| An efficient data format for mass spectrometry-based proteomics. | |
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MedLine Citation:
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PMID: 20674389 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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The diverse range of mass spectrometry (MS) instrumentation along with corresponding proprietary and nonproprietary data formats has generated a proteomics community driven call for a standardized format to facilitate management, processing, storing, visualization, and exchange of both experimental and processed data. To date, significant efforts have been extended towards standardizing XML-based formats for mass spectrometry data representation, despite the recognized inefficiencies associated with storing large numeric datasets in XML. The proteomics community has periodically entertained alternate strategies for data exchange, e.g., using a common application programming interface or a database-derived format. However, these efforts have yet to gain significant attention, mostly because they have not demonstrated significant performance benefits over existing standards, but also due to issues such as extensibility to multidimensional separation systems, robustness of operation, and incomplete or mismatched vocabulary. Here, we describe a format based on standard database principles that offers multiple benefits over existing formats in terms of storage size, ease of processing, data retrieval times, and extensibility to accommodate multidimensional separation systems. |
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Authors:
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Anuj R Shah; Jennifer Davidson; Matthew E Monroe; Anoop M Mayampurath; William F Danielson; Yan Shi; Aaron C Robinson; Brian H Clowers; Mikhail E Belov; Gordon A Anderson; Richard D Smith |
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Publication Detail:
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Type: Journal Article Date: 2010-07-07 |
Journal Detail:
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Title: Journal of the American Society for Mass Spectrometry Volume: 21 ISSN: 1879-1123 ISO Abbreviation: J. Am. Soc. Mass Spectrom. Publication Date: 2010 Oct |
Date Detail:
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Created Date: 2010-09-24 Completed Date: 2010-12-30 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9010412 Medline TA: J Am Soc Mass Spectrom Country: United States |
Other Details:
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Languages: eng Pagination: 1784-8 Citation Subset: IM |
Copyright Information:
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Copyright © 2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved. |
Affiliation:
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Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Database Management Systems* Databases, Factual* Mass Spectrometry* Proteomics* |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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