road 38, Haidian District, Beijing, 100191, China.
| | - Li-Jun Zhong
- Medical and Health Analytical Center, Peking University Health Science Center, Beijing, 100191, China
| | - Peng Zhang
- Zhuzhou Qianjin Pharmaceutical Co., Ltd., Zhuzhou, 412003, China
| | - Yun Gong
- Zhuzhou Qianjin Pharmaceutical Co., Ltd., Zhuzhou, 412003, China
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4
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González-Gomariz J, Serrano G, Tilve-Álvarez CM, Corrales FJ, Guruceaga E, Segura V. UPEFinder: A Bioinformatic Tool for the Study of Uncharacterized Proteins Based on Gene Expression Correlation and the PageRank Algorithm. J Proteome Res 2020; 19:4795-4807. [PMID: 33155801 DOI: 10.1021/acs.jproteome.0c00364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Human Proteome Project (HPP) is leading the international effort to characterize the human proteome. Although the main goal of this project was first focused on the detection of missing proteins, a new challenge arose from the need to assign biological functions to the uncharacterized human proteins and describe their implications in human diseases. Not only the proteins with experimental evidence (uPE1 proteins) but also the uncharacterized missing proteins (uMPs) were the objects of study in this challenge, neXt-CP50. In this work, we developed a new bioinformatic approach to infer biological annotations for the uPE1 proteins and uMPs based on a "guilt-by-association" analysis using public RNA-Seq data sets. We used the correlation of these proteins with the well-characterized PE1 proteins to construct a network. In this way, we applied the PageRank algorithm to this network to identify the most relevant nodes, which were the biological annotations of the uncharacterized proteins. All of the generated information was stored in a database. In addition, we implemented the web application UPEFinder (https://upefinder.proteored.org) to facilitate the access to this new resource. This information is especially relevant for the researchers of the HPP who are interested in the generation and validation of new hypotheses about the functions of these proteins. Both the database and the web application are publicly available (https://github.com/ubioinformat/UPEfinder).
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Affiliation(s)
| | - Guillermo Serrano
- Bioinformatics Platform, CIMA University of Navarra, Pamplona E-31008, Spain
| | - Carlos M Tilve-Álvarez
- Fundación Profesor Nóvoa-Santos, Instituto de Investigación Biomédica da Coruña, Coruña E-15006, Spain
| | - Fernando J Corrales
- Proteomics Unit, National Center for Biotechnology, CSIC, Madrid E-28049, Spain
| | - Elizabeth Guruceaga
- IdiSNA, Navarra Institute for Health Research, Pamplona E-31008, Spain.,Bioinformatics Platform, CIMA University of Navarra, Pamplona E-31008, Spain
| | - Victor Segura
- Tracasa Instrumental, Sarriguren E-31621, Spain.,Sección de Ingeniería del Dato, Dirección General de Telecomunicaciones y Digitalización, Gobierno de Navarra, Sarriguren E-31621, Spain
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5
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Zhang Y, Zhang K, Bu F, Hao P, Yang H, Liu S, Ren Y. D283 Med, a Cell Line Derived from Peritoneal Metastatic Medulloblastoma: A Good Choice for Missing Protein Discovery. J Proteome Res 2020; 19:4857-4866. [DOI: 10.1021/acs.jproteome.0c00743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yuanliang Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Keren Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Fanyu Bu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
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6
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Vandenbrouck Y, Pineau C, Lane L. The Functionally Unannotated Proteome of Human Male Tissues: A Shared Resource to Uncover New Protein Functions Associated with Reproductive Biology. J Proteome Res 2020; 19:4782-4794. [PMID: 33064489 DOI: 10.1021/acs.jproteome.0c00516] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the context of the Human Proteome Project, we built an inventory of 412 functionally unannotated human proteins for which experimental evidence at the protein level exists (uPE1) and which are highly expressed in tissues involved in human male reproduction. We implemented a strategy combining literature mining, bioinformatics tools to collate annotation and experimental information from specific molecular public resources, and efficient visualization tools to put these unknown proteins into their biological context (protein complexes, tissue and subcellular location, expression pattern). The gathered knowledge allowed pinpointing five uPE1 for which a function has recently been proposed and which should be updated in protein knowledge bases. Furthermore, this bioinformatics strategy allowed to build new functional hypotheses for five other uPE1s in link with phenotypic traits that are specific to male reproductive function such as ciliogenesis/flagellum formation in germ cells (CCDC112 and TEX9), chromatin remodeling (C3orf62) and spermatozoon maturation (CCDC183). We also discussed the enigmatic case of MAGEB proteins, a poorly documented cancer/testis antigen subtype. Tools used and computational outputs produced during this study are freely accessible via ProteoRE (http://www.proteore.org), a Galaxy-based instance, for reuse purposes. We propose these five uPE1s should be investigated in priority by expert laboratories and hope that this inventory and shared resources will stimulate the interest of the community of reproductive biology.
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Affiliation(s)
- Yves Vandenbrouck
- Univ. Grenoble Alpes, INSERM, CEA, IRIG-BGE, U1038, F-38000 Grenoble, France
| | - Charles Pineau
- Univ. Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35042 Rennes cedex, France
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Michel Servet 1, 1211 Geneva 4, Switzerland
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7
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Sanchez A, Kuras M, Murillo JR, Pla I, Pawlowski K, Szasz AM, Gil J, Nogueira FCS, Perez-Riverol Y, Eriksson J, Appelqvist R, Miliotis T, Kim Y, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Ekedahl H, Horvatovich P, Sugihara Y, Welinder C, Wieslander E, Kwon HJ, Domont GB, Malm J, Rezeli M, Betancourt LH, Marko-Varga G. Novel functional proteins coded by the human genome discovered in metastases of melanoma patients. Cell Biol Toxicol 2020; 36:261-272. [PMID: 31599373 PMCID: PMC7320927 DOI: 10.1007/s10565-019-09494-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/02/2019] [Indexed: 12/18/2022]
Abstract
In the advanced stages, malignant melanoma (MM) has a very poor prognosis. Due to tremendous efforts in cancer research over the last 10 years, and the introduction of novel therapies such as targeted therapies and immunomodulators, the rather dark horizon of the median survival has dramatically changed from under 1 year to several years. With the advent of proteomics, deep-mining studies can reach low-abundant expression levels. The complexity of the proteome, however, still surpasses the dynamic range capabilities of current analytical techniques. Consequently, many predicted protein products with potential biological functions have not yet been verified in experimental proteomic data. This category of 'missing proteins' (MP) is comprised of all proteins that have been predicted but are currently unverified. As part of the initiative launched in 2016 in the USA, the European Cancer Moonshot Center has performed numerous deep proteomics analyses on samples from MM patients. In this study, nine MPs were clearly identified by mass spectrometry in MM metastases. Some MPs significantly correlated with proteins that possess identical PFAM structural domains; and other MPs were significantly associated with cancer-related proteins. This is the first study to our knowledge, where unknown and novel proteins have been annotated in metastatic melanoma tumour tissue.
