GlycoWorkbench: Semi-Automatic Interpretation and Annotation of Mass Spectra of Glycans

Introduction

GlycoWorkbench is a suite of software tools designed for rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data. The graphical interface of GlycoWorkbench provides an environment in which structure models can be rapidly assembled, their mass computed, their fragments automatically matched with MSⁿ data and the results compared to assess the best candidate. GlycoWorkbench can greatly reduce the time needed for the interpretation and annotation of mass spectra of glycans.

Contact:  info@glycoworkbench.org

Download (requires Java™ version 6 or greater)

Latest 2.1 series (build 140 released on 10/05/2012)

 Windows  Mac OS X  Linux

For more information on alternative packages and possible complications see the instructions below

Launching

• Windows - Click on the desktop icon to launch
• Mac OS X - Extract the zip archive and double click on GlycoWorkbench.jar
• Linux - Run "java -jar eurocarb-glycoworkbench-1.0rc.jar"

How to cite

If you are using GlycoWorkbench or GlycanBuilder for preparing your articles, or if you employed the GlycanBuilder applet in your web interface, please cite:

A.Ceroni, K. Maass, H.Geyer, R.Geyer, A.Dell and S.M.Haslam: GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans Journal of Proteome Research, 7 (4), 1650--1659, 2008 ( PMID: 18311910)

A.Ceroni, A.Dell and S.M.Haslam: The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures Source Code for Biology and Medicine, 2007,2:3 ( PMID: 17683623)

Manual

See the GlycoWorkbench  wiki manual for more information.

Acknowledgements

First we must thank both past and present members of Professor Anne Dell's Biopolymer mass spectrometry group within which the majority of the development of this tool has taken place. We must also give a big thanks to the Glycoconjugate biochemistry group at JLUG and especially to Tobias Lehr, which have provided continuous testing and feedback to GlycoWorkbench and made it possible to reach its current level of functionality.

Thanks go to those projects which have provided free of charge some great Java libraries, sharing the result of their work with all the development community. Many features of this software would not be possible without their effort. We should always remember to support open source and open access policies.

The component for loading raw spectra files has been realized using the fantastic library developed by Jayson Falkner and his colleagues at ProteomeCommons. They are working really hard to extend the support to all available formats in close collaboration with the MS instrumentation vendors. These guys really need all the appraisal and the support from the mass spectrometry community.

The components for displaying graphs have been realized using the JFreeChart library, from the JFree collection of Java free software projects.

The export to SVG, EPS and PDF has been made possible by the Batik toolkit from the Apache XML Graphics Project, part of the Apache Software Foundation for open source software.

The new look of GlycoWorkbench series 2 has been made possible by the Flamingo and Substance libraries created by Kirill Grouchnikov ( http://pushing-pixels.org). All new artwork within GlycoWorkbench series 2 was created by Dr Claire Strain-Damerell using the excellent Inkscape vector graphics drawing tool.

Last but not least we thank the  GlycomeDB Project for hosting the new web presence of GlycoWorkbench?.

Other versions

• 2.0 series (build 96)  Windows  Mac OS X  Linux
• 1.3 series  Windows  Mac OS X  Linux

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Installation Instructions

1. Make sure that your system has version 6 or latter of Java installed
2. Download the correct package for your system
3. To manually launch GlycoWorkbench run "java -jar -Xmx300M eurocarb-glycoworkbench-1.0rc.jar"

More detailed installation instructions can be found  in the manual

Windows

• Windows Installer (recommended)  winsetup_x86 or  winsetup_x86-64
• Windows Archive  zip_archive_x86 or  zip_archive_x86-64

You only require the 64bit version of GlycoWorkbench if your default JRE is a 64bit (x86-64) one.

If you have installed GlycoWorkbench using the provided installation package - you'll find a corresponding entry within your start menu to launch GlycoWorkbench.

If the installer doesn't work for you - download and extract the above ZIP archive to your directory of choice; GlycoWorkbench can be launched with the enclosed executable. Please refer to the included README file, if you are having problems launching GlycoWorkbench.

News: 12/07/2010, some users are still reporting issues launching GlycoWorkbench; it appears to be an issue with some combinations of Java and Windows that are installed. Please email  info@glycoworkbench.org with the following details

• Java version(s) (please list all) - found within Add/Remove programs (or uninstall program on newer versions of Windows)
• Windows Version (if your not sure run the builtin program "winver") - including if it's 64bit or not.

