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.