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PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor.

Heazlewood JL, Durek P, Hummel J, Selbig J, Weckwerth W, Walther D, Schulze WX - Nucleic Acids Res. (2007)

Bottom Line: The database is searchable by protein accession number, physical peptide characteristics, as well as by experimental conditions (tissue sampled, phosphopeptide enrichment method).An analysis of the current annotated Arabidopsis proteome yielded in 27,782 predicted phosphoserine sites distributed across 17,035 proteins.These prediction results are summarized graphically in the database together with the experimental phosphorylation sites in a whole sequence context.

View Article: PubMed Central - PubMed

Affiliation: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley 6009, WA, Australia.

ABSTRACT
The PhosPhAt database provides a resource consolidating our current knowledge of mass spectrometry-based identified phosphorylation sites in Arabidopsis and combines it with phosphorylation site prediction specifically trained on experimentally identified Arabidopsis phosphorylation motifs. The database currently contains 1187 unique tryptic peptide sequences encompassing 1053 Arabidopsis proteins. Among the characterized phosphorylation sites, there are over 1000 with unambiguous site assignments, and nearly 500 for which the precise phosphorylation site could not be determined. The database is searchable by protein accession number, physical peptide characteristics, as well as by experimental conditions (tissue sampled, phosphopeptide enrichment method). For each protein, a phosphorylation site overview is presented in tabular form with detailed information on each identified phosphopeptide. We have utilized a set of 802 experimentally validated serine phosphorylation sites to develop a method for prediction of serine phosphorylation (pSer) in Arabidopsis. An analysis of the current annotated Arabidopsis proteome yielded in 27,782 predicted phosphoserine sites distributed across 17,035 proteins. These prediction results are summarized graphically in the database together with the experimental phosphorylation sites in a whole sequence context. The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt) provides a valuable resource to the plant science community and can be accessed through the following link http://phosphat.mpimp-golm.mpg.de.

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Schematic diagram outlining the structure of the PhosPhAt service illustrating the two main query entry points to query experimental data and pSer prediction information. Both services merge into a common output at the ‘Summary Page’ on which the prediction results are displayed on top of the page and all experimental phosphopeptides for the given AGI code are listed below. In instances where no experimental phosphopeptides are available, only the prediction result will be displayed. External links to published references at PubMed and MS/MS data at the ProMex mass spectral library (17) are also shown.
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Figure 1: Schematic diagram outlining the structure of the PhosPhAt service illustrating the two main query entry points to query experimental data and pSer prediction information. Both services merge into a common output at the ‘Summary Page’ on which the prediction results are displayed on top of the page and all experimental phosphopeptides for the given AGI code are listed below. In instances where no experimental phosphopeptides are available, only the prediction result will be displayed. External links to published references at PubMed and MS/MS data at the ProMex mass spectral library (17) are also shown.

Mentions: The database is comprised of two distinct tables (Figure 1): the first table (phosphat) contains the experimental phosphopeptide information and comprises data from several published large- and medium-scale phosphoproteomic analyses (9,12–15) as well as unpublished sites identified in authors’ labs. Each entry is a unique experimentally measured precursor ion (m/z) and not a composite entry. This is an important feature of the PhosPhAt database as it tracks each piece of experimental data, and provides links also to the actual experimental mass spectra deposited in PROMEX [http://promex.mpimp-golm.mpg.de; (17)]. With a link to this spectral library on the ‘Result Table’ users can download the precursor mass-to-charge ratio and the corresponding CID-spectrum. This data is crucial for the design of multiple reaction monitoring (MRM) experiments for targeted phosphopeptide-quantification on a triple quadrupole or ion trap mass spectrometer (10,18).Figure 1.


PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor.

Heazlewood JL, Durek P, Hummel J, Selbig J, Weckwerth W, Walther D, Schulze WX - Nucleic Acids Res. (2007)

Schematic diagram outlining the structure of the PhosPhAt service illustrating the two main query entry points to query experimental data and pSer prediction information. Both services merge into a common output at the ‘Summary Page’ on which the prediction results are displayed on top of the page and all experimental phosphopeptides for the given AGI code are listed below. In instances where no experimental phosphopeptides are available, only the prediction result will be displayed. External links to published references at PubMed and MS/MS data at the ProMex mass spectral library (17) are also shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238998&req=5

Figure 1: Schematic diagram outlining the structure of the PhosPhAt service illustrating the two main query entry points to query experimental data and pSer prediction information. Both services merge into a common output at the ‘Summary Page’ on which the prediction results are displayed on top of the page and all experimental phosphopeptides for the given AGI code are listed below. In instances where no experimental phosphopeptides are available, only the prediction result will be displayed. External links to published references at PubMed and MS/MS data at the ProMex mass spectral library (17) are also shown.
Mentions: The database is comprised of two distinct tables (Figure 1): the first table (phosphat) contains the experimental phosphopeptide information and comprises data from several published large- and medium-scale phosphoproteomic analyses (9,12–15) as well as unpublished sites identified in authors’ labs. Each entry is a unique experimentally measured precursor ion (m/z) and not a composite entry. This is an important feature of the PhosPhAt database as it tracks each piece of experimental data, and provides links also to the actual experimental mass spectra deposited in PROMEX [http://promex.mpimp-golm.mpg.de; (17)]. With a link to this spectral library on the ‘Result Table’ users can download the precursor mass-to-charge ratio and the corresponding CID-spectrum. This data is crucial for the design of multiple reaction monitoring (MRM) experiments for targeted phosphopeptide-quantification on a triple quadrupole or ion trap mass spectrometer (10,18).Figure 1.

Bottom Line: The database is searchable by protein accession number, physical peptide characteristics, as well as by experimental conditions (tissue sampled, phosphopeptide enrichment method).An analysis of the current annotated Arabidopsis proteome yielded in 27,782 predicted phosphoserine sites distributed across 17,035 proteins.These prediction results are summarized graphically in the database together with the experimental phosphorylation sites in a whole sequence context.

View Article: PubMed Central - PubMed

Affiliation: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley 6009, WA, Australia.

ABSTRACT
The PhosPhAt database provides a resource consolidating our current knowledge of mass spectrometry-based identified phosphorylation sites in Arabidopsis and combines it with phosphorylation site prediction specifically trained on experimentally identified Arabidopsis phosphorylation motifs. The database currently contains 1187 unique tryptic peptide sequences encompassing 1053 Arabidopsis proteins. Among the characterized phosphorylation sites, there are over 1000 with unambiguous site assignments, and nearly 500 for which the precise phosphorylation site could not be determined. The database is searchable by protein accession number, physical peptide characteristics, as well as by experimental conditions (tissue sampled, phosphopeptide enrichment method). For each protein, a phosphorylation site overview is presented in tabular form with detailed information on each identified phosphopeptide. We have utilized a set of 802 experimentally validated serine phosphorylation sites to develop a method for prediction of serine phosphorylation (pSer) in Arabidopsis. An analysis of the current annotated Arabidopsis proteome yielded in 27,782 predicted phosphoserine sites distributed across 17,035 proteins. These prediction results are summarized graphically in the database together with the experimental phosphorylation sites in a whole sequence context. The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt) provides a valuable resource to the plant science community and can be accessed through the following link http://phosphat.mpimp-golm.mpg.de.

Show MeSH