Version History
Version 5.5.0 (Released Jul 1, 2013)
- Added: Peak list can now be exported into ASCII with column headers.
- Added: Mass to Formula tool is now able to calculate negative compositions.
- Improved: Form parameters updated in Protein Prospector tools.
- Fixed: Mass to Formula tool crashed when no composition was found.
- Fixed: Correct scan number is now parsed from mzML format.
Version 5.4.1 (Released Dec 25, 2012)
- Fixed: Internal server has been disabled for OS X.
- Fixed: An issue with crashing plot canvas.
- Fixed: An issue with crashing Envelope Fit tool.
Version 5.4.0 (Released Nov 18, 2012)
- Improved: Multiple documents overlay in Mass Defect Plot panel.
- Improved: On Linux, system user’s folder is now used for configs and presets.
- Fixed: Incorrect handling of C-terminal modification in Peptide Fragmentation panel.
- Fixed: Incorrect calculation of some mass defects.
- Fixed: An issue with peak picking crashing on some documents.
- Fixed: An issue with mzML files with incorrect base peak intensity.
- Fixed: An issue with mzML files with unspecified retention time units.
- Fixed: Incorrect zooming style in Scan Selection dialog.
- Fixed: Updated link to ChemSpider from Mass to Formula panel.
- Fixed: Updated link to Human Metabolom Database from Mass to Formula tool.
Version 5.3.0 (Released Aug 27, 2012)
- Added: Mass Defect Plot to clusterize peaks based on their mass defect.
- Added: Swap Data function is now available in the Batch Processing panel.
- Added: Line style can be set for profile mass spectra.
- Improved: Open multiple documents via command line.
- Fixed: An issue with negatively charged ions matching.
Version 5.2.0 (Released Jul 1, 2012)
- Added: New spectrum canvas view option to allow ranges outside current documents boundaries.
- Improved: File association now works on all platforms via listening on port 65456.
- Improved: More detailed Spectrum Ruler info for charge and neutral mass.
- Fixed: In some cases, document selection in batch processing was unpredictable.
Version 5.1.0 (Released May 17, 2012)
- Added: Mass to Formula tool now compares theoretical isotopic pattern with acquired data.
- Added: Isotopic pattern can be modeled using either symmetrical or asymmetrical peak shapes.
- Added: Artificial spectra can be modeled using either symmetrical or asymmetrical peak shapes.
- Added: Compare Peak Lists tool now shows additional table with combined peak list.
- Added: Compare Peak Lists tool now enables intensity ratio threshold for highlighting peaks.
- Added: Unmatched peaks can now be removed from Peak Differences tool table.
- Added: Neutral mass can be calculated and shown by Spectrum Ruler tool.
- Improved: Peak list generated by Isotopic Pattern tool is calculated from final envelope.
- Changed: Baseline shift removed from normalization.
- Fixed: Preview in Math Operations tool did not work correctly.
- Fixed: An issue with re-creating configuration files.
- Fixed: Peak list updating in Match panel plot.
Version 5.0.1 (Released Mar 28, 2012)
- Improved: Molecular formula of the peptide is shown in custom-type Sequence Editor.
- Fixed: Sequence Search tool did not work.
- Fixed: Sequence info did not update correctly while switching sequences.
- Fixed: Applying processing tools with no document selected may cause application to crash.
- Fixed: An issue with mzML files with different data array bits.
Version 5.0.0 (Released Mar 2, 2012)
- Added: Mass to Formula tool to generate molecular formula from given m/z value.
- Added: Batch Processing tool to apply multiple processing steps to multiple documents at once.
- Added: Minor axis ticks can be shown in spectrum canvas.
- Added: Peak area can be calculated and shown by Spectrum Ruler tool.
- Added: Protein charge state can be calculated and shown by Spectrum Ruler tool.
- Added: Overlay function added to Math Operations panel.
- Added: Combine All, Average All and Overlay All functions added to Math Operations panel.
- Added: Photoshop-like method to see/enable just one document while hiding others.
- Added: Sequence modifications can be applied specifically to N or C terminus.
- Added: New view option to show/hide labels' Group name.
- Improved: Part of the mMass's processing core is now written in C.
- Improved: Faster calculation of Math Operations.
- Improved: Faster loading of single-scan documents from mzML, mzXML and mzData.
- Improved: Information shown by Spectrum Ruler tool can be set via application menu View.