Linux

• Linux Archive  zip_archive_x86 or  zip_archive_x86-64

Download and extract the correct ZIP archive into your directory of choice - run the program by clicking on the provided jar.

Mac OS X

The Mac OS X version of GlycoWorkbench doesn't get as much testing as the Linux and Windows builds. The last version that was known to work can be found  here - that's not to say that the latest version doesn't work. For more information on Mac OS X support please check the  Mac OS X section of the manual

• Cocoa API (64bit) Archive  zip_archive_cocoa_x86-64
• Cocoa API (32bit) Archive  zip_archive_cocoa_32
• Carbon API (32bit) Archive  zip_archive_carbon_32

Run GlycoWorkbench by clicking on the GlycoWorkbench.jar file (you might need to click open afterwards).

Manual

A short GlycoWorkbench_short_manual.1.2.4105.pdf ShortManual can also be downloaded.

ChangeLog

2.1 Stable (Build 139) 09/05/2012

• Fixed blocking behavior of settings dialog box on various flavors of Windows.

2.1 Stable (Build 137) 04/05/2012

• GlycoWorkbench appears to have always read the attribute "is_msms" as "is_msm" which meant that if a user manually changed the MS level it would not be reflected in the interface if the user saved and then re-opened the session.
• Fixed a NullPointerException being thrown when a session is opened which contains imported spectra and then the user attempts to reassign the spectra.

2.1 Stable (Build 134) 03/05/2012

• Fixed an issue that could prevent the report dialog box from being shown.

2.1 Stable (Build 132) 19/04/2012

• Improved peak parsing routine to allow for three column CSV formatted files where the third column can be relative intensity or charge state.

2.1 Stable (Build 131) 11/04/2012

• Before computing peak centroids we now store the current config, destroy the current instance, and reload the config (to get around the same issue we see on GlycoWorkbench first run)

2.1 Stable (Build 128) 04/04/2012

• Fixed bug which stopped the cascade annotation routine from finding matching peaks within an accuracy window
• Changed structure pull threshold from 0.0001 PPM to 2 Da
• Fixed multiple issues resulting in a scans MS level being incorrectly set
• Fixed issues relating to peak picking and cascading annotations
• Ribbon is now minimized by default to free up some vertical space
• Quick access buttons have been added
• Fixed multiple issues with FileChooser dialog boxes not defaulting to the correct FileFilter
• Fixed issues with the linkage and structure tool bars not wrapping correctly (better support for small screens)
• Split spectrum toolbar in two (better support for small screens)
• Wiki help page is manipulated by GlycoWorkbench to remove left and top tool bar areas

2.1 Stable (Build 110) 31/10/2011

• Updated Windows executables so that they are compatible with JRE 7
• Minor updates to the handling of WGGDS resources
• Delayed start-up of Profiler plugin for faster startup
• Updated manual (in the previous version the new URL wasn't deployed correctly)
• Slight change to the work flow of a cascade annotation

2.1 Stable (Build 105) 09/09/2011

• Added isotope specification support for all molecules
• Added heavy permethylation as a derivatization
• Added amine substituent
• De-selecting "Show reducing end" now works for all reducing ends
• Added ability to copy in silco generated fragment m/z values to peak list (for testing purposes)
• Annotation system can now try (if asked) all possible ion combinations (i.e. glycan structure is 2Na, annotator will try all 2Na and 1Na fragments)
• Added ability to customize core types gallery
• Added ability to customize terminal types gallery
• Added ability to add custom Residues
• Added ability to create custom substituents
• Added ability to create custom reducing ends
• Added ability to create custom modifications
• Added ability to store definition files (Residues, etc.) on a remote server
• Added ability to customize all symbolic notations (including adding new residues)
• Added ability to customize Residue fragmentation
• Redirected help system to new version 2.1 manual (although not finished quite yet)
• Added ability to customize builtin structure dictionaries
• Completed support for WGGDS web service databases

2.0 Stable (Build 96) 19/08/2011

• Changes to profiler database search options
• Removed sequences from dictionaries with nested repeats
• Structures on the glycan canvas with repeating units can now be copied and pasted
• m/z is calculated for structures with repeating units of specified size (i.e. min and max are equal)
• Support for WGGDS substructure queries (disabled for now)

2.0 Stable (Build 93) 03/08/2011

• Fixed bug which caused GWB to throw an exception on startup when the remembered ion count for H2PO4 >0

