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mMass Changelog

What's new in mMass 5.5.0

Jul 2, 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.

New in mMass 5.4.1 (Dec 27, 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.

New in mMass 5.4.0 (Nov 19, 2012)

  • Improved: Multiple documents overlay in Mass Defect Plot panel.
  • 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.

New in mMass 5.3.0 (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.

New in mMass 5.2.0 (Jul 2, 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.

New in mMass 5.1.0 (May 18, 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.

New in mMass 5.0.1 (Mar 29, 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.

New in mMass 5.0.0 (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.

New in mMass 4.0.0 (Dec 5, 2011)

  • 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.

New in mMass 3.12.1 (Aug 29, 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.

New in mMass 3.12.0 (Jul 15, 2011)

  • 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.

New in mMass 3.11.0 (May 10, 2011)

  • 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.

New in mMass 3.10.0 (Feb 23, 2011)

  • 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.

New in mMass 3.9.0 (Dec 16, 2010)

  • New: Compare Peak Lists tool to compare peak lists between multiple documents.
  • New: Simple math functions are now available to add, subtract and multiply spectra.
  • New: Peptides, fragments or compounds lists can be filtered to show matched/unmatched items.
  • New: Sequences from digest list, fragments list or peptide search list can be copied into clipboard.
  • New: Duplicate copy of selected document can be made via pop-up menu in Documents Panel.
  • New: Distance measurement tool shows current distance in both m/z and ppm (bottom bar only).
  • Improved: 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.

New in mMass 3.8.0 (Aug 21, 2010)

  • New: TIC and BPC chromatograms are now available in scan selection dialog.
  • New: Support for mzML data format.
  • New: Spectrum intensity offset (visual only) can now be set either manually or using new mouse tool.
  • New: Intensity bar is now available in Spectrum Panel.
  • New: Height of position bar and intensity bar can now be set in Canvas Properties.
  • New: New view option to show/hide spectrum data points.
  • Improved: Peak width is assigned automatically when overlaying theoretical isotopic patterns.
  • Fixed: Incorrect charge calculation in Deisotoping module.
  • Fixed: Incorrect file extension for files converted by CompassXport.

New in mMass 3.7.0 (Jul 19, 2010)

  • 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.

New in mMass 3.6.0 (Jul 6, 2010)

  • 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.

New in mMass 3.5.0 (Jun 4, 2010)

  • New: Possibility to vertically flip spectra in Spectrum Viewer.
  • New: -H2O can now be searched in Compounds Search tool.
  • Fixed: Normalized view did not worked for non-profile spectra.

New in mMass 3.4.0 (May 13, 2010)

  • 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.

New in mMass 3.3.0 (Apr 9, 2010)

  • Simple periodic table of the elements is available with direct links to Wikipedia and The Photographic Periodic Table of the Elements.
  • Since the Bruker's raw data format is changing for every instrument (particularly the calibration method) I cannot guarantee correct data import. Therefore I've decided to remove native support for such data. However, a new feature has been implemented to use Bruker's own CompassXport tool to import the raw data from different Bruker's MS instruments. The CompassXport tool is available for free at www.bdal.de and must be installed on your computer. Many of the Bruker's MS instruments are now supported, unfortunately, this works on MS Windows only.
  • Single charge state is calculated in the Sequence Search tool, because it is much faster and makes more sense.
  • The bