PrestOMIC, an open source application for dissemination of proteomic datasets by individual laboratories

被引:5
作者
Howes, Charles G. [1 ]
Foster, Leonard J.
机构
[1] Univ British Columbia, UBC Ctr Proteom, Dept Biochem & Mol Biol, Vancouver, BC V6T 1Z4, Canada
[2] Packets Consulting Inc, Burnaby, BC V6T 1Z4, Canada
关键词
D O I
10.1186/1477-5956-5-8
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Background: Technological advances in mass spectrometry and other detection methods are leading to larger and larger proteomics datasets. However, when papers describing such information are published the enormous volume of data can typically only be provided as supplementary data in a tabular form through the journal website. Several journals in the proteomics field, together with the Human Proteome Organization's (HUPO) Proteomics Standards Initiative and institutions such as the Institute for Systems Biology are working towards standardizing the reporting of proteomics data, but just defining standards is only a means towards an end for sharing data. Data repositories such as ProteomeCommons. org and the Open Proteomics Database allow for public access to proteomics data but provide little, if any, interpretation. Results & conclusion: Here we describe PrestOMIC, an open source application for storing mass spectrometry-based proteomic data in a relational database and for providing a user-friendly, searchable and customizable browser interface to share one's data with the scientific community. The underlying database and all associated applications are built on other existing open source tools, allowing PrestOMIC to be modified as the data standards evolve. We then use PrestOMIC to present a recently published dataset from our group through our website.
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页数:8
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共 27 条
  • [1] Mass spectrometry-based proteomics
    Aebersold, R
    Mann, M
    [J]. NATURE, 2003, 422 (6928) : 198 - 207
  • [2] BASIC LOCAL ALIGNMENT SEARCH TOOL
    ALTSCHUL, SF
    GISH, W
    MILLER, W
    MYERS, EW
    LIPMAN, DJ
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) : 403 - 410
  • [3] [Anonymous], The Apache HTTP Server Project
  • [4] *BIOPERL, MAINP BIOPERL
  • [5] Minimum information about a microarray experiment (MIAME) - toward standards for microarray data
    Brazma, A
    Hingamp, P
    Quackenbush, J
    Sherlock, G
    Spellman, P
    Stoeckert, C
    Aach, J
    Ansorge, W
    Ball, CA
    Causton, HC
    Gaasterland, T
    Glenisson, P
    Holstege, FCP
    Kim, IF
    Markowitz, V
    Matese, JC
    Parkinson, H
    Robinson, A
    Sarkans, U
    Schulze-Kremer, S
    Stewart, J
    Taylor, R
    Vilo, J
    Vingron, M
    [J]. NATURE GENETICS, 2001, 29 (04) : 365 - 371
  • [6] ArrayExpress - a public repository for microarray gene expression data at the EBI
    Brazma, A
    Parkinson, H
    Sarkans, U
    Shojatalab, M
    Vilo, J
    Abeygunawardena, N
    Holloway, E
    Kapushesky, M
    Kemmeren, P
    Lara, GG
    Oezcimen, A
    Rocca-Serra, P
    Sansone, SA
    [J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (01) : 68 - 71
  • [7] The need for guidelines in publication of peptide and protein identification data - Working group on publication guidelines for peptide and protein identification data
    Carr, S
    Aebersold, R
    Baldwin, M
    Burlingame, A
    Clauser, K
    Nesvizhskii, A
    [J]. MOLECULAR & CELLULAR PROTEOMICS, 2004, 3 (06) : 531 - 533
  • [8] Quantitative comparison of caste differences in honeybee hemolymph
    Chan, Queenie W. T.
    Howes, Charles G.
    Foster, Leonard J.
    [J]. MOLECULAR & CELLULAR PROTEOMICS, 2006, 5 (12) : 2252 - 2262
  • [9] Open source system for analyzing, validating, and storing protein identification data
    Craig, R
    Cortens, JP
    Beavis, RC
    [J]. JOURNAL OF PROTEOME RESEARCH, 2004, 3 (06) : 1234 - 1242
  • [10] Proteomics
    de Hoog, CL
    Mann, M
    [J]. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 2004, 5 : 267 - 293