Mascp - Recent changes [en]

Gator

2010-08-31T13:50:06Z

MASCP Gator Interface:

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-	<td align=center><p><strong>Due to issues associated with browser non-conformity, we recommend using any of the following browsers</strong></p></td>	+	<td align=center><p><strong>Due to issues associated with browser non-conformity, we recommend using any of the following browsers to obtain correct rendering</strong></p></td>
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-	'''The interface and data delivery have been designed to be as intuitive ~~as possible for~~ the ~~end~~ user:'''	+	''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:''

Databases

2010-08-30T20:11:42Z

Post-Translational Modification:

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	AtProteome assembles proteomic data of about 13.000 proteins and provides information about identified proteotypic peptides, abundances and tissue and organelle-specific appearance.		AtProteome assembles proteomic data of about 13.000 proteins and provides information about identified proteotypic peptides, abundances and tissue and organelle-specific appearance.

-	'''[http://~~www~~.~~promexdb~~.~~org~~/ ProMEX]'''	+	'''[http://promex.pph.univie.ac.at/promex/ ProMEX]'''

	ProMEX is a mass spectral library, consisting of tryptic peptide product ion spectra  from protein samples of ''Arabidopsis thaliana'', ''Medicago truncatula'', ''Chlamydomonas reinhardtii'', Tomato and Potato. The database serves as a reference and can be used for protein identification in uncharacterized samples. Protein identification by ProMEX is linked to other molecular levels of biological organization such as [http://csbdb.mpimp.golm.mpg.de/csbdb/gmd/gmd.html metabolite], [http://www.genome.jp/kegg/pathway.html pathway] and [http://csbdb.mpimp-golm.mpg.de/csbdb/dbxp/ath/ath_xpmgq.html transcript] data. The database is further connected to annotation and classification services via [http://www.biomoby.org/ BioMoby]. ProMEX allows also text searches based on AGI code, metadata such as experimental information of the samples, and mass spectrometric instrument parameters.		ProMEX is a mass spectral library, consisting of tryptic peptide product ion spectra  from protein samples of ''Arabidopsis thaliana'', ''Medicago truncatula'', ''Chlamydomonas reinhardtii'', Tomato and Potato. The database serves as a reference and can be used for protein identification in uncharacterized samples. Protein identification by ProMEX is linked to other molecular levels of biological organization such as [http://csbdb.mpimp.golm.mpg.de/csbdb/gmd/gmd.html metabolite], [http://www.genome.jp/kegg/pathway.html pathway] and [http://csbdb.mpimp-golm.mpg.de/csbdb/dbxp/ath/ath_xpmgq.html transcript] data. The database is further connected to annotation and classification services via [http://www.biomoby.org/ BioMoby]. ProMEX allows also text searches based on AGI code, metadata such as experimental information of the samples, and mass spectrometric instrument parameters.
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	While the PPDB database has its main focus on chloroplasts (see above), recent analysis of leaf samples have produced a significant collection of mapped PTMs including deamidation, hydroxylation, propionylation, formylation, amino acid substitutions and acetylation.		While the PPDB database has its main focus on chloroplasts (see above), recent analysis of leaf samples have produced a significant collection of mapped PTMs including deamidation, hydroxylation, propionylation, formylation, amino acid substitutions and acetylation.

-	'''[http://phosphoproteome.psc.database.riken.jp/ Plant Phosphoproteome Database]'''	+	'''[http://phosphoproteome.psc.database.riken.jp/ Plant Phosphoproteome Database (RIPP-DB)]'''

	The Plant Phosphoproteome Database provides information on phosphopeptides which were identified from Arabidopsis and rice cells by LC-MS/MS-based shotgun phosphoproteomics approach.		The Plant Phosphoproteome Database provides information on phosphopeptides which were identified from Arabidopsis and rice cells by LC-MS/MS-based shotgun phosphoproteomics approach.

Gator

2010-08-30T19:13:08Z

Statistics (June 2010):

←Older revision		Revision as of 19:13, 30 August 2010
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	== '''The MASCP Gator V1.0 Release Edition''' ==		== '''The MASCP Gator V1.0 Release Edition''' ==

-	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 pulls information on-the-fly from a variety of proteomics resources.	+	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 [http://www.masc-proteomics.org/ MASCP Proteomics Subcommittee] have developed a proteomics aggregation utility called the [http://gator.masc-proteomics.org/ MASCP Gator], that pulls information on-the-fly from a variety of proteomics resources.

