NCBI Peptidome: a new repository for mass spectrometry proteomics data.

Nucleic Acids Research
Li JiDouglas J Slotta

Abstract

Peptidome is a public repository that archives and freely distributes tandem mass spectrometry peptide and protein identification data generated by the scientific community. Data from all stages of a mass spectrometry experiment are captured, including original mass spectra files, experimental metadata and conclusion-level results. The submission process is facilitated through acceptance of data in commonly used open formats, and all submissions undergo syntactic validation and curation in an effort to uphold data integrity and quality. Peptidome is not restricted to specific organisms, instruments or experiment types; data from any tandem mass spectrometry experiment from any species are accepted. In addition to data storage, web-based interfaces are available to help users query, browse and explore individual peptides, proteins or entire Samples and Studies. Results are integrated and linked with other NCBI resources to ensure dissemination of the information beyond the mass spectroscopy proteomics community. Peptidome is freely accessible at http://www.ncbi.nlm.nih.gov/peptidome.

References

Jun 3, 2004·Proteomics·David M Creasy, John S Cottrell
Dec 15, 2004·Journal of Proteome Research·Robertson CraigRonald C Beavis
Dec 31, 2005·Nucleic Acids Research·Philip JonesRolf Apweiler
Mar 9, 2007·Nature Biotechnology
Feb 9, 2008·Nature Biotechnology·Suresh MathivananAkhilesh Pandey
Oct 23, 2008·Nucleic Acids Research·Eric W SayersJian Ye
Jul 10, 2009·Nature Biotechnology·Douglas J SlottaRon Edgar

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Citations

May 17, 2011·Database : the Journal of Biological Databases and Curation·Viswanadham SridharaLewis Y Geer
Nov 17, 2009·Nucleic Acids Research·Eric W SayersJian Ye
Nov 26, 2010·Nucleic Acids Research·Eric W SayersJian Ye
Jan 5, 2011·Nucleic Acids Research·Michael Y Galperin, Guy R Cochrane
Dec 7, 2011·Nucleic Acids Research·Michael Y Galperin, Xosé M Fernández-Suárez
Sep 8, 2011·Infection and Immunity·Joseph J GillespieBruno W Sobral
Mar 23, 2011·Genome Génome / Conseil National De Recherches Canada·Peng-Fei QiYou-Liang Zheng
Jul 5, 2011·Bioorganicheskaia khimiia·E A PonomarenkoA V Lisitsa
Sep 2, 2010·Nature Methods·Tommy NilssonJohn J M Bergeron
Aug 1, 2012·Journal of the American Society for Mass Spectrometry·Konstantinos ThalassinosScott J Geromanos
Mar 26, 2013·Science China. Life Sciences·Weimin ZhuXiaoling Yang
Sep 8, 2011·Proteomics·Matthew P CampbellNicolle H Packer
Dec 15, 2012·Molecular BioSystems·Thilo MuthLennart Martens
Dec 3, 2016·Nucleic Acids Research·Shujiro OkudaYasushi Ishihama
Jul 14, 2011·Proteomics·Benoît ValotMichel Zivy
Mar 2, 2011·Proteomics·Kathryn S LilleyLaurent Gatto
Feb 18, 2011·Proteomics·Julia M BurkhartAlbert Sickmann

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Software Mentioned

The
OMSSA
PRIDE
PeptideAtlas
Petidome
Tranche
Human
Mascot
Entrez
Peptidome

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