About PRIDE Inspector

The key features include:

• Fast loading of mzML and PRIDE XML files.
• Search, access and download all PRIDE public database experiments. New
• Different views on spectra, chromatogram, protein, peptides and metadata.
• Visualize quantification data for both protein and peptide identifications. New
• Experiment summary on key measurements of experiment quality. New
• Download additional protein details, such as: protein name, sequence. New
• Visualize protein sequences and their peptide/PTM coverage. New
• Decoy filter on both protein and peptide identifications. New
• Visualization for all spectra and chromatograms, including automatic MS2 fragment ion annotations.
• Possibility to perform a quality assessment of the data using a statistical view with different charts.
• User-friendly download facility for private PRIDE experiments.

The data formats supported by PRIDE Inspector are:

• mzML 1.1
• PRIDE XML 2.1

Note: We do have plans to support additional formats like mzIdentML in the near future.

PRIDE Inspector Publication

When you use PRIDE Inspector, please cite the following publication:

• Wang et al., Nat Biotechnol 2012; 30:130-132. PDF File. PubMed record.

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Getting PRIDE Inspector

Installation Requirements

• Java: Java JRE 1.6(or above), which you can download for free here. (Note: most computers should have Java installed already).
• Operating System: The current verion has been tested on Windows 7, Windows Vista, Linux and Max OS X, it should also work on other platforms. If you come across any problems on your platform, please contact the PRIDE Help Desk.
• Memory: MS dataset can be very large sometimes, in order to get good performence from PRIDE Inspector, we recommend you to have 1G of free memory.

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Launch via Webstart

Click here to launch directly the latest PRIDE Inspector.

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Download

You can get the latest PRIDE Inspector from our Download Section, and download pride-inspector-X.Y.zip (where X and Y represent the version of the software). Unzipping the file, creates the following directory structure:

  pride-inspector-X.Y
     pride-inspector-X.Y.jar
     log
     lib
     examples
     config

To start the software, simply double-click the file named pride-inspector-X.Y.jar. If this fails, try to download and install Java 1.5 or above, as explained in the previous section. (The program can also be started from the command line using the following command: java -jar pride-inspector-X.Y.jar.)

The zip file contains also an examples folder with 2 sample files: one in mzML format (mzml-example.mzML) and the other in PRIDE xml format (pride-example.xml) so you can upload them in pride inspector and try the application. There is and additional folder, config, that contains a file called config.props where you can modify the amount of memory assigned to your application (only change if you are trying to view files and is causing the software crash because of a "Out of memory..." exception). The additional 2 directories, lib and log, contain all the java libraries necessary for the application to run and some debugging information if the application crashes.

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Disclaimer

1. Disclaimer on shared peptides problem

Please be aware that usually only one of the possible peptide to protein mappings are kept in PRIDE. In shotgun proteomics experiments, protein inference needs to be taken into account when interpreting protein identifications reported that are based on non-ambiguous (or shared) peptides.

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FAQs

1. What to do if PRIDE Inspector runs out of memory?

Although PRIDE Inspector is design to handle large datasets with small memory footprint, it can still run out of memory if many files or public experiments are opened at the same time. If you have seen such a warning message in a popup window, you should try to increase the memory allocation for the program.This can be done by editing the config.props file, this file is located in the config folder of the installation directory. In the file, change the pride.inspector.max.memory=1024 to a higher number, for instance, pride.inspector.max.memory=2048 will give PRIDE Inspector 2G of memory. Please note that you will need to restart PRIDE Inspector in order for the change to take effect. It is also important to know that on a 32-bit operating system you can not increase this value beyond 2000.

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Getting Help

If you have questions or need additional help, please contact the PRIDE Helpdesk at the EBI: pride-support at ebi.ac.uk (replace at with @). To help us better identify the problem, you can also include a (preferably zipped) copy of the pride-inspector.log from the log folder.

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Source Code

You can browse the source code here: Browse code repository

Alternatively, non-members may check out a read-only working copy anonymously over HTTP:

svn checkout http://pride-toolsuite.googlecode.com/svn/pride-inspector/trunk pride-inspector-read-only

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Screenshots

(Click on a screenshot to see the full size version)

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