1
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Bairoch A. Meet the Editorial Board Member. CURR PROTEOMICS 2022. [DOI: 10.2174/157016461904220907111423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Amos Bairoch
- Department of Human Protein Sciences
Swiss-Prot Group
Swiss Institute of Bioinformatics
Geneva
Switzerland
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2
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Zhang Y, Lin Z, Tan Y, Bu F, Hao P, Zhang K, Yang H, Liu S, Ren Y. Exploration of Missing Proteins by a Combination Approach to Enrich the Low-Abundance Hydrophobic Proteins from Four Cancer Cell Lines. J Proteome Res 2019; 19:401-408. [DOI: 10.1021/acs.jproteome.9b00590] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Yuanliang Zhang
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhilong Lin
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Yifan Tan
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Fanyu Bu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Keren Zhang
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
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3
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Abstract
Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA- and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry-based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease. We frame central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today. We use this framework to assess existing data and to ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?" We also explore prospects for improving measurements to better regularize protein-level biology and efficiently associate PTMs to function and phenotype.
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4
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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: 1.1] [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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5
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Zhang Y, Lin Z, Hao P, Hou K, Sui Y, Zhang K, He Y, Li H, Yang H, Liu S, Ren Y. Improvement of Peptide Separation for Exploring the Missing Proteins Localized on Membranes. J Proteome Res 2018; 17:4152-4159. [DOI: 10.1021/acs.jproteome.8b00409] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuanliang Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Zhilong Lin
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Kexia Hou
- The Second Maternal and Child Health Care Center of Huangdao District, 236 Fuchunjiang Road, Qingdao 266555, Shandong, China
| | - Yuanyuan Sui
- The Second Maternal and Child Health Care Center of Huangdao District, 236 Fuchunjiang Road, Qingdao 266555, Shandong, China
| | - Keren Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Yanbin He
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Hong Li
- Pulmonary Function Room, Shenzhen Seventh People’s Hospital, 2010 Wutong Road, Yantian District, Shenzhen, Guangdong 518081, 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
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
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6
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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: 1.9] [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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7
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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: 2.3] [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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8
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Yang MH, Chen WJ, Fu YS, Huang B, Tsai WC, Arthur Chen YM, Lin PC, Yuan CH, Tyan YC. Utilizing glycine N-methyltransferasegene knockout mice as a model for identification of missing proteins in hepatocellular carcinoma. Oncotarget 2017; 9:442-452. [PMID: 29416626 PMCID: PMC5787479 DOI: 10.18632/oncotarget.23064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/13/2017] [Indexed: 11/25/2022] Open
Abstract
Glycine N-methyltransferase is a tumor suppressor gene for hepatocellular carcinoma, which can activate DNA methylation by inducing the S-adenosylmethionine to S-adenosylhomocystine. Previous studies have indicated that the expression of Glycine N-methyltransferase is inhibited in hepatocellular carcinoma. To confirm and identify missing proteins, the pathologic analysis of the tumor-bearing mice will provide critical histologic information. Such a mouse model is applied as a screening tool for hepatocellular carcinoma as well as a strategy for missing protein discovery. In this study we designed an analysis platform using the human proteome atlas to compare the possible missing proteins to human whole chromosomes. This will integrate the information from animal studies to establish an optimal technique in the missing protein biomarker discovery.