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Affiliation(s)
- Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden.
| | - Magdalena Kuras
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Jimmy Rodriguez Murillo
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Indira Pla
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
| | - Krzysztof Pawlowski
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
- Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - A Marcell Szasz
- Cancer Center, Semmelweis University, Budapest, 1083, Hungary
| | - Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Fábio C S Nogueira
- Proteomics Unit, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD Hinxton, Cambridge, UK
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | | | - Yonghyo Kim
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Skåne University Hospital, Lund University, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Henrik Ekedahl
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Yutaka Sugihara
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Ho Jeong Kwon
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Gilberto B Domont
- Proteomics Unit, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
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8
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Lenčo J, Khalikova MA, Švec F. Dissolving Peptides in 0.1% Formic Acid Brings Risk of Artificial Formylation. J Proteome Res 2020; 19:993-999. [DOI: 10.1021/acs.jproteome.9b00823] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Maria A. Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - František Švec
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
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9
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Shan S, Xu F, Bleyer M, Becker S, Melbaum T, Wemheuer W, Hirschfeld M, Wacker C, Zhao S, Schütz E, Brenig B. Association of α/β-Hydrolase D16B with Bovine Conception Rate and Sperm Plasma Membrane Lipid Composition. Int J Mol Sci 2020; 21:E627. [PMID: 31963602 PMCID: PMC7014312 DOI: 10.3390/ijms21020627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 02/01/2023] Open
Abstract
We have identified a Holstein sire named Tarantino who had been approved for artificial insemination that is based on normal semen characteristics (i.e., morphology, thermoresistance, motility, sperm concentration), but had no progeny after 412 first inseminations, resulting in a non-return rate (NRdev) of -29. Using whole genome association analysis and next generation sequencing, an associated nonsense variant in the α/β-hydrolase domain-containing 16B gene (ABHD16B) on bovine chromosome 13 was identified. The frequency of the mutant allele in the German Holstein population was determined to be 0.0018 in 222,645 investigated cattle specimens. The mutant allele was traced back to Whirlhill Kingpin (bornFeb. 13th, 1959) as potential founder. The expression of ABHD16B was detected by Western blotting and immunohistochemistry in testis and epididymis of control bulls. A lipidome comparison of the plasma membrane of fresh semen from carriers and controls showed significant differences in the concentration of phosphatidylcholine (PC), diacylglycerol (DAG), ceramide (Cer), sphingomyelin (SM), and phosphatidylcholine (-ether) (PC O-), indicating that ABHD16B plays a role in lipid biosynthesis. The altered lipid contents may explain the reduced fertilization ability of mutated sperms.
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Affiliation(s)
- Shuwen Shan
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Fangzheng Xu
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Martina Bleyer
- Pathology Unit, German Primate Center, Leibniz-Institute for Primate Research Goettingen, 37077 Goettingen, Germany
| | - Svenja Becker
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Torben Melbaum
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Wilhelm Wemheuer
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Marc Hirschfeld
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
- Department of Obstetrics and Gynecology, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Christin Wacker
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Shuhong Zhao
- Key Lab of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ekkehard Schütz
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
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10
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Lisitsa AV, Petushkova NA, Levitsky LI, Zgoda VG, Larina OV, Kisrieva YS, Frankevich VE, Gamidov SI. Comparative Analysis of the Performаnce of Mascot and IdentiPy Algorithms on a Benchmark Dataset Obtained by Tandem Mass Spectrometry Analysis of Testicular Biopsies. Mol Biol 2019. [DOI: 10.1134/s0026893319010096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Zhang Y, Wen Z, Washburn MP, Florens L. Evaluating Chromatographic Approaches for the Quantitative Analysis of a Human Proteome on Orbitrap-Based Mass Spectrometry Systems. J Proteome Res 2019; 18:1857-1869. [PMID: 30884231 DOI: 10.1021/acs.jproteome.9b00036] [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] [Indexed: 02/08/2023]
Abstract
The Orbitrap is now a core component of several different instruments. However, evaluating the capabilities of each system is lacking in the field. Here, we compared the performance of multidimensional protein identification (MudPIT) on Velos Pro Orbitrap and Velos Orbitrap Elite mass spectrometers to reversed phase liquid chromatography (RPLC) on a Q-Exactive Plus and an Orbitrap Fusion Lumos. Using HeLa cell protein digests, we carried out triplicate analyses of 16 different chromatography conditions on four different instrumentation platforms. We first optimized RPLC conditions by varying column lengths, inner diameters, and particle sizes. We found that smaller particle sizes improve results but only with smaller inner diameter microcapillary columns. We then selected one chromatography condition on each system and varied gradient lengths. We used distributed normalized spectral abundance factor (dNSAF) values to determine quantitative reproducibility. With Pearson product-moment correlation coefficient r values routinely above 0.96, single RPLC on both the QE+ and Orbitrap Lumos outperformed MudPIT on the Orbitrap Elite mass spectrometer. In addition, when comparing dNSAF values measured for the same proteins across the different platforms, RPLC on the Orbitrap Lumos had greater sensitivity than MudPIT, as demonstrated by the detection and quantification of histone deacetylase complex components. Data are available via ProteomeXchange with identifier 10.6019/PXD009875.
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Affiliation(s)
- Ying Zhang
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States
| | - Zhihui Wen
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States
| | - Michael P Washburn
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States.,Department of Pathology and Laboratory Medicine , University of Kansas Medical Center , Kansas City , Kansas 66160 , United States
| | - Laurence Florens
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States
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12
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González-Gomariz J, Guruceaga E, López-Sánchez M, Segura V. Proteogenomics in the context of the Human Proteome Project (HPP). Expert Rev Proteomics 2019; 16:267-275. [PMID: 30654666 DOI: 10.1080/14789450.2019.1571916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION The technological and scientific progress performed in the Human Proteome Project (HPP) has provided to the scientific community a new set of experimental and bioinformatic methods in the challenging field of shotgun and SRM/MRM-based Proteomics. The requirements for a protein to be considered experimentally validated are now well-established, and the information about the human proteome is available in the neXtProt database, while targeted proteomic assays are stored in SRMAtlas. However, the study of the missing proteins continues being an outstanding issue. Areas covered: This review is focused on the implementation of proteogenomic methods designed to improve the detection and validation of the missing proteins. The evolution of the methodological strategies based on the combination of different omic technologies and the use of huge publicly available datasets is shown taking the Chromosome 16 Consortium as reference. Expert commentary: Proteogenomics and other strategies of data analysis implemented within the C-HPP initiative could be used as guidance to complete in a near future the catalog of the human proteins. Besides, in the next years, we will probably witness their use in the B/D-HPP initiative to go a step forward on the implications of the proteins in the human biology and disease.
