Gator
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The MASCP Gator v1.1
Proteomics has become a critical tool in the functional understanding of plant processes at the molecular level. Proteomics-based studies have contributed to the ever expanding array of data in modern biology, with many generating web portals and online resources. Many of these resources reflect specialist research areas with significant and novel information that is not currently captured by centralized repositories. Consequently the MASCP Proteomics Subcommittee have developed a proteomics aggregation utility called the MASCP Gator, that queries information from a variety of online proteomics resources.
- NEWS September 2011
We have now incorporated the Arabidopsis Gelmap database and will include parameters regarding experimental pI and MWt into the MASCP Gator. We have also added the Arabidopsis P3DB phosphorylation database as a track to the MASCP Gator which provides experimentally determined ortrhologous phosphorylation sites mapped to Arabidopsis proteins. This enables the identification of previously uncharacterized phosphorylation sites (MS incompatible) in Arabidopsis
MASCP Gator Interface
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The Arabidopsis Proteomics Aggregator MASCP Gator |
The interface and data delivery have been designed to be visually intuitive with the utility providing a proteomics overview of an AGI with little input from the user:
Using the MASCP Gator
1. To view proteomics data for a given Arabidopsis protein, simply type or paste the AGI into the query window at the top of the page and use return on the keyboard or the retrieve button on the web page. A protein description from TAIR will also be displayed for the AGI.
2. Data will now be downloaded from the various data sources. To check whether communication with data sources was successful, the page footer indicates a green ball (success) or red ball (failure). Simply refresh or reload to re-establish communications with any data sources that have produced communication errors (red ball). If still unsuccessful, it is likely that the resource is down. This panel also provides links to the relevant databases.
3. A schematic of the protein (scale bar) with identified peptides represented as tracks beneath the protein will now be updated with newly acquired data. Sites of post translational modification are displayed as symbols e.g. P for phosphorylation. By default, a hydropathy plot is the last track displayed. The control panel (dark box) on the left provides advanced control functions.
4. To obtain sequence context for the arrayed MS/MS derived peptides, a zoom function can be employed by the mouse wheel (while hovering the cursor over tracks) or by using the plus (+) or minus (-) button on the control panel. The display can be panned left and right by mouse left click and holding while moving the mouse left or right. The original display can be obtained by using the Reset button on the control panel.
5. The discrete number of peptides, source of data (e.g. organ, experiment), sequence context and identification of overlapping peptides sequences can be obtained by toggling the triangle button next to the specific data source (database) on the control panel. Links back to an AGI entry or an MS/MS data entry for each data source is available through the computer screen symbol (square) in the control panel next to each track.
6. Post translational modification context on both the protein sequence and peptides is also obtained through the zoom and toggle features.
7. Manipulation of tracks is available through the options button on the control panel which displays an options box where tracks can be toggled on and off as well as re-arranged by grabbing and moving with a mouse.
8. Subcellular localization information is obtained from the SUBA database and is displayed as a tag-cloud. For this type of display, the larger the font the more evidence for this localization is available. A GREEN colored font indicates subcellular evidence by a fluorescent protein tag, a RED colored font indicates subcellular information by proteomics and a GRAY colored font indicates predicted subcellular localization. Hovering the cursor over a location will display a number which corresponds to the times identified at this subcellular location.
9. Evidence for the presence of a protein in a specific plant organ represents aggregated data from AtProteome, AtPeptide and PhosPhAt. This information is also displayed as a tag-cloud where the size of the font indicates the number of times a peptide or AGI was identified in that organ type. Hovering the cursor over a specific organ description will display the actual number of times the peptide / AGI was identified in this organ.
Advanced Search (Multiple AGI)
Data for multiple AGIs can be obtained through the advanced search feature. Results from this component also provide the raw underlying data that is used to create the single AGI overview page.
1. Simply paste a list of AGIs in the window and click 'Update' to retrieve data.
2. Data is loaded sequentially for each AGI from each data source. If all data loaded and the communication was successful a green square appears beside the AGI. If an error occurs, an orange marker will appear with the short name of the database that caused a problem. Simply reload or refresh the page to correct any communication issues. Data can be downloaded in a comma delimited format by using the 'Save' button.
3. The list of AGIs can be edited or modified by clicking the 'Edit' button to re-enable the entry pane.
4. Explanation of column headings:
- Phosphorylation: Residue with experimentally determined phosphorylation site e.g. 210 indicates residue phosphorylated.
- Phosphomodulation: Experimentally determined phosphorylation site / peptide with other MS/MS data suggesting a non-modified residue also exists e.g. 122-135:124 indicates an unmodified peptide in the region 122-135 which overlaps to a phosphorylated residue at 124.
- MS Localization: The 'winner takes all' subcellular location derived from proteomic studies. Multiple locations are possible e.g. 2 studies identify the AGI in the mitochondria and 2 separate studies identify the AGI in the plastid (mitochondrion,plastid)
- FP Localization: The 'winner takes all' subcellular localization from fluorescent protein studies. Multiple locations are possible e.g. a study localizes the AGI in the peroxisome and another studies localizes the AGI in the cytosol (peroxisome,cytosol).
- Organ Spectral Count: The raw number of spectra identified from different plant organ types. Caution should be used with this information as no analysis has been undertaken on these values. Therefore they should only be used to indicate the presence of an AGI in a organ and not used to compare relative expression unless further validation / analysis are conducted.
MASCP Gator Architecture
Citation
If you find the MASCP Gator useful please cite the following article:
Joshi, H.J., Hirsch-Hoffmann, M., Baerenfaller, K., Gruissem, W., Baginsky, S., Schmidt, R., Schulze, W.X., Sun, Q., van Wijk, K., Egelhofer, V., Wienkoop, S., Weckwerth, W., Bruley, C., Rolland, R., Toyoda, T., Nakagam, H., Jones, A., Briggs, S.P., Castleden, I., Tanz, S., Millar, A.H., and Heazlewood, J.L. (2011). MASCP Gator: An aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiol. 155, 259-270.
Statistics (September 2011) TAIR10
Database |
Number of Proteins |
Unique Proteins |
6,346 |
188 |
|
14,582 |
1,765 |
|
6,172 |
1,049 |
|
1,035 |
2 |
|
16,769 |
3,484 |
|
4,449 |
423 |
|
1,323 |
0 |
|
2,244 |
0 |
|
3,866 |
313 |
|
614 |
7 |
|
|
|
|
|
Total (unique) |
7,231 |
|
Total (shared) |
14,686 |
|
Total (non-redundant) |
21,917 |