mMass - Open Source MS Tool

Jan 05, 2012 - Happy new year mMass users!

Dec 02, 2011 - mMass 4.0 released

Version 4.0 of mMass software has been released with additional new features and bug fixes.

• New: Additional Sequence Editor to define custom peptide sequence with non-standard amino acids.
• New: Peptide sequence can be set as linear or cyclic.
• New: N-terminal modifications can be saved in presets.
• New: Internal monomer library with more that 500 building blocks according to NORINE database. (Please make sure you place the monomers.xml file into your configs folder under MS Windows or Linux.)
• New: Monomer Library Editor to allow user-defined monomers and corresponding neutral losses.
• New: Improved Peptide Fragmentation tool with more fragmentation pathways.
• New: Gaussian smoothing filter.
• New: Overall matched intensity is calculated and shown in Match panel and Sample Report.
• New: Envelope Fit tool to determine heavy atoms exchange (e.g for HDX experiments).
• New: Monoisotopic mass determination for large proteins with isotopically resolved envelope.
• New: Charge state is shown in the bottom bar for Measure Distance tool and current difference.
• New: Save All feature to save all opened documents at once.
• New: Current document’s path is shown in Document Info panel.
• New: Charge column is shown for annotations and sequence matches in Sample Report.
• New: User’s Guide PDF is accessible via application menu Help.
• Changed: Definition of the z-series ions according to Mascot.
• Changed: Polished icons to better fit into OS X Lion.
• Fixed: An issue with mzData time parameter.

Sep 06, 2011 - LIPID MAPS database updated

New database of lipids is available in download section.

Aug 28, 2011 - mMass 3.12.1 released

Version 3.12.1 of mMass software has been released with important bug fixes.

• Fixed: Application sometimes crashed while closing last document.
• Fixed: Some peaks were skipped when peak picking height was set to 100%.
• Fixed: Calibration curve sometimes did not fit well.

Jul 14, 2011 - mMass 3.12 released

Version 3.12 of mMass software has been released with additional new features and bug fixes.

• New: Deconvolution tool to generate deconvoluted peak list from peaks with assigned charge.
• New: New document can be created directly from clipboard data.
• New: Different application layouts are available via Window menu.
• New: Group name parameter can be specified for any peak via Peak Editor.
• New: Group name column can be shown in Peaklist Panel.
• New: For Label Envelope tool, final intensity can be calculated as envelope max, sum or average.
• Improved: Faster calculation of complex isotopic distributions.
• Improved: Spectrum Generator tool is using native peak’s FWHM value to generate spectra.
• Changed: Unified toolbar for all platforms.
• Fixed: Isotopic envelope was not calculated correctly for single-isotope compounds.
• Fixed: Peak list was not updated correctly after applying math functions.
• Fixed: Some toolbars were not drawn correctly in floating panels.
• Fixed: Peak lists concatenation (A+B) did not work correctly.

May 31, 2011 - ASMS 2011 - Denver

Would you like to talk about mMass? Do you have some ideas for new features? Please meet me near my poster (ThP418) at ASMS 2011 in Denver. I am looking forward to talking with you.

May 10, 2011 - mMass 3.11 released

Version 3.11 of mMass software has been released with additional new features and bug fixes.

• New: Simple Spectrum Generator tool for artificial mass spectra generation.
• New: Cancel button for long-running tasks.
• New: All peak picking tools are using baseline calculated according to Baseline Correction panel.
• New: Live threshold line preview is shown for Peak Picking tool according to current settings.
• New: Label Envelope tool to label isotopes or envelope centroid or to “measure” peak charge.
• New: Isotope mass shift correction parameter in Deisotoping panel.
• New: Support for MGF (Mascot Generic Format) data format.
• New: User annotations and sequence matches can be shown as “labels” in Spectrum Viewer.
• New: Peaklist Panel columns can be enabled or disabled.
• New: A.i. value can be shown in Peaklist Panel.
• New: Neutral mass is calculated and can be shown in Peaklist Panel.
• New: Left-click+Alt/Ctrl on a document title in Documents Panel hides other documents.
• New: Scale y-axis simply by mouse scroll with the cursor positioned in the y-axis area.
• New: Sequence accession number can be specified in Sequence Editor.
• New: Direct links to protein databases are available in Report via protein accession numbers.
• New: H3PO4 neutral loss added to Sequence Fragmentation panel.
• New: Semi-specific mass search in Sequence Panel can be enabled.
• Improved: Various speed improvements for high-resolution data.
• Improved: Application closing is much faster.
• Changed: Parameters of manual peak picking tools were moved to corresponding processing panels.
• Fixed: Documents loading queue.
• Fixed: Sequence Editor popup menu now behaves correctly.
• Fixed: Specifity filter in Sequence Modifications panel correctly handles terminal amino acids.
• Fixed: Metadata (e.g. operator, contact) are correctly loaded from mzData, mzXML and mzML.
• Fixed: Resolved an issue causing axis labels overlapping.

Apr 25, 2011 - Follow mMass on Twitter

mMass is now on twitter as @mmassorg. Follow the latest news, announcements of the new features in current development version or send me your own requests.

Feb 24, 2011 - mMass 3.10 for Linux

Thanks to the Sebastian Gibb from the University of Leipzig (Germany) you can now download mMass for different Linux distributions - Fedora, Mandriva, openSUSE and Debian. Thank you Sebastian!

Feb 23, 2011 - mMass 3.10 released

Version 3.10 of mMass software has been released with additional new features and bug fixes.

• New: Mass Filter tool to annotate or remove contaminant masses.
• New: Set Mass Range tool to specify current mass range in Spectrum Panel.
• New: Font and line scaling can be specified in Export Spectrum Image tool.
• New: Peak list filter can be specified in Match panel and protein identification tools.
• New: IDs for NCBI PubChem Compounds and NORINE peptide database are recognized in Report.
• Improved: New items in Peptide Fragmentation panel.
• Changed: Data normalization tool moved to Processing Panel.
• Changed: All annotations and sequence matches are removed when processing tools are applied.