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Affiliation(s)
- José González-Gomariz
- a Bioinformatics Platform, Center for Applied Medical Research , University of Navarra , Pamplona , Spain.,b IdiSNA , Navarra Institute for Health Research , Pamplona , Spain
| | - Elizabeth Guruceaga
- a Bioinformatics Platform, Center for Applied Medical Research , University of Navarra , Pamplona , Spain.,b IdiSNA , Navarra Institute for Health Research , Pamplona , Spain
| | - Macarena López-Sánchez
- a Bioinformatics Platform, Center for Applied Medical Research , University of Navarra , Pamplona , Spain
| | - Victor Segura
- a Bioinformatics Platform, Center for Applied Medical Research , University of Navarra , Pamplona , Spain.,b IdiSNA , Navarra Institute for Health Research , Pamplona , Spain
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13
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Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Snyder M, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project. J Proteome Res 2018; 17:4031-4041. [PMID: 30099871 PMCID: PMC6387656 DOI: 10.1021/acs.jproteome.8b00441] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Human Proteome Project (HPP) annually reports on progress throughout the field in credibly identifying and characterizing the human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2018-01-17, the baseline for this sixth annual HPP special issue of the Journal of Proteome Research, contains 17 470 PE1 proteins, 89% of all neXtProt predicted PE1-4 proteins, up from 17 008 in release 2017-01-23 and 13 975 in release 2012-02-24. Conversely, the number of neXtProt PE2,3,4 missing proteins has been reduced from 2949 to 2579 to 2186 over the past two years. Of the PE1 proteins, 16 092 are based on mass spectrometry results, and 1378 on other kinds of protein studies, notably protein-protein interaction findings. PeptideAtlas has 15 798 canonical proteins, up 625 over the past year, including 269 from SUMOylation studies. The largest reason for missing proteins is low abundance. Meanwhile, the Human Protein Atlas has released its Cell Atlas, Pathology Atlas, and updated Tissue Atlas, and is applying recommendations from the International Working Group on Antibody Validation. Finally, there is progress using the quantitative multiplex organ-specific popular proteins targeted proteomics approach in various disease categories.
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Affiliation(s)
- Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Christopher M. Overall
- Life Sciences Institute, Faculty of Dentistry, University of British Columbia, 2350 Health Sciences Mall, Room 4.401, Vancouver, BC Canada V6T 1Z3
| | | | - Jochen M. Schwenk
- Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Room 425, Building #114, Yonsei University,50 Yonsei-ro, Seodaemoon-ku, Seoul 120-749, Korea
| | - Jennifer E. Van Eyk
- Advanced Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker Laboratories, Barbra Streisand Women’s Heart Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Siqi Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, United States
| | - Michael Snyder
- Department of Genetics, Stanford University, Alway Building, 300 Pasteur Drive, 3165 Porter Drive, Palo Alto, 94304, United States
| | - Mark S. Baker
- Department of Biomedical Sciences, Macquarie University, NSW 2109, Australia
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
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14
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Sabatier P, Saei AA, Wang S, Zubarev RA. Dynamic Proteomics Reveals High Plasticity of Cellular Proteome: Growth-Related and Drug-Induced Changes in Cancer Cells are Comparable. Proteomics 2018; 18:e1800118. [PMID: 30382632 DOI: 10.1002/pmic.201800118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 09/26/2018] [Indexed: 11/10/2022]
Abstract
In chemical proteomics, the changes occurring in cellular proteomes upon drug treatment are used to identify the drug targets and the mechanism of action. However, proteomes of cultured cells undergo also natural alteration associated with changes in the media, attaining a degree of confluence as well as due to cell division and cell metabolism. These changes are implicitly assumed to be smaller in magnitude than the drug-induced changes that ultimately lead to cell demise. In this study, it is shown that growth-related proteome changes in the untreated control group are comparable in magnitude to drug-induced changes over the course of 48 h treatment. In two well-characterized cancer cell lines, growth-related effects assessed with deep proteomics analysis (10 481 proteins quantified with at least two peptides) show common trends, the steady downregulation of cell division processes, and the upregulation of metabolism-related pathways. The magnitude of these variations, which are present even before reaching 100% confluence reveals unexpectedly high plasticity of the cellular proteome. This finding reinforces the need, generally accepted in theory but not always followed in practice, to use a time-matched control when measuring drug-induced proteome changes.
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Affiliation(s)
- Pierre Sabatier
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, SE, 17 177, Stockholm, Sweden
| | - Amir Ata Saei
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, SE, 17 177, Stockholm, Sweden
| | - Shiyu Wang
- Department of Biostatistics, Yale School of Public Health, Yale University, 60 College Street, New Haven, CT, 06510, USA
| | - Roman A Zubarev
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, SE, 17 177, Stockholm, Sweden.,Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia
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15
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Gao X, Li H, Li H, Dong S, Chu J, Guo H, Zhao Q. Sensitive determination of nine anticoagulant rodenticides in blood by high resolution mass spectrometry with supported liquid extraction pretreatment. Forensic Sci Int 2018; 292:39-44. [DOI: 10.1016/j.forsciint.2018.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 12/14/2022]
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16
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Siddiqui O, Zhang H, Guan Y, Omenn GS. Chromosome 17 Missing Proteins: Recent Progress and Future Directions as Part of the neXt-MP50 Challenge. J Proteome Res 2018; 17:4061-4071. [PMID: 30280577 DOI: 10.1021/acs.jproteome.8b00442] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Chromosome-centric Human Proteome Project (C-HPP), announced in September 2016, is an initiative to accelerate progress on the detection and characterization of neXtProt PE2,3,4 "missing proteins" (MPs) with a mandate to each chromosome team to find about 50 MPs over 2 years. Here we report major progress toward the neXt-MP50 challenge with 43 newly validated Chr 17 PE1 proteins, of which 25 were based on mass spectrometry, 12 on protein-protein interactions, 3 on a combination of MS and PPI, and 3 with other types of data. Notable among these new PE1 proteins were five keratin-associated proteins, a single olfactory receptor, and five additional membrane-embedded proteins. We evaluate the prospects of finding the remaining 105 MPs coded for on Chr 17, focusing on mass spectrometry and protein-protein interaction approaches. We present a list of 35 prioritized MPs with specific approaches that may be used in further MS and PPI experimental studies. Additionally, we demonstrate how in silico studies can be used to capture individual peptides from major data repositories, documenting one MP that appears to be a strong candidate for PE1. We are close to our goal of finding 50 MPs for Chr 17.
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Affiliation(s)
- Omer Siddiqui
- Department of Electronic Engineering and Computer Science , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Hongjiu Zhang
- Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Internal Medicine , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Internal Medicine , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Human Genetics and School of Public Health , University of Michigan , Ann Arbor , Michigan 48109 , United States
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17
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Sun J, Shi J, Wang Y, Chen Y, Li Y, Kong D, Chang L, Liu F, Lv Z, Zhou Y, He F, Zhang Y, Xu P. Multiproteases Combined with High-pH Reverse-Phase Separation Strategy Verified Fourteen Missing Proteins in Human Testis Tissue. J Proteome Res 2018; 17:4171-4177. [PMID: 30280576 DOI: 10.1021/acs.jproteome.8b00397] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Subsequent to conducting the Chromosome-Centric Human Proteome Project, we have focused on human testis-enriched missing proteins (MPs) since 2015. For protein coverage to be enhanced, a multiprotease strategy was used for separation of samples by 10% SDS-PAGE. For the separating efficiency to be improved, a high-pH reverse phase (RP) separation strategy was applied to fractionate complex samples in this study. A total of 11,558 proteins was identified, which is the largest proteome data set for single human tissue sample so far. On the basis of this large-scale data set, we verified 14 MPs (PE2) in neXtProt (2018-01) after spectrum quality analysis, isobaric post-translational modification, and single amino acid variant filtering, and synthesized peptide matching. Tissue expression analysis showed that 3 of 14 MPs were testis-specific proteins. Functional analysis showed that 10 of 14 MPs were closely related to liver tumor, liver carcinoma, and hepatocellular carcinoma. Another 100 MPs were listed as candidates but required additional verification information. All MS data sets have been deposited into the ProteomeXchange with the identifier PXD009737.
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Affiliation(s)
- Jinshuai Sun
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Jiahui Shi
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yihao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yang Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Degang Kong
- Department of Hepatopancreatobiliary Surgery , The Second Affiliated Hospital of Tianjin Medical University , Tianjin 300211 , China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Fengsong Liu
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China
| | - Zhitang Lv
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China
| | - Yue Zhou
- Demo Laboratory of Thermofisher Scientific China , Shanghai 200120 , China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yao Zhang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Ping Xu
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China.,Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science , Wuhan University , Wuhan 430072 , China
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18
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He C, Sun J, Shi J, Wang Y, Zhao J, Wu S, Chang L, Gao H, Liu F, Lv Z, He F, Zhang Y, Xu P. Digging for Missing Proteins Using Low-Molecular-Weight Protein Enrichment and a “Mirror Protease” Strategy. J Proteome Res 2018; 17:4178-4185. [DOI: 10.1021/acs.jproteome.8b00398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Cuitong He
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Jinshuai Sun
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Jiahui Shi
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Yihao Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Jialing Zhao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
- Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430072, China
| | - Shujia Wu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
- Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430072, China
| | - Lei Chang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Huiying Gao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Fengsong Liu
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Zhitang Lv
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Fuchu He
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Yao Zhang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
- Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430072, China
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19
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Weldemariam MM, Han CL, Shekari F, Kitata RB, Chuang CY, Hsu WT, Kuo HC, Choong WK, Sung TY, He FC, Chung MCM, Salekdeh GH, Chen YJ. Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane Proteins. J Proteome Res 2018; 17:4138-4151. [DOI: 10.1021/acs.jproteome.8b00407] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mehari Muuz Weldemariam
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 112, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
| | - Faezeh Shekari
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Ching-Yu Chuang
- Genomics Research Center, Academia Sinica, Taiepei 115, Taiwan
| | | | | | | | | | - Fu-Chu He
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, 102206 China
| | - Maxey Ching Ming Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, 14 Science Drive 4, singapore, 117543 Singpore
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 112, Taiwan
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20
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Melaine N, Com E, Bellaud P, Guillot L, Lagarrigue M, Morrice NA, Guével B, Lavigne R, Velez de la Calle JF, Dojahn J, Pineau C. Deciphering the Dark Proteome: Use of the Testis and Characterization of Two Dark Proteins. J Proteome Res 2018; 17:4197-4210. [DOI: 10.1021/acs.jproteome.8b00387] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nathalie Melaine
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Pascale Bellaud
- H2P2 Core Facility, UMS BioSit, Univ Rennes, Rennes F-35040, France
| | - Laetitia Guillot
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Mélanie Lagarrigue
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Nick A. Morrice
- Sciex, Phoenix House Lakeside Drive Centre Park, Warrington WA1 1RX, U.K
| | - Blandine Guével
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Régis Lavigne
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | | | - Jörg Dojahn
- Sciex, Landwehrstr. 54, 64293 Darmstadt, Germany
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
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21
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Paik YK, Overall CM, Deutsch EW, Van Eyk JE, Omenn GS. Progress and Future Direction of Chromosome-Centric Human Proteome Project. J Proteome Res 2018; 16:4253-4258. [PMID: 29191025 DOI: 10.1021/acs.jproteome.7b00734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This special issue of JPR celebrates the fifth anniversary of the Chromosome-Centric Human Proteome Project (C-HPP). We present 27 manuscripts in four categories: (i) Metrics of Progress and Resources, (ii) Missing Protein Detection and Validation, (iii) Analytical Methods and Quality Assessment, and (iv) Protein Functions and Disease. We briefly introduce key messages from each paper, mostly from C-HPP teams and some from the Biology and Disease-driven HPP. From the first few months of the C-HPP NeXt-MP50 Missing Proteins Challenge, authors report 73 missing protein detections that meet the HPP guidelines using several novel approaches. Finally, we discuss future directions.
