mMass - Open Source MS Tool

Mar 03, 2010 - Version 3.1 released - Comments 0

New version of mMass is now available for download. Beside some minor bug fixes, there are many important new features:

• In addition to Mascot search tools a new interface for the excelent ProFound tool is now available for protein identifications. I would like to express my thanks to David Fenyo for his support.
• Thanks to Eoin Fahy from the excelent LipidMaps.org server we now have a permission to put their lipid database into mMass. You can use the Compounds Search tool to search for thousands of lipids and their corresponding adducts. In addition, if you annotate your matched peaks and make an Analysis Report, each lipid ID provides a direct link to LipidMaps.org to see the structure and other information.
• Protein or peptide sequences can now be imported from any mMass document (include modifications) or FASTA format. If you are using some sequences quite often it can be very handy to put all of them into a single mMass document and create your personal sequence library. You can then skip over the boring sequence editing, just import the sequence you like and all of its modifications as well.
• If you are using manual peak labeling (Label Peak tool) every labeled peak can now be set as monoisotopic automatically. In the spectrum Tools Properties (bottom toolbar) check "Set as monoisotopic" checkbox.
• Spectrum tools can now be selected via the main menu (Tools) or using a shortcut. In addition, new mouse cursors reflects currently selected tool.
• If you are opening multiple scans from a huge LC-MS file repeatedly, corresponding scan list is retained in a memory to speed-up the loading process.
• The peak-picking algorithm has been improved to correctly resolve adjacent peaks in high-resolution data.
• There has been some bugs in the Mascot Sequence Query tool which are now fixed.
• Some of the functions in mMass core library has been changed to be more "Pythonic".

Enjoy this new version and let me know your comments.

Feb 01, 2010 - mMass 3.0 - Comments 0

New version of mMass is finally available. I've put a lot of energy into making this program as stable and reliable as possible but you know... Please feel free to send me your comments or suggestions for further development. I hope you find the new mMass useful for your own work. Have fun...

• Read the mMass User's Guide!
• It is not really necessary, however, due to the small changes in colors definitions I'd recommend to use the new configuration files if you are updating from any testing version ("mMass/configs" folder under MS Windows and Linux and "~/Library/Application Support/mMass/"folder under MacOS X).
• If you are updating from the version 2.4 or any older, please remove the old version completely.

Jan 21, 2010 - Version 3.0 RC2 released

Unfortunately, the bug in the sequence modifications as mentioned recently, were not fixed correctly. Therefore a new version is now available.

Jan 19, 2010 - Version 3.0 RC released

Release Candidate version of mMass is now available for download and testing. I hope it will be the last testing version and final mMass 3.0 will be available soon. One of the major update is mMass User's Guide describing all the mMass's features. Other changes are as follows:

• bug fix: if a fixed modification was applied to amino acid type rather than to exact position, this modification was calculated only once, even if more amino acids of that type were presented
• bug fix: selecting "Show specific modifications only" with no amino acid selected caused application crash
• bug fix: "treshold" renamed to "threshold" in all configs files (an automatic update is temporarily incorporated, so you don't have to edit anything)
• bug fix: escaping illegal characters in all config files
• bug fix: calculation of isotopic pattern from formula containing specific isotope caused application crash
• improved: removed "peak width" parameter from peak picking algorithm
• improved: additional keyboard shortcuts
• other minor fixes and improvements

Jan 19, 2010 - RSS feed available - Comments 0

The RSS feed is finally available for mMass.org so you can watch for changes by Google reader etc.

Jan 19, 2010 - Comments are back

You can comment mMass's news again.

Jan 18, 2010 - A bug found in the sequence modifications

Please note that there is a bug (known from today): if fixed modification is applied to amino acid type rather than to exact position, this modification is calculated only once, even if more amino acids of that type are presented in a sequence. This is already fixed in the upcoming version. The new version will be available later this week. I really apologize for the inconvenience.

Jan 04, 2010 - mMass failed to start on some Windows computers - Comments 0

On some windows computers you can expect following error: This application has failed to start because the application configuration is incorrect. If so, please download and install runtime components of Visual C++ Libraries from Microsoft's website.

Dec 14, 2009 - Version 3.0 beta 1 released

New testing version of mMass 3.0 has been released. Read „readme.txt“ before you use mMass. If you are running mMass from the source code, please note that there is a C part which needs to be compiled first. Feel free to send me any comments, requests, bug reports etc.

• changed: processing methods moved to configs/presets.xml file together with operator presets
• changed: mascot servers definitions moved to configs/mascot.xml file
• changed: (OS X only) in order to retain user configurations after updating mMass all the configuration files are now located in ~/Library/Application Support/mMass/
• new feature: operator presets in Document Info Panel
• new feature: direct recalibration using data from Match Panel
• new feature: search for specified formula in Compound Search Tool
• improved: active sorting in report tables
• improved: relative intensity for annotations and matches in report
• improved: MeOH and ACN adducts in Compound Search Tool
• improved: Mascot Search form shows number of selected modifications
• improved: Match Panel behavior
• bug fix: fixed links to mMass webpage
• bug fix: mascot modifications were not loaded from config
• bug fix: fragments types were not loaded from config
• bug fix: sequence editing is now disabled if no document is selected
• bug fix: validated code of HTML report

Dec 03, 2009 - MS Tools

Nice set of tools for H/D exchange experiments has been published on our laboratory webpage.

• H/D Exchange Calculator - Calculates number of exchangeable hydrogens, monoisotopic and average masses and displays a simple peptide statistics.
• H/D Experiment Planner - Creates a time schedule for H/D exchange experiments.
• Draw Map - Creates a graphical representation of protein sequence coverage.
• Draw H/D Heat Map - Draws graphical representation of H/D exchange using color gradients.
• Draw H/D Protection Plot - Creates a protection plot based on data from H/D exchange and allows comparison of various conditions.
• JMol Scripter - Visualization of H/D data on protein structure using JMol.