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  ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites

Hummel, J., Niemann, M., Wienkoop, S., Schulze, W., Steinhauser, D., Selbig, J., et al. (2007). ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites. BMC Bioinformatics, 8, 216. doi:10.1186/1471-2105-8-216.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-290B-B Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0019-075D-D
Genre: Journal Article

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 Creators:
Hummel, J.1, 2, Author              
Niemann, M.3, Author
Wienkoop, S.4, Author              
Schulze, W.3, Author
Steinhauser, D.5, 6, Author              
Selbig, J.1, Author              
Walther, D.2, Author              
Weckwerth, W.4, Author              
Affiliations:
1BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753315              
2BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753303              
3External Organizations, ou_persistent22              
4Integrative Proteomics and Metabolomics, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753334              
5Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753340              
6Systems Metabolomics, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, Am Mühlenberg 1, 14476 Potsdam-Golm, DE, ou_1797285              

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Free keywords: compound identification arabidopsis-thaliana library quantification extraction peptides csb.db
 Abstract: Background: In the last decade, techniques were established for the large scale genome-wide analysis of proteins, RNA, and metabolites, and database solutions have been developed to manage the generated data sets. The Golm Metabolome Database for metabolite data (GMD) represents one such effort to make these data broadly available and to interconnect the different molecular levels of a biological system [1]. As data interpretation in the light of already existing data becomes increasingly important, these initiatives are an essential part of current and future systems biology. Results: A mass spectral library consisting of experimentally derived tryptic peptide product ion spectra was generated based on liquid chromatography coupled to ion trap mass spectrometry ( LC-IT-MS). Protein samples derived from Arabidopsis thaliana, Chlamydomonas reinhardii, Medicago truncatula, and Sinorhizobium meliloti were analysed. With currently 4,557 manually validated spectra associated with 4,226 unique peptides from 1,367 proteins, the database serves as a continuously growing reference data set and can be used for protein identification and quantification in uncharacterized biological samples. For peptide identification, several algorithms were implemented based on a recently published study for peptide mass fingerprinting [2] and tested for false positive and negative rates. An algorithm which considers intensity distribution for match correlation scores was found to yield best results. For proof of concept, an LC-IT-MS analysis of a tryptic leaf protein digest was converted to mzData format and searched against the mass spectral library. The utility of the mass spectral library was also tested for the identification of phosphorylated tryptic peptides. We included in vivo phosphorylation sites of Arabidopsis thaliana proteins and the identification performance was found to be improved compared to genome-based search algorithms. Protein identification by ProMEX is linked to other levels of biological organization such as metabolite, pathway, and transcript data. The database is further connected to annotation and classification services via BioMoby. Conclusion: The ProMEX protein/ peptide database represents a mass spectral reference library with the capability of matching unknown samples for protein identification. The database allows text searches based on metadata such as experimental information of the samples, mass spectrometric instrument parameters or unique protein identifier like AGI codes. ProMEX integrates proteomics data with other levels of molecular organization including metabolite, pathway, and transcript information and may thus become a useful resource for plant systems biology studies. The ProMEX mass spectral library is available at http://promex.mpimp-golm.mpg.de/.

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Language(s): eng - English
 Dates: 2007-06-232007
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: ISI: ISI:000248130900001
DOI: 10.1186/1471-2105-8-216
ISSN: 1471-2105 (Electronic)1471-2105 (Linking)
URI: ://000248130900001http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920535/pdf/1471-2105-8-216.pdf?tool=pmcentrez
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Title: BMC Bioinformatics
Source Genre: Journal
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Pages: - Volume / Issue: 8 Sequence Number: - Start / End Page: 216 Identifier: -