The Arabidopsis Protein Phosphorylation Site Database
Home Bulk Downloads Data submission Background Database P-Hotspots Kinome Facts & Figures Imprint
 
System requirements:
  • JavaScript enabled
  • Windows, Mac or Linux
  • Firefox (1.5+), Opera 9+, IE 7+, Safari 3.1+, Google Chrome 1.0+
Logo of MPG Logo of MPIMP

Background


About PhosPhAt

Phosphorylation site database: The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt 3.0) contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups. Specific information about the peptide properties, their annotated biological function as well as the experimental and analytical context is given. For a majority of peptides, the actual annotated mass spectrum is displayed in interactive manner.

Phosphorylation site predictor: The PhosPhAt service has a built-in plant specific phosphorylation site predictor trained on the experimental dataset for Serine, threonine and tyrosine phosphorylation (pSer, pThr, pTyr). Protein sequences or Arabidopsis AGI gene identifier can be submitted to the predictor.



Structure

Query Forms

The query forms. Basic and advanced search parameters. Prediction query.

Result Tables

The "Result Tables" will be displayed as a new tab named "Your Results" when the 'submit' button on the query forms is pressed. Data is presented in a tabular form in which the user can chose the displayed fields and apply custom grouping and sorting. The headers for each column refer to the parameters available for each peptides and are further outlined below (see Definitions).


Result Table multi


The nomenclature used for indicating modifications in the peptide sequence follow the Publication Guidelines as set out by Molecular & Cellular Proteomics. An experimentally confirmed or validated site is indicated with a lowercase p and is contained in brackets e.g. (pS). Ambiguous pSTY sites are presented as lower case characters and each potential candidate (not necessarily all STY residues) is contained in a set of brackets e.g. (s)(s). Following this convention, any oxidized Met residues that have been clamed by the matching process are annotated as (oxM). If no statement can be made on the location of the phosphorylation site, the modified tryptic peptide sequence is displayed with the remark 'site not determined'.

Details page for single result

Beside details about the result data, this view also displays the spectrum and quantitative data (if available).

Result Table multi

Result Table multi

Protein prediction

The "Summary Page" is accessed either by navigating from the result list or is directly displayed after pressing 'submit' button on the "Prediction Query" form. This page summarizes all information in the PhoPhAt Database for a given Arabidopsis loci. Prediction results are displayed graphically and experimental peptides are displayed in a tabular form to which custom sorting and grouping functions can be applied.
At the top of the page the protein sequence (current as of TAIR8) for the AGI code is displayed. Experimentally determined phosphorylation sites are displayed as colored residues (S, T or Y).

Result Table multi

Sequence prediction

It is also possible to get a prediction for a specified sequence. It is accessible through the prediction form, filling out the sequence field. The sequence can contain up to 2000 amino acids.

Result Table multi

Definitions

AGI code: Arabidopsis Genome Initiative code. The code allocated to each gene by the Arabidopsis Genome Initiative (e.g. AT1G02280.1). The decimal point indicates the splice variant, the default splice variant is .1.
Charge: Sort and group a result by selecting ions (peptides) with a specific charge state. Number ranges are inclusive e.g. 2 to 3 would select ions that have charge states M+2H and M+3H. Use 2 to 2 to select ions with charge state M+2H only.
Compartment: Sort, group or limit a query for phosphopeptides identified from a specific cellular compartment. Be aware of inclusive and exclusive sets generating the same or no data when using these options.
Dalton Identical to mass or molecular weight.
Enrichment: Search for phosphopeptides isolated using a specific enrichment strategy. Be aware of inclusive and exclusive sets generating the same or no data when using these options. Current strategies include enrichment of peptides from a complex mixtures e.g. IMAC, TiO2, ZrO2 and double enrichment strategies using phosphoprotein enrichment (MOAC) followed by a phosphopeptide enrichment.
Enzyme: Search for phosphopeptides identified using a specific protease. Be aware of inclusive and exclusive sets generating the same or no data when using these options. Currently only tryptic phosphopeptide information are available.
Instrument: Search for phosphopeptides identified using a specific type of mass spectrometer. Be aware of inclusive and exclusive sets generating the same or no data when using these options.
Mass: Mass or molecular weight being the sum of the atomic masses relative to carbon 12.00000.
Mascot Score: Sort your results using the score (Mascot). Roughly, for high mass accuracy instruments, scores above 24 indicate a true hit with p<0.05, but lower scoring peptides may have been validated manually. Be aware that some data does not use this scoring method.
No. oxM: Group a result by peptides with a specific number of oxidised methionines.
No. pSTY: Group a result by the number of phosphorylated STY experimentally found in each given peptide.
Peptide: Search with a peptide sequence to find a phosphopeptide. No match will occur if the query sequence is outside peptide sequence in database e.g. NRTIDVLLYVDR will not match TIDVLLYVDR.
Peptide w. mod: The modified peptide sequence annotated using the modification nomenclature outlined in the Publication Guidelines of Molecular & Cellular Proteomics. Location of the phosphorylation site clearly derived from the mass spectrum is indicated with a lowercase p and is contained in brackets e.g. (pS). Ambiguous location of pSTY sites are presented as lower case characters and each potential candidate (not necessarily all STY residues) is contained in a set of brackets e.g. (s)(s). In these cases, the peptide sequence and the number of phosphorylation sites in the peptide could be derived from the mass spectrum, but not the precise location within the sequence. If no statement can be made on the location of the phosphorylation site, the modified tryptic peptide sequence is displayed with the remark 'site not determined'.
Following this convention, any oxidized Met residues that have been clamed by the matching process are annotated as (oxM). For cystein residues a * indicates carbamidomethylation.
PhosPhAt redundant: Other entries (listed as AGI codes) in the experimental dataset that also matched this phosphopeptide. This is not an exhaustive list of all instances of this peptide in the Arabiodpsis proteome. The database relies on the initial experimenter to undertake rigorous MS/MS matching and therefore in instances where not all redundancies (AGI codes) for a specific peptide are listed, it is assumed that there was a strong reason to make this limited call e.g. other peptides (not necessarily phosphopeptides) from the sample also matching the protein which produced the phosphopepide.
ppm: Sort a result by ppm mass accuracy of the identified peptide. The percent accuracy (difference between the precursor mass (expt) and precursor mass (calc)) expressed as parts per million (ppm) e.g. a 100 ppm error for peptide of 1000 Da is 0.1 Da.
Precursor Mass of the ion (phosphopeptide) measured by the mass spectrometer, expressed as mass / charge (m/z).
PTM Score: Sort a result by PTM score as derived from validation of the position of each phosphorylation site within the peptide sequence (MSQuant). A score above 30 indicates a 'good hit'. Be aware that some data does not use this scoring method.
PubMed PubMed identification code provides a link to PubMed entries at NCBI. Associated with published data.
Species: Currently only data from Arabidopsis is available. In the future, data from other plant species may be incorporated.
TAIR: The Arabidopsis Information Resource official proteome annotation releases. Currently TAIR10.
TAIR Description: Search by description according to Arabidopsis Information Resource official genome annotation release 8 (non-Boolean).
Tissue: Limit a query for phosphopeptides identified from a specific tissue. Be aware of inclusive and exclusive sets generating the same or no data when using these options.
Treatment: Search for phosphopetides identified from a specific treatment or stress. Be aware of inclusive and exclusive sets generating the same or no data when using these options.
Xcorr: Limit search using an Xcorr score (SEQUEST) cut-off. A score above 2 indicates a 'good hit'. Be aware that most data does not use this scoring method and therefore will not be retrieved with this option.