- Improved: Drawing of individual peaks in pattern simulator can be disabled to speed up calculation.
- Fixed: Multiple files selection in Open dialog.
- Fixed: Application sometimes crashed when peaks were labeled with Sequence panel opened.
Version 4.0.0 (Released Dec 2, 2011)
- Added: New Sequence Editor to define custom peptide sequence with non-standard amino acids.
- Added: Peptide sequence can be set as linear or cyclic.
- Added: N-terminal modifications can be saved in presets.
- Added: Internal monomer library with more that 500 building blocks from NORINE database.
- Added: Monomer Library Editor for user-defined monomers and corresponding neutral losses.
- Added: Improved Peptide Fragmentation tool with more fragmentation pathways.
- Added: Gaussian smoothing filter.
- Added: Overall matched intensity is calculated and shown in Match panel and Sample Report.
- Added: Envelope Fit tool to determine heavy atoms exchange (e.g for HDX experiments).
- Added: Monoisotopic mass determination for large proteins with isotopically resolved envelope.
- Added: Charge state is shown in the bottom bar for Measure Distance tool and current difference.
- Added: Save All feature to save all opened documents at once.
- Added: Current document’s path is shown in Document Info panel.
- Added: Charge column is shown for annotations and sequence matches in Sample Report.
- Added: 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.
Version 3.12.1 (Released Aug 28, 2011)
- 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.
Version 3.12.0 (Released Jul 14, 2011)
- Added: Deconvolution tool to generate deconvoluted peak list from peaks with assigned charge.
- Added: New document can be created directly from clipboard data.
- Added: Different application layouts are available via Window menu.
- Added: Group name parameter can be specified for any peak via Peak Editor.
- Added: Group name column can be shown in Peaklist Panel.
- Added: For Label Envelope tool, 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.
Version 3.11.0 (Released May 10, 2011)
- Added: Simple Spectrum Generator tool for artificial mass spectra generation.
- Added: Cancel button for long-running tasks.
- Added: All the peak picking tools are using baseline according to Baseline Correction panel.
- Added: Live threshold line preview is shown for Peak Picking tool according to current settings.
- Added: Label Envelope tool to label isotopes or envelope centroid or to “measure” peak charge.
- Added: Isotope mass shift correction parameter in Deisotoping panel.
- Added: Support for MGF (Mascot Generic Format) data format.
- Added: User annotations and sequence matches can be shown as “labels” in Spectrum Viewer.
- Added: Peaklist Panel columns can be enabled or disabled.
- Added: A.i. value can be shown in Peaklist Panel.
- Added: Neutral mass is calculated and can be shown in Peaklist Panel.
- Added: Left-click+Alt/Ctrl on a document title in Documents Panel hides other documents.
- Added: Scale y-axis simply by mouse scroll with the cursor positioned in the y-axis area.
- Added: Sequence accession number can be specified in Sequence Editor.
- Added: Direct links to protein databases are available in Sample Report via protein accession numbers.
- Added: H3PO4 neutral loss added to Sequence Fragmentation panel.
- Added: 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.
Version 3.10.0 (Released Feb 23, 2011)
- Added: Mass Filter tool to annotate or remove contaminant masses.
- Added: Set Mass Range tool to specify current mass range in Spectrum Viewer.
- Added: Font and line scaling can be specified in Export Spectrum Image tool.
- Added: Peak list filter can be specified in Match panel and protein identification tools.
- Added: IDs for PubChem Compounds and NORINE peptide database are recognized in Report.
- Added: 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.
Version 3.9.0 (Released Dec 15, 2010)
- Added: Compare Peak Lists tool to compare peak lists between multiple documents.
- Added: Simple math functions are now available to add, subtract and multiply spectra.
- Added: Peptides, fragments or compounds lists can be filtered to show matched/unmatched items.
- Added: Sequences from digest, fragments or peptide search lists can be copied into clipboard.
- Added: Duplicate copy of selected document can be make via pop-up menu in Documents Panel.
- Added: Distance measurement tool shows current distance in both m/z and ppm (bottom bar only).
- Added: Multiple documents can be opened at once using Open dialog.
- Fixed: Correct drawing of spectra with no continuous baseline (typically for SIM experiments).
- Fixed: FWHM and resolution columns in a peak list can now be copied into clipboard as well.