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Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center and Department of Biochemistry, Yonsei University
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia
| | | | - Jennifer E Van Eyk
- Advanced Clinical BioSystems Research Institute , Department of Medicine, Cedars-Sinai Medical Centre
| | - Gilbert S Omenn
- Institute for Systems Biology.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan
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22
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Lee SE, Song J, Bösl K, Müller AC, Vitko D, Bennett KL, Superti-Furga G, Pandey A, Kandasamy RK, Kim MS. Proteogenomic Analysis to Identify Missing Proteins from Haploid Cell Lines. Proteomics 2018; 18:e1700386. [DOI: 10.1002/pmic.201700386] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/14/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Seung-Eun Lee
- Department of Applied Chemistry College of Applied Science; Kyung Hee University; Yongin-si Republic of Korea
- Department of Biomedical Science and TechnologyKyung Hee Medical Science Research Institute; Kyung Hee University; Yongin-si Republic of Korea
| | - JongKeon Song
- Department of Applied Chemistry College of Applied Science; Kyung Hee University; Yongin-si Republic of Korea
| | - Korbinian Bösl
- Centre of Molecular Inflammation Research (SFF-CEMIR), and Department of Clinical and Molecular Medicine (IKOM); Norwegian University of Science and Technology; Trondheim Norway
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Dijana Vitko
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
- Center for Physiology and Pharmacology; Medical University of Vienna; Vienna Austria
| | - Akhilesh Pandey
- Department of Applied Chemistry College of Applied Science; Kyung Hee University; Yongin-si Republic of Korea
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore MD USA
| | - Richard K. Kandasamy
- Centre of Molecular Inflammation Research (SFF-CEMIR), and Department of Clinical and Molecular Medicine (IKOM); Norwegian University of Science and Technology; Trondheim Norway
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
- Centre for Molecular Medicine Norway (NCMM) Nordic EMBL Partnership; University of Oslo and Oslo University Hospital; Oslo Norway
| | - Min-Sik Kim
- Department of Applied Chemistry College of Applied Science; Kyung Hee University; Yongin-si Republic of Korea
- Department of Biomedical Science and TechnologyKyung Hee Medical Science Research Institute; Kyung Hee University; Yongin-si Republic of Korea
- Global Center for Pharmaceutical Ingredient Materials; Kyung Hee University; Yongin-si Republic of Korea
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23
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Paik YK, Overall CM, Deutsch EW, Hancock WS, Omenn GS. Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV. J Proteome Res 2018; 15:3945-3950. [PMID: 27809547 DOI: 10.1021/acs.jproteome.6b00803] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center and Department of Biochemistry, Yonsei University
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia
| | | | | | - Gilbert S Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan
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24
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Elguoshy A, Hirao Y, Xu B, Saito S, Quadery AF, Yamamoto K, Mitsui T, Yamamoto T. Identification and Validation of Human Missing Proteins and Peptides in Public Proteome Databases: Data Mining Strategy. J Proteome Res 2017; 16:4403-4414. [PMID: 28980472 DOI: 10.1021/acs.jproteome.7b00423] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In an attempt to complete human proteome project (HPP), Chromosome-Centric Human Proteome Project (C-HPP) launched the journey of missing protein (MP) investigation in 2012. However, 2579 and 572 protein entries in the neXtProt (2017-1) are still considered as missing and uncertain proteins, respectively. Thus, in this study, we proposed a pipeline to analyze, identify, and validate human missing and uncertain proteins in open-access transcriptomics and proteomics databases. Analysis of RNA expression pattern for missing proteins in Human protein Atlas showed that 28% of them, such as Olfactory receptor 1I1 ( O60431 ), had no RNA expression, suggesting the necessity to consider uncommon tissues for transcriptomic and proteomic studies. Interestingly, 21% had elevated expression level in a particular tissue (tissue-enriched proteins), indicating the importance of targeting such proteins in their elevated tissues. Additionally, the analysis of RNA expression level for missing proteins showed that 95% had no or low expression level (0-10 transcripts per million), indicating that low abundance is one of the major obstacles facing the detection of missing proteins. Moreover, missing proteins are predicted to generate fewer predicted unique tryptic peptides than the identified proteins. Searching for these predicted unique tryptic peptides that correspond to missing and uncertain proteins in the experimental peptide list of open-access MS-based databases (PA, GPM) resulted in the detection of 402 missing and 19 uncertain proteins with at least two unique peptides (≥9 aa) at <(5 × 10-4)% FDR. Finally, matching the native spectra for the experimentally detected peptides with their SRMAtlas synthetic counterparts at three transition sources (QQQ, QTOF, QTRAP) gave us an opportunity to validate 41 missing proteins by ≥2 proteotypic peptides.
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Affiliation(s)
- Amr Elguoshy
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan.,Graduate School of Science and Technology, Niigata University , Niigata 950-2181, Japan.,Biotechnology Department - Faculty of Agriculture, Al-azhar University , Cairo 11651, Egypt
| | - Yoshitoshi Hirao
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan
| | - Bo Xu
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan
| | - Suguru Saito
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan
| | - Ali F Quadery
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan
| | - Keiko Yamamoto
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan
| | - Toshiaki Mitsui
- Graduate School of Science and Technology, Niigata University , Niigata 950-2181, Japan
| | - Tadashi Yamamoto
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan
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25
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Poverennaya EV, Ilgisonis EV, Ponomarenko EA, Kopylov AT, Zgoda VG, Radko SP, Lisitsa AV, Archakov AI. Why Are the Correlations between mRNA and Protein Levels so Low among the 275 Predicted Protein-Coding Genes on Human Chromosome 18? J Proteome Res 2017; 16:4311-4318. [PMID: 28956606 DOI: 10.1021/acs.jproteome.7b00348] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work targeted (selected reaction monitoring, SRM, PASSEL: PASS00697) and panoramic (shotgun LC-MS/MS, PRIDE: PXD00244) mass-spectrometric methods as well as transcriptomic analysis of the same samples using RNA-Seq and PCR methods (SRA experiment IDs: SRX341198, SRX267708, SRX395473, SRX390071) were applied for quantification of chromosome 18 encoded transcripts and proteins in human liver and HepG2 cells. The obtained data was used for the estimation of quantitative mRNA-protein ratios for the 275 genes of the selected chromosome in the selected tissues. The impact of methodological limitations of existing analytical proteomic methods on gene-specific mRNA-protein ratios and possible ways of overcoming these limitations for detection of missing proteins are also discussed.