2.0 Stable (Build 91) 28/07/2011

• Added support for Cl- and H2PO4-

2.0 Stable (Build 90) 27/07/2011

• Added ability to add all peaks from a peak list to a report
• Added checkbox to clear existing annotations before carrying out an annotation run
• Updated DJNativeSwing and SWT libraries to latest version - (required to allow the GWB help system to work with newer web browsers)
• Added missing avalon library - which was preventing PDF export

2.0 Alpha 2 (Build 83) 20/12/2010

• Fixed broken Glyco-Peakfinder plugin
• Fixed potential issues with the update link
• Fixed possible exception being thrown on startup

2.0 Alpha 2 (Build 66) 22/10/2010

• Individual panels can now be detached
• Notification when a new version has been released
• Simplification of application menu
• Fixed broken linkage bar
• Restored the majority of keyboard short cuts
• Improved open button behaviour
• Updated icons and other LAF issues

2.0 Alpha 2 (Build 48) 07/09/2010

• Permanent display of linkage and recent residue bar.
• Option to not save loaded spectra in GWP file.
• Clicking the save button in application bar, saves the GWS by default.
• LAF updates: Default theme now Office Blue, themes shown by unqualified name, icon loading change for faster startup.
• Changed location of Manual to wiki.glycoworkbench.org
• Improved error handling.
• Fixed missing AppData? directory on none English versions of Windows.

2.0 Alpha 2 (Build 42) 26/07/2010

• Fixed peak editor delete bug
• Altered glycan contextual ribbon activation behaviour
• UI speed ups

2.0 Alpha 2 (Build 35) 13/07/2010

• Restored about menu .
• Fixed Mac OS X specific issues.

2.0 Alpha 2 (Build 25) 12/07/2010

• Added missing JNA library (Unix users affected)
• Changed resize policy of a RibbonTask? for compatibility with Mac OS X and Linux users.

2.0 Alpha 2 (Build 15) 07/07/2010

#New Features

• S3 support (suitability for use within GWB is being prototyped, might still be removed)
• Automatic building of all packages and subsequent publication.

#Changes

• Refactored the residue contextual ribbon tasks [id: 2]
• Three packages are now created for Mac OS X (Carbon 32bit, Cocoa 32bit and Cocoa 64bit). [id:11]
• Both 32 and 64bit packages are generated for Linux.
• Switched Windows launcher to WinRun4J
• New Startup script for Mac OS X (possibly to be replaced by a complete DMG)

#FIXED

• Restored peak list paste support [id:6]
• Fixed broken Buker peak list import [id:7]
• Fixed exception being thrown when empty peak is deleted [id:12]
• Fixed two UI jitter bugs [id: 16 and 17]
• Tooltip support refactored via RichTooltip [id: 3]
• Accelerator key support refactored via RichTooltip [id: 4]
• Fixed some dialog boxes being too small [id: 8]
• Converted all remaining GIF icons to PNGs [id:15]
• Fixed high CPU load when displaying the fragment editor [id: 18]
• Icons are now shown for terminals with unknown linkage [id: 5]
• Fixed insert residue gallery being shown within the structure ribbon rather than the add residue gallery. (Prevented structures from being drawn from scratch). [id: 19]

Version 2.0 alpha 09/06/2010 (missing 64bit Windows Zip)

• Cascade annotation of MS^{n data sets}
• Migration to Office style ribbon interface
• Additional icons
• Ribbon support for plugins
• New splash screen and logo
• Implementation of Mediawiki help system.
• Help system, detection of internet connection.
• Bug fixes for peak list editor (introduced in version 1.3)
• Fixed broken jar click support (non-functional in version 1.3)

Version 1.3 21/05/2010

• Moved user configuration into home directory
• Initial integration of SWT browser (for future EurocarbDB integration)
• Updated help system. (will be heavily revised in next revision)
• Minor bug fixes.
• Splash screen for Linux and Mac OS X users
• Added charge field to Peak list panel

Version 1.1

Build 3480 - 22/09/2008

• GAG profiling tool
• in-silico fragmentation of sulfated glycans
• graphic display of the peak list, similar to the spectra panel
• residue properties toolbar
• copy tables in spreadsheets with structures as compositions
• search databases by sub-structure
• close dialogs by pressing Escape
• select OK in dialogs by pressing Enter
• added executable, icons and splashscreen for Windows users
• fixed export to SVG

see all changes

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