- Fixed: Option to enable/disable notation marks now works correctly.
Version 3.8.0 (Released Aug 20, 2010)
- Added: TIC and BPC chromatograms are now available in scan selection dialog.
- Added: Support for mzML data format.
- Added: Spectrum intensity offset (visual only) can be set either manually or using new mouse tool.
- Added: Intensity bar is now available in Spectrum Panel.
- Added: Height of position bar and intensity bar can now be set in Canvas Properties.
- Added: New view option to show/hide spectrum data points.
- Added: Peak width is assigned automatically when overlaying theoretical isotopic patterns.
- Fixed: Incorrect charge calculation in Deisotoping tool.
- Fixed: Incorrect file extension for files converted by CompassXport.
Version 3.7.0 (Released Jul 19, 2010)
- Added: Simplified interface for Protein Prospector tools MS-Fit and MS-Tag.
- Added: FWHM and resolution is now calculated for each peak and shown in Peaklist Panel.
- Added: Global modifications can now be stored as presets.
- Added: 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.
Version 3.6.0 (Released Jul 5, 2010)
- Added: Match Summary is now available for each data matching.
- Added: Remove shoulder peaks option is now available for FTMS data peak-picking.
- Added: All annotations and sequence matches can now be removed at once from Document panel.
- Added: Compounds and reference masses can now be imported using corresponding library editor.
- Added: Spectrum flipping is now accessible from the View menu.
- Improved: Faster peak-picking, especially when Adaptive threshold option is used.
- 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.
Version 3.5.0 (Released Jun 4, 2010)
- Added: Possibility to vertically flip spectra in Spectrum Viewer.
- Added: -H2O can now be searched in Compounds Search tool.
- Fixed: Normalized view did not worked for centroid spectra.
Version 3.4.0 (Released May 12, 2010)
- Added: Radical ions can now be calculated in Mass Calculator and Compounds Search tools.
- Added: Single-point linear calibration has been enabled.
- Added: Calibration curve is now shown in the calibration error plot.
- Added: Current peak list is now shown as a background in error plots (calibration, data matching).
- Added: New view option to enable/disable normalized view of opened documents.
- Added: New view option to enable/disable notation marks.
- Added: All annotations and matches can now be highlighted by selecting a document root.
- Added: Theoretical and matched sequence coverage is now shown in Protein Digest tool.
- Added: Final composition of ion is validated in ion series calculations.
- Added: Automatic checking for available updates has been added.
- Added: Application preferences for updates and CompassXport utility has been added.
- Fixed: Mass Calculator - calculation of ions with negative agent charge.
- Fixed: Mass Calculator - pattern modeling with complex charging agent.
- Fixed: Normalization now includes baseline shift.
Version 3.3.0 (Released Apr 9, 2010)
- Added: Periodic Table of the elements has been added.
- Added: Bruker's raw data are imported using CompassXport tool (MSW only).
- Improved: Mass Search tool - better filtering.
- Fixed: Small fixes in manual peak picking.
- Fixed: Dropping documents to mMass caused the source window to freeze until loading finished.
- Fixed: Mass Search tool - Enzyme endings selection did not worked.
- Fixed: Mass Search tool - Max charge has been replaced by Charge.
Version 3.2.0 (Released Mar 14, 2010)
- Added: Isotopic Pattern panel is now collapsable.
- Added: Hidden modifications can now be enabled in Mascot Search interface.
- Added: Modified documents are marked by asterisk.
- Improved: Relative intensity for annotations and matches is now calculated on-the-fly.
Version 3.1.0 (Released Mar 3, 2010)
- Added: Lipid database (by LIPID MAPS Consortium) has been added to Compounds Search tool.
- Added: ProFound Search interface has been implemented.
- Added: Sequences can now be imported form mMass’s and FASTA files.
- Added: Manually labeled peak can now be automatically set as monoisotopic.
- Added: Specific cursor images for spectrum tools has been added.
- Added: Scan list buffer is now used to speed-up loading of multi-scan documents.
- Improved: Peak-picking algorithm has been improved.
- Improved: More "Pythonic" syntax in the mspy module.
- Improved: Spectrum tools are now accessible from the main menu as well.
- Fixed: Multiple fixes in Mascot Search interface.
Version 3.0.0 (Released Feb 1, 2010)
- Complete mMass redesign - new user interface, new features and new source code architecture.