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Affiliation(s)
| | | | | | | | - Victor G Zgoda
- Institute of Biomedical Chemistry RAS , 119121 Moscow, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry RAS , 119121 Moscow, Russia
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26
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Li S, He Y, Lin Z, Xu S, Zhou R, Liang F, Wang J, Yang H, Liu S, Ren Y. Digging More Missing Proteins Using an Enrichment Approach with ProteoMiner. J Proteome Res 2017; 16:4330-4339. [PMID: 28960076 DOI: 10.1021/acs.jproteome.7b00353] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Human Proteome Project (HPP) aims at mapping entire human proteins with a systematic effort upon all the emerging techniques, which would enhance understanding of human biology and lay a foundation for development of medical applications. Until now, 2563 missing proteins (MPs, PE2-4) are still undetected even using the most sensitive approach of protein detection. Herein, we propose that enrichment of low-abundance proteins benefits MPs finding. ProteoMiner is an equalizing technique by reducing high-abundance proteins and enriching low-abundance proteins in biological liquids. With triton X-100/TBS buffer extraction, ProteoMiner enrichment, and peptide fractionation, 20 MPs (at least two non-nested unique peptides with more than eight a.a. length) with 60 unique peptides were identified from four human tissues including eight membrane/secreted proteins and five nucleus proteins. Then 15 of them were confirmed with two non-nested unique peptides (≥9 a.a.) identified by matching well with their chemically synthetic peptides in PRM assay. Hence, these results demonstrated ProteoMiner as a powerful means in discovery of MPs.
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Affiliation(s)
- Siqi Li
- BGI-Shenzhen , Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Yanbin He
- BGI-Shenzhen , Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Zhilong Lin
- BGI-Shenzhen , Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Shaohang Xu
- BGI-Shenzhen , Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Ruo Zhou
- BGI-Shenzhen , Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Feng Liang
- BGI-Shenzhen , Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Jian Wang
- BGI-Shenzhen , Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Huanming Yang
- BGI-Shenzhen , Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310008, China
| | - Siqi Liu
- BGI-Shenzhen , Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Yan Ren
- BGI-Shenzhen , Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
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27
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Wang Y, Chen Y, Zhang Y, Wei W, Li Y, Zhang T, He F, Gao Y, Xu P. Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue. J Proteome Res 2017; 16:4352-4363. [PMID: 28959888 DOI: 10.1021/acs.jproteome.7b00340] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although 5 years of the missing proteins (MPs) study have been completed, searching for MPs remains one of the core missions of the Chromosome-Centric Human Proteome Project (C-HPP). Following the next-50-MPs challenge of the C-HPP, we have focused on the testis-enriched MPs by various strategies since 2015. On the basis of the theoretical analysis of MPs (2017-01, neXtProt) using multiprotease digestion, we found that nonconventional proteases (e.g. LysargiNase, GluC) could improve the peptide diversity and sequence coverage compared with Trypsin. Therefore, a multiprotease strategy was used for searching more MPs in the same human testis tissues separated by 10% SDS-PAGE, followed by high resolution LC-MS/MS system (Q Exactive HF). A total of 7838 proteins were identified. Among them, three PE2 MPs in neXtProt 2017-01 have been identified: beta-defensin 123 ( Q8N688 , chr 20q), cancer/testis antigen family 45 member A10 ( P0DMU9 , chr Xq), and Histone H2A-Bbd type 2/3 ( P0C5Z0 , chr Xq). However, because only one unique peptide of ≥9 AA was identified in beta-defensin 123 and Histone H2A-Bbd type 2/3, respectively, further analysis indicates that each falls under the exceptions clause of the HPP Guidelines v2.1. After a spectrum quality check, isobaric PTM and single amino acid variant (SAAV) filtering, and verification with a synthesized peptide, and based on overlapping peptides from different proteases, these three MPs should be considered as exemplary examples of MPs found by exceptional criteria. Other MPs were considered as candidates but need further validation. All MS data sets have been deposited to the ProteomeXchange with identifier PXD006465.
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Affiliation(s)
- Yihao Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China.,Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine , Beijing 100850, China
| | - Yang Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yao Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University , Guangzhou 510275, China
| | - Wei Wei
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Tao Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yue Gao
- Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine , Beijing 100850, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University , Wuhan 430072, China.,Graduate School, Anhui Medical University , Hefei 230032, China.,Tianjin Baodi Hospital , Tianjin 301800, China
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28
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Hwang H, Park GW, Park JY, Lee HK, Lee JY, Jeong JE, Park SKR, Yates JR, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS. Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases. J Proteome Res 2017; 16:4425-4434. [PMID: 28965411 DOI: 10.1021/acs.jproteome.7b00223] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human Proteome Project aims to map all human proteins including missing proteins as well as proteoforms with post translational modifications, alternative splicing variants (ASVs), and single amino acid variants (SAAVs). neXtProt and Ensemble databases are usually used to provide curated information on human coding genes. However, to find these proteoforms, we (Chr #11 team) first introduce a streamlined pipeline using customized and concatenated neXtProt and GENCODE originated from Ensemble, with controlled false discovery rate (FDR). Because of large sized databases used in this pipeline, we found more stringent FDR filtering (0.1% at the peptide level and 1% at the protein level) to claim novel findings, such as GENCODE ASVs and missing proteins, from human hippocampus data set (MSV000081385) and ProteomeXchange (PXD007166). Using our next generation proteomic pipeline (nextPP) with neXtProt and GENCODE databases, two missing proteins such as activity-regulated cytoskeleton-associated protein (ARC, Chr 8) and glutamate receptor ionotropic, kainite 5 (GRIK5, Chr 19) were additionally identified with two or more unique peptides from human brain tissues. Additionally, by applying the pipeline to human brain related data sets such as cortex (PXD000067 and PXD000561), spinal cord, and fetal brain (PXD000561), seven GENCODE ASVs such as ACTN4-012 (Chr.19), DPYSL2-005 (Chr.8), MPRIP-003 (Chr.17), NCAM1-013 (Chr.11), EPB41L1-017 (Chr.20), AGAP1-004 (Chr.2), and CPNE5-005 (Chr.6) were identified from two or more data sets. The identified peptides of GENCODE ASVs were mapped onto novel exon insertions, alternative translations at 5'-untranslated region, or novel protein coding sequence. Applying the pipeline to male reproductive organ related data sets, 52 GENCODE ASVs were identified from two testis (PXD000561 and PXD002179) and a spermatozoa (PXD003947) data sets. Four out of 52 GENCODE ASVs such as RAB11FIP5-008 (Chr. 2), RP13-347D8.7-001 (Chr. X), PRDX4-002 (Chr. X), and RP11-666A8.13-001 (Chr. 17) were identified in all of the three samples.
