Software:Prequips

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	[[Image:Prequips_icon.png|thumb|Prequips logo.]]		[[Image:Prequips_icon.png|thumb|Prequips logo.]]
-	Prequips is an application for integration and exploration of proteomics mass spectrometry data. It handles both MS level 1 and MS level 2 data. The [[Prequips:FAQ|FAQ]] might answer many of your questions.
-	'''The [[Software:Prequips:Inclusion List Builder| Inclusion List Builder]] extension for Prequips facilitates directed LC-MS/MS analyses.'''	+	Prequips is a software environment for integration, visualization and analysis of LC-MS/MS data.
		+	*Integration*: The software is capable of integrating mass spectrometry data at the raw data, peptide and protein level. Furthermore, this data can be linked to other data types such as microarray data or sequence information. Currently data can be read from mzXML, pepXML, Bioworks (tabular), and protXML files.
-	== Key Features ==	+	*Visualization*: Prequips includes tabular data viewers as well as spectrum and chromatogram plots. It also provides an overview of the data as a 2-D gel-like image, which is a essential tool for quality control. All visualizations are interactive and linked to each other, making visual data exploration straightforward.
-	* Interactive, graphical user interface.	+	*Analysis*: Through implementation of the Gaggle interface [http://gaggle.systemsbiology.net] mass spectrometry data can be exchanged with programs such as Cytoscape, TIGR MeV, R and Firefox. This enables analysis and interactive exploration of large heterogeneous data sets without manual data conversion.
-	* Reads mzXML, pepXML and protXML (if corresponding plug-ins are installed).	+
-	* Interacts with other applications such as Cytoscape through the Gaggle.	+
-	Note that "feature" in Eclipse slang refers to a set of plug-ins that implement a certain functionality of the software.	+	Prequips is written in Java and based on the Eclipse Rich Client platform. It runs on all operating systems supporting Java 1.5 or later.
-	== Using Prequips ==	+	'''The [[Software:Prequips:Inclusion List Builder| Inclusion List Builder]] extension for Prequips facilitates directed LC-MS/MS analyses.'''
-		+
-	Go to \\isb-2\public\ngehlenb and select the *.zip file with the highest release number. Consult the [[Prequips:FAQ|FAQ]] to find out how to use individual features. A manual doesn't exist at the moment.	+
-		+
-	== Developing Prequips ==	+
-		+
-	To modify the Prequips core application or to develop Prequips extensions an Eclipse installation is required. Refer to the notes on [[Prequips:Eclipse_Setup|how to setup Eclipse]] to find out which Eclipse features are required and on how to check out Prequips from the Subversion repository.	+
-		+
-	== Updating a Prequips Installation ==	+
-		+
-	Prequips uses the same update mechanisms as the Eclipse RCP that it is based on. To search for new extensions to the software go to '''Help > Search for Extensions'''. This will automatically contact the local update site (not accessible from outside the Institute for Systems Biology) and search for features that can be used with your version of Prequips.	+
-		+
-	== Screenshot Gallery ==	+
-		+
-	<gallery>	+
-	image:Prequips027.png|An older screenshot showing several profile and map viewers.	+
-	</gallery>	+
	== More ==		== More ==

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Revision as of 22:37, 23 October 2008

Prequips is a software environment for integration, visualization and analysis of LC-MS/MS data.

• Integration*: The software is capable of integrating mass spectrometry data at the raw data, peptide and protein level. Furthermore, this data can be linked to other data types such as microarray data or sequence information. Currently data can be read from mzXML, pepXML, Bioworks (tabular), and protXML files.

• Visualization*: Prequips includes tabular data viewers as well as spectrum and chromatogram plots. It also provides an overview of the data as a 2-D gel-like image, which is a essential tool for quality control. All visualizations are interactive and linked to each other, making visual data exploration straightforward.

• Analysis*: Through implementation of the Gaggle interface [1] mass spectrometry data can be exchanged with programs such as Cytoscape, TIGR MeV, R and Firefox. This enables analysis and interactive exploration of large heterogeneous data sets without manual data conversion.

Prequips is written in Java and based on the Eclipse Rich Client platform. It runs on all operating systems supporting Java 1.5 or later.

The Inclusion List Builder extension for Prequips facilitates directed LC-MS/MS analyses.

More

1. FAQ is the recommened source of information for users.
2. Bugs is where you can post your bug reports.
3. Wishlist is self-explanatory.