Abstract
BackgroundTechnological 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 & conclusionHere 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.
Highlights
Technological advances in mass spectrometry and other detection methods are leading to larger and larger proteomics datasets
In the case of such studies the journal article focuses on the interpretation of the sequence data while the actual sequence is deposited into public databases maintained by the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI) or other institutions
Underlying database The microarray community agreed on the MIAME (Minimum Information About a Microarray Experiment) standards in 2001 [15] but the proteomics community is still far from an agreement on an analogous MIAPE despite the best efforts of the Human Proteome Organization's (HUPO) Proteomics Standards Initiative (HUPO-PSI) [16]
Summary
Technological advances in mass spectrometry and other detection methods are leading to larger and larger proteomics datasets. 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.
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