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Affiliation(s)
- Heeyoun Hwang
- Biomedical Omics Group, Korea Basic Science Institute , Cheongju 28119, Republic of Korea
| | - Gun Wook Park
- Biomedical Omics Group, Korea Basic Science Institute , Cheongju 28119, Republic of Korea
| | - Ji Yeong Park
- Biomedical Omics Group, Korea Basic Science Institute , Cheongju 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon, Republic of Korea
| | - Hyun Kyoung Lee
- Biomedical Omics Group, Korea Basic Science Institute , Cheongju 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon, Republic of Korea
| | - Ju Yeon Lee
- Biomedical Omics Group, Korea Basic Science Institute , Cheongju 28119, Republic of Korea
| | - Ji Eun Jeong
- Biomedical Omics Group, Korea Basic Science Institute , Cheongju 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon, Republic of Korea
| | - Sung-Kyu Robin Park
- Department of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Kyung-Hoon Kwon
- Biomedical Omics Group, Korea Basic Science Institute , Cheongju 28119, Republic of Korea
| | - Young Mok Park
- Center for Cognition and Sociality, Institute for Basic Science , Daejeon, Republic of Korea
| | - Hyoung-Joo Lee
- Yonsei Proteome Research Center and Department of Integrated OMICS for Biomedical Science, and Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University , Seoul, Republic of Korea
| | - Young-Ki Paik
- Yonsei Proteome Research Center and Department of Integrated OMICS for Biomedical Science, and Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University , Seoul, Republic of Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute , Cheongju 28119, Republic of Korea
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute , Cheongju 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon, Republic of Korea
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29
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Guruceaga E, Garin-Muga A, Prieto G, Bejarano B, Marcilla M, Marín-Vicente C, Perez-Riverol Y, Casal JI, Vizcaíno JA, Corrales FJ, Segura V. Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach. J Proteome Res 2017; 16:4374-4390. [PMID: 28960077 PMCID: PMC5737412 DOI: 10.1021/acs.jproteome.7b00388] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
The Human Proteome
Project (HPP) aims deciphering the complete
map of the human proteome. In the past few years, significant efforts
of the HPP teams have been dedicated to the experimental detection
of the missing proteins, which lack reliable mass spectrometry evidence
of their existence. In this endeavor, an in depth analysis of shotgun
experiments might represent a valuable resource to select a biological
matrix in design validation experiments. In this work, we used all
the proteomic experiments from the NCI60 cell lines and applied an
integrative approach based on the results obtained from Comet, Mascot,
OMSSA, and X!Tandem. This workflow benefits from the complementarity
of these search engines to increase the proteome coverage. Five missing
proteins C-HPP guidelines compliant were identified, although further
validation is needed. Moreover, 165 missing proteins were detected
with only one unique peptide, and their functional analysis supported
their participation in cellular pathways as was also proposed in other
studies. Finally, we performed a combined analysis of the gene expression
levels and the proteomic identifications from the common cell lines
between the NCI60 and the CCLE project to suggest alternatives for
further validation of missing protein observations.
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Affiliation(s)
- Elizabeth Guruceaga
- Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , Pamplona 31008, Spain.,IdiSNA, Navarra Institute for Health Research , Pamplona 31008, Spain
| | - Alba Garin-Muga
- Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , Pamplona 31008, Spain
| | - Gorka Prieto
- Department of Communications Engineering, University of the Basque Country (UPV/EHU) , Bilbao 48013, Spain
| | | | - Miguel Marcilla
- Proteomics Unit, Spanish National Biotechnology Centre, CSIC , Madrid 28049, Spain
| | | | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, U.K
| | | | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, U.K
| | - Fernando J Corrales
- Proteomics Unit, Spanish National Biotechnology Centre, CSIC , Madrid 28049, Spain
| | - Victor Segura
- Bioinformatics Unit, Center for Applied Medical Research, University of Navarra , Pamplona 31008, Spain.,IdiSNA, Navarra Institute for Health Research , Pamplona 31008, Spain
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30
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Omenn GS, Lane L, Lundberg EK, Overall CM, Deutsch EW. Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project. J Proteome Res 2017; 16:4281-4287. [PMID: 28853897 DOI: 10.1021/acs.jproteome.7b00375] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Human Proteome Organization (HUPO) Human Proteome Project (HPP) continues to make progress on its two overall goals: (1) completing the protein parts list, with an annual update of the HUPO draft human proteome, and (2) making proteomics an integrated complement to genomics and transcriptomics throughout biomedical and life sciences research. neXtProt version 2017-01-23 has 17 008 confident protein identifications (Protein Existence [PE] level 1) that are compliant with the HPP Guidelines v2.1 ( https://hupo.org/Guidelines ), up from 13 664 in 2012-12 and 16 518 in 2016-04. Remaining to be found by mass spectrometry and other methods are 2579 "missing proteins" (PE2+3+4), down from 2949 in 2016. PeptideAtlas 2017-01 has 15 173 canonical proteins, accounting for nearly all of the 15 290 PE1 proteins based on MS data. These resources have extensive data on PTMs, single amino acid variants, and splice isoforms. The Human Protein Atlas v16 has 10 492 highly curated protein entries with tissue and subcellular spatial localization of proteins and transcript expression. Organ-specific popular protein lists have been generated for broad use in quantitative targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology and disease.
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Affiliation(s)
- Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan , 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States.,Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Human Protein Science, University of Geneva , CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Emma K Lundberg
- SciLifeLab Stockholm and School of Biotechnology, KTH, Karolinska Institutet Science Park , Tomtebodavägen 23, SE-171 65 Solna, Sweden
| | - Christopher M Overall
- Life Sciences Institute, Faculty of Dentistry, University of British Columbia , 2350 Health Sciences Mall, Room 4.401, Vancouver, British Columbia V6T 1Z3, Canada
| | - Eric W Deutsch
- Institute for Systems Biology , 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
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31
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Carapito C, Duek P, Macron C, Seffals M, Rondel K, Delalande F, Lindskog C, Fréour T, Vandenbrouck Y, Lane L, Pineau C. Validating Missing Proteins in Human Sperm Cells by Targeted Mass-Spectrometry- and Antibody-based Methods. J Proteome Res 2017; 16:4340-4351. [DOI: 10.1021/acs.jproteome.7b00374] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Christine Carapito
- Laboratoire
de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, 25 Rue Becquerel, Strasbourg F-67087, France
| | - Paula Duek
- CALIPHO
Group, SIB-Swiss Institute of Bioinformatics, CMU, rue Michel-Servet
1, CH-1211 Geneva
4, Switzerland
| | - Charlotte Macron
- Laboratoire
de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, 25 Rue Becquerel, Strasbourg F-67087, France
| | - Marine Seffals
- H2P2
Core facility, UMS BioSit, University of Rennes 1, Rennes F-35040, France
| | - Karine Rondel
- Protim,
Inserm U1085, Irset, Campus de Beaulieu, Rennes F-35042, France
| | - François Delalande
- Laboratoire
de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, 25 Rue Becquerel, Strasbourg F-67087, France
| | - Cecilia Lindskog
- Department
of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thomas Fréour
- Service de
Médecine de la Reproduction, CHU de Nantes, 38 boulevard
Jean Monnet, Nantes F-44093, France
- Inserm UMR1064, Nantes F-44093, France
| | - Yves Vandenbrouck
- CEA, DRF, BIG,
Laboratoire de Biologie à Grande Echelle, 17, rue des Martyrs, Grenoble F-38054, France
- Inserm U1038, Grenoble F-38054, France
- Grenoble-Alpes University, Grenoble F-38054, France
| | - Lydie Lane
- CALIPHO
Group, SIB-Swiss Institute of Bioinformatics, CMU, rue Michel-Servet
1, CH-1211 Geneva
4, Switzerland
- Department
of Human Protein Sciences, Faculty of Medicine, University of Geneva, 1, rue Michel-Servet, 1211 Geneva 4, Switzerland
| | - Charles Pineau
- Protim,
Inserm U1085, Irset, Campus de Beaulieu, Rennes F-35042, France
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32
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Miotello G, Ktari A, Gueddou A, Nouioui I, Ghodhbane-Gtari F, Armengaud J, Gtari M. Proteogenomics data for deciphering Frankia coriariae interactions with root exudates from three host plants. Data Brief 2017; 14:73-76. [PMID: 28765834 PMCID: PMC5526514 DOI: 10.1016/j.dib.2017.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/22/2017] [Accepted: 07/05/2017] [Indexed: 10/28/2022] Open
Abstract
Frankia coriariae BMG5.1 cells were incubated with root exudates derived from compatible (Coriaria myrtifolia), incompatible (Alnus glutinosa) and non-actinorhizal (Cucumis melo) host plants. Bacteria cells and their exoproteomes were analyzed by high-throughput proteomics using a Q-Exactive HF high resolution tandem mass spectrometer incorporating an ultra-high-field orbitrap analyzer. MS/MS spectra were assigned with two protein sequence databases derived from the closely-related genomes from strains BMG5.1 andDg1, the Frankia symbiont of Datisca glomerata. The tandem mass spectrometry data accompanying the manuscript describing the database searches and comparative analysis (Ktari et al., 2017, doi.org/10.3389/fmicb.2017.00720) [1] have been deposited to the ProteomeXchange with identifiers PXD005979 (whole cell proteomes) and PXD005980 (exoproteome data).
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Affiliation(s)
- Guylaine Miotello
- CEA, DRF/JOLIOT/DMTS/SPI/Li2D, Lab Innovative Technologies for Detection and Diagnostic, Bagnols-sur-Cèze, France
| | - Amir Ktari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Abdellatif Gueddou
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Imen Nouioui
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Jean Armengaud
- CEA, DRF/JOLIOT/DMTS/SPI/Li2D, Lab Innovative Technologies for Detection and Diagnostic, Bagnols-sur-Cèze, France
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
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Omenn GS. Advances of the HUPO Human Proteome Project with broad applications for life sciences research. Expert Rev Proteomics 2017; 14:109-111. [PMID: 27935328 PMCID: PMC5335864 DOI: 10.1080/14789450.2017.1270763] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/07/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Gilbert S Omenn
- a Departments of Computational Medicine & Bioinformatics , Internal Medicine, Human Genetics, and School of Public Health, University of Michigan , Ann Arbor , MI , USA
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Omenn GS, Lane L, Lundberg EK, Beavis RC, Overall CM, Deutsch EW. Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications. J Proteome Res 2016; 15:3951-3960. [PMID: 27487407 PMCID: PMC5129622 DOI: 10.1021/acs.jproteome.6b00511] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The HUPO Human Proteome Project (HPP) has two overall goals: (1) stepwise completion of the protein parts list-the draft human proteome including confidently identifying and characterizing at least one protein product from each protein-coding gene, with increasing emphasis on sequence variants, post-translational modifications (PTMs), and splice isoforms of those proteins; and (2) making proteomics an integrated counterpart to genomics throughout the biomedical and life sciences community. PeptideAtlas and GPMDB reanalyze all major human mass spectrometry data sets available through ProteomeXchange with standardized protocols and stringent quality filters; neXtProt curates and integrates mass spectrometry and other findings to present the most up to date authorative compendium of the human proteome. The HPP Guidelines for Mass Spectrometry Data Interpretation version 2.1 were applied to manuscripts submitted for this 2016 C-HPP-led special issue [ www.thehpp.org/guidelines ]. The Human Proteome presented as neXtProt version 2016-02 has 16,518 confident protein identifications (Protein Existence [PE] Level 1), up from 13,664 at 2012-12, 15,646 at 2013-09, and 16,491 at 2014-10. There are 485 proteins that would have been PE1 under the Guidelines v1.0 from 2012 but now have insufficient evidence due to the agreed-upon more stringent Guidelines v2.0 to reduce false positives. neXtProt and PeptideAtlas now both require two non-nested, uniquely mapping (proteotypic) peptides of at least 9 aa in length. There are 2,949 missing proteins (PE2+3+4) as the baseline for submissions for this fourth annual C-HPP special issue of Journal of Proteome Research. PeptideAtlas has 14,629 canonical (plus 1187 uncertain and 1755 redundant) entries. GPMDB has 16,190 EC4 entries, and the Human Protein Atlas has 10,475 entries with supportive evidence. neXtProt, PeptideAtlas, and GPMDB are rich resources of information about post-translational modifications (PTMs), single amino acid variants (SAAVSs), and splice isoforms. Meanwhile, the Biology- and Disease-driven (B/D)-HPP has created comprehensive SRM resources, generated popular protein lists to guide targeted proteomics assays for specific diseases, and launched an Early Career Researchers initiative.
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Affiliation(s)
- Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Human Protein Science, University of Geneva, CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Emma K. Lundberg
- SciLifeLab Stockholm and School of Biotechnology, KTH, Karolinska Institutet Science Park, Tomtebodavägen 23, SE-171 65 Solna, Sweden
| | - Ronald C. Beavis
- Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Christopher M. Overall
- Biochemistry and Molecular Biology, and Oral Biological and Medical Sciences University of British Columbia, 2350 Health Sciences Mall, Room 4.401, Vancouver, BC V6T 1Z3, Canada
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
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