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Affiliation(s)
- Ming-Hui Yang
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wan-Jou Chen
- Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yaw-Syan Fu
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Bin Huang
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wan-Chi Tsai
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Ming Arthur Chen
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Po-Chiao Lin
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Cheng-Hui Yuan
- Mass Spectrometry Laboratory, Department of Chemistry, National University of Singapore, Singapore
| | - Yu-Chang Tyan
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
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9
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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: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [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
| | - Consuelo Marín-Vicente
- Functional
Proteomics, Department of Cellular and Molecular Medicine and Proteomic Facility, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Yasset Perez-Riverol
- European
Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K.
| | - J. Ignacio Casal
- Functional
Proteomics, Department of Cellular and Molecular Medicine and Proteomic Facility, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, Madrid 28040, Spain
| | - 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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10
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Paik YK, Omenn GS, Hancock WS, Lane L, Overall CM. Advances in the Chromosome-Centric Human Proteome Project: looking to the future. Expert Rev Proteomics 2017; 14:1059-1071. [PMID: 29039980 DOI: 10.1080/14789450.2017.1394189] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION The mission of the Chromosome-Centric Human Proteome Project (C-HPP), is to map and annotate the entire predicted human protein set (~20,000 proteins) encoded by each chromosome. The initial steps of the project are focused on 'missing proteins (MPs)', which lacked documented evidence for existence at protein level. In addition to remaining 2,579 MPs, we also target those annotated proteins having unknown functions, uPE1 proteins, alternative splice isoforms and post-translational modifications. We also consider how to investigate various protein functions involved in cis-regulatory phenomena, amplicons lncRNAs and smORFs. Areas covered: We will cover the scope, historic background, progress, challenges and future prospects of C-HPP. This review also addresses the question of how we can best improve the methodological approaches, select the optimal biological samples, and recommend stringent protocols for the identification and characterization of MPs. A new strategy for functional analysis of some of those annotated proteins having unknown function will also be discussed. Expert commentary: If the project moves well by reshaping the original goals, the current working modules and team work in the proposed extended planning period, it is anticipated that a progressively more detailed draft of an accurate chromosome-based proteome map will become available with functional information.
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Affiliation(s)
- Young-Ki Paik
- a Yonsei Proteome Research Center and Department of Biochemistry , Yonsei University , Seoul , Korea
| | - Gilbert S Omenn
- b Department of Computational Medicine & Bioinformatics , University of Michigan , Ann Arbor , MI , USA
| | - William S Hancock
- c Department of Chemical Biology , Northeastern University , Boston , Massachusetts 02115 , USA
| | - Lydie Lane
- d Department of Human Protein Sciences, Faculty of Medicine , University of Geneva , Geneva , Switzerland.,e Swiss Institute of Bioinformatics , Geneva , Switzerland
| | - Christopher M Overall
- f Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry , University of British Columbia , Vancouver , Canada
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11
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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: 2.4] [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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12
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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: 48] [Impact Index Per Article: 6.0] [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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13
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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: 2.1] [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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Segura V, Garin-Muga A, Guruceaga E, Corrales FJ. Progress and pitfalls in finding the 'missing proteins' from the human proteome map. Expert Rev Proteomics 2017; 14:9-14. [PMID: 27885863 DOI: 10.1080/14789450.2017.1265450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/23/2016] [Indexed: 01/09/2023]
Abstract
The Human Proteome Project was launched with two main goals: the comprehensive and systematic definition of the human proteome map and the development of ready to use analytical tools to measure relevant proteins in their biological context in health and disease. Despite the great progress in this endeavour, there is still a group of reluctant proteins with no, or scarce, experimental evidence supporting their existence. These are called the 'missing proteins' and represent one of the biggest challenges to complete the human proteome map. Areas covered: This review focuses on the description of the missing proteome based on the HUPO standards, the analysis of the reasons explaining the difficulty of detecting missing proteins and the strategies currently used in the search for missing proteins. The present and future of the quest for the missing proteins is critically revised hereafter. Expert commentary: An overarching multidisciplinary effort is currently being done under the HUPO umbrella to allow completion of the human proteome map. It is expected that the detection of missing proteins will grow in the coming years since the methods and the best tissue/cell type sample for their search are already on the table.
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Affiliation(s)
- Victor Segura
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| | - Alba Garin-Muga
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| | - Elizabeth Guruceaga
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| | - Fernando J Corrales
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
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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: 7.0] [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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