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      A draft map of the human proteome

      research-article
      Author(s): 1 , 2 , 3 , 1 , 4 , 3 , 3 , 1 , 2 , 3 , 3 , 5 , 5 , 3 , 3 , 1 , 6 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 1 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 3 , 7 , 3 , 1 , 1 , 1 , 2 , 1 , 1 , 2 , 8 , 9 , 10 , 11 , 12 , 1 , 10 , 11 , 13 , 14 , 3 , 15 , 16 , 1 , 17 , 16 , 18 , 15 , 3 , 15 , 16 , 19 , 5 , 15 , 16 , 17 , 3 , * , 1 , 2 , 3 , 4 , 15 , 16 , 20 , *
      Publication date PMC-release:
      Journal: Nature

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          Abstract

          The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet. Here, we present a draft map of the human proteome using high resolution Fourier transform mass spectrometry. In-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells resulted in identification of proteins encoded by 17,294 genes accounting for ~84% of the total annotated protein-coding genes in humans. A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream ORFs. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) will complement available human genome and transcriptome data to accelerate biomedical research in health and disease.

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          The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

          Juan Antonio Vizcaíno, Richard Côté, Attila Csordas … (2012)
          The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.
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            TANDEM: matching proteins with tandem mass spectra.

            Robertson Craig, Ronald C Beavis (2004)
            Tandem mass spectra obtained from fragmenting peptide ions contain some peptide sequence specific information, but often there is not enough information to sequence the original peptide completely. Several proprietary software applications have been developed to attempt to match the spectra with a list of protein sequences that may contain the sequence of the peptide. The application TANDEM was written to provide the proteomics research community with a set of components that can be used to test new methods and algorithms for performing this type of sequence-to-data matching. The source code and binaries for this software are available at http://www.proteome.ca/opensource.html, for Windows, Linux and Macintosh OSX. The source code is made available under the Artistic License, from the authors.
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              The UCSC Genome Browser database: extensions and updates 2013

              Laurence R. Meyer, Ann Zweig, Angie S. Hinrichs … (2012)
              The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation ‘tracks’ are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.
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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 0410462
                Journal ID (pubmed-jr-id): 6011
                Journal ID (nlm-ta): Nature
                Journal ID (iso-abbrev): Nature
                Title: Nature
                ISSN (Print): 0028-0836
                ISSN (Electronic): 1476-4687
                Publication date Nihms-submitted: 1 October 2014
                Publication date (Print): 29 May 2014
                Publication date PMC-release: 20 April 2015
                Volume: 509
                Issue: 7502
                Pages: 575-581
                Affiliations
                [1 ]McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
                [2 ]Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
                [3 ]Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
                [4 ]Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130, USA
                [5 ]The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
                [6 ]Department of Pathology, Universidad de La Frontera, Center of Genetic and Immunological Studies-Scientific and Technological Bioresource Nucleus, Temuco 4811230, Chile
                [7 ]School of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
                [8 ]Department of Neurosurgery, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
                [9 ]Department of Internal Medicine Armed Forces Medical College, Pune 411040, India
                [10 ]Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
                [11 ]Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
                [12 ]Department of Chemical and Biomolecular Engineering and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
                [13 ]Department of Neurology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
                [14 ]Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
                [15 ]The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
                [16 ]Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
                [17 ]Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
                [18 ]Departments of Immunology and Urology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
                [19 ]Department of Obstetrics and Gynecology, Johns Hopkins University School of Medicine Baltimore, MD 21205
                [20 ]Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130, USA
                Author notes
                Correspondence and requests for materials should be addressed to H.G. ( harsha@ 123456ibioinformatics.org ) or A.P. ( pandey@ 123456jhmi.edu )
                [§]

                Current address as Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

                Article
                Manuscript ID: NIHMS581490
                DOI: 10.1038/nature13302
                PMC ID: 4403737
                PubMed ID: 24870542
                SO-VID: 62940d9e-fd14-42bb-9473-3d34303e0b6b
                License:

                Reprints and permissions information is available at www.nature.com/reprints.

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