mMass - Open Source MS Tool

Jul 19, 2010 - mMass 3.7 released - Comments 0

Version 3.7 of mMass software has been released with additional new features and important bug fixes.

• New: Simplified interface for Protein Prospector tools MS-Fit and MS-Tag. (Since I did not received any response from original developers, current implementation is rather experimental.)
• New: FWHM and resolution are now calculated for each peak and are shown in Peaklist Panel.
• New: Global sequence modifications can now be stored as presets.
• New: Spectrum polarity can now be set in Document Info panel.
• Fixed: Application crashed when "None" document was sent into Calibration Panel.
• Fixed: Some of the potential peaks were skipped in Shoulder Peaks Removal algorithm.
• Fixed: Data matching for negative spectra was not possible with Ignore charge option unchecked.

Jul 05, 2010 - mMass 3.6 released

Version 3.6 of mMass software has been released with additional new features and important bug fixes.

• New: Match Summary is now available for each data matching.
• New: Remove shoulder peaks option is now available for FTMS data peak-picking. Since I have only some data from our FTICR instrument, please let me know if you would have any problem with this feature on your FTMS data.
• New: All annotations and sequence matches can now be removed at once, using context menu in Documents Panel.
• New: Compounds and calibration masses can now be imported using corresponding library editor and can be shared easily. See User's Guide for more info.
• Improved: Faster peak-picking, especially when Adaptive threshold option is used.
• Improved: Spectrum flipping is now accessible from the View menu.
• Improved: Updated lipids library.
• Fixed: Loading of some mzXML files with parameter "compressionType=none" was not possible.
• Fixed: Application crashed on a single right-click in Isotopic pattern panel.

Jun 04, 2010 - mMass 3.5 released

One of the most requested feature in the recent ASMS conference was possibility to flip spectra to enable more efficient comparison. Check this new feature in mMass 3.5, released today.

• New: Possibility to vertically flip spectra in Spectrum Viewer. (Right-click on the document in Document Panel and choose "Flip Spectrum".
• New: -H2O can now be searched in Compounds Search tool.
• Fixed: Normalized view did not worked for non-profile spectra.

May 31, 2010 - Thanks for visiting mMass poster at ASMS

I just want to thank all those mMass users who visited my poster at ASMS. It was very nice to speak with you and couple of new ideas raised up for future versions of mMass. The poster PDF is available for download (3MB).

May 23, 2010 - mMass at 58th ASMS Conference, Salt Lake City, Utah

mMass will be presented at the 58th ASMS Conference in Salt Lake City, Utah. I would be very pleased to see you, answer your questions and talk about your feature requests.

mMass reloaded - advances in the popular cross-platform software for precise analysis of mass spectrometric data - Session: WP01, Bioinformatics III, Slot/Poster Number: 023, Wednesday, Poster Hall

May 17, 2010 - mMass in Analytical Chemistry - Comments 2

I am pleased to inform you that mMass has been accepted for publishing in Analytical Chemistry journal. You can read the article entitled mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data. Thank you, all the mMass users and contributors!

May 17, 2010 - mMass 3.4.0 RPM package for OpenSUSE available

Thanks to Sebastian Gibb the RPM package of mMass 3.4 is available for OpenSUSE Linux.

May 12, 2010 - mMass 3.4 released

Version 3.4 of mMass software has been released with additional new features and important bug fixes.

• Radical ions can now be calculated in Mass Calculator and Compounds Search tools.
• Single-point linear calibration has been enabled.
• Calibration curve is shown in calibration error plot.
• Current peaklist is shown as a background in error plots (calibration, data matching).
• New view option has been added to enable/disable normalized view of all opened documents.
• New view option has been added to enable/disable annotation marks.
• If you select your document root in the documents tree panel, all annotations and matches will be highlighted in the spectrum.
• Theoretical and matched sequence coverage shown in Protein Digest tool.
• Final ion composition is validated in ion series calculations.
• Automatic checking for available updates has been added.
• App preferences for updates and compassXport utility has been added.
• Fixed: Mass Calculator - calculation of ions with negative agent charge.
• Fixed: Mass Calculator - pattern moddeling with complex charging agent.
• Fixed: normalization calculates baseline shift as well.

Apr 30, 2010 - Data Re-Calibration Screencast

New video tutorial has been published, showing you how to re-calibrate your data in mMass. In this video you will learn how to perform the following tasks:

• how to perform external calibration,
• how to perform internal calibration,
• how to use matched peptides for calibration,
• how to use user annotations for calibration.

Apr 15, 2010 - Personal Sequence Database Screencast

New video tutorial has been published, showing you how to create your own personal database of protein or peptide sequences. In this video you will learn how to perform the following tasks:

• how to get a protein sequence from UniProt,
• how to apply fixed and variable modifications,
• how to import sequence into an analysis.