	== MASCP Gator Interface ==		== MASCP Gator Interface ==
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	<td align=center><p><strong>[http://www.mozilla.com/ Firefox], [http://www.google.com/chrome Google Chrome], [http://www.google.com/chromeframe Google Chrome frame] or [http://www.apple.com/safari/ Safari].</strong></p></td>		<td align=center><p><strong>[http://www.mozilla.com/ Firefox], [http://www.google.com/chrome Google Chrome], [http://www.google.com/chromeframe Google Chrome frame] or [http://www.apple.com/safari/ Safari].</strong></p></td>
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		+	<td align=center><p><strong></strong></p></td>
		+	</tr>
		+	<tr>
		+	<td align=center><p><strong>The Arabidopsis Proteomics Aggregator [http://gator.masc-proteomics.org/ MASCP Gator]</strong></p></td>
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-	<td width="150"><p>SUBA</p></td>	+	<td width="150"><p>[http://suba.plantenergy.uwa.edu.au/ SUBA]</p></td>
	<td width="150"><p align="center">4,685</p></td>		<td width="150"><p align="center">4,685</p></td>
-	<td width="150"><p align="center">~~138~~</p></td>	+	<td width="150"><p align="center">134</p></td>
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-	<td width="150"><p>AtProteome</p></td>	+	<td width="150"><p>[http://fgcz-atproteome.unizh.ch/ AtProteome]</p></td>
	<td width="150"><p align="center">13,029</p></td>		<td width="150"><p align="center">13,029</p></td>
-	<td width="150"><p align="center">1,~~679~~</p></td>	+	<td width="150"><p align="center">1,644</p></td>
	</tr>		</tr>
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-	<td width="150"><p>PPDB</p></td>	+	<td width="150"><p>[http://ppdb.tc.cornell.edu/ PPDB]</p></td>
	<td width="150"><p align="center">6,425</p></td>		<td width="150"><p align="center">6,425</p></td>
-	<td width="150"><p align="center">1,~~376~~</p></td>	+	<td width="150"><p align="center">1,369</p></td>
	</tr>		</tr>
	<tr>		<tr>
-	<td width="150"><p>ProMEX</p></td>	+	<td width="150"><p>[http://promex.pph.univie.ac.at/promex/ ProMEX]</p></td>
	<td width="150"><p align="center">~1,000</p></td>		<td width="150"><p align="center">~1,000</p></td>
	<td width="150"><p align="center">ND</p></td>		<td width="150"><p align="center">ND</p></td>
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	<tr>		<tr>
-	<td width="150"><p>AtPeptide</p></td>	+	<td width="150"><p>[http://proteomics.ucsd.edu/Software/ArabidopsisProteogenomics.html AtPeptide]</p></td>
	<td width="150"><p align="center">16,769</p></td>		<td width="150"><p align="center">16,769</p></td>
-	<td width="150"><p align="center">4,~~628~~</p></td>	+	<td width="150"><p align="center">4,536</p></td>
	</tr>		</tr>
	<tr>		<tr>
-	<td width="150"><p>PhosPhAt</p></td>	+	<td width="150"><p>[http://phosphat.mpimp-golm.mpg.de/ PhosPhAt]</p></td>
	<td width="150"><p align="center">4,859</p></td>		<td width="150"><p align="center">4,859</p></td>
-	<td width="150"><p align="center">~~577~~</p></td>	+	<td width="150"><p align="center">521</p></td>
	</tr>		</tr>
	<tr>		<tr>
-	<td width="150"><p>RIPP DB</p></td>	+	<td width="150"><p>[http://phosphoproteome.psc.database.riken.jp/ RIPP-DB]</p></td>
-	<td width="150"><p align="center">ND</p></td>	+	<td width="150"><p align="center">2,244</p></td>
-	<td width="150"><p align="center">ND</p></td>	+	<td width="150"><p align="center">82</p></td>
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-	~~<td width="150"><p>Total (unique)</p></td>~~
	<td width="150"><p align="center"> </p></td>		<td width="150"><p align="center"> </p></td>
-	<td width="150"><p align="center">8,~~398~~</p></td>	+	<td width="150"><p align="center">Total (unique)</p></td>
		+	<td width="150"><p align="center">8,286</p></td>
	</tr>		</tr>
	<tr>		<tr>
-	~~<td width="150"><p>Total (shared)</p></td>~~
	<td width="150"><p align="center"> </p></td>		<td width="150"><p align="center"> </p></td>
-	<td width="150"><p align="center">12,~~930~~</p></td>	+	<td width="150"><p align="center">Total (shared)</p></td>
		+	<td width="150"><p align="center">13,125</p></td>
	</tr>		</tr>
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-	~~<td width="150"><p>Total (non-redundant)</p></td>~~
	<td width="150"><p align="center"> </p></td>		<td width="150"><p align="center"> </p></td>
-	<td width="150"><p align="center">21,~~328~~</p></td>	+	<td width="150"><p align="center">Total (non-redundant)</p></td>
		+	<td width="150"><p align="center">21,411</p></td>
	</tr>		</tr>
	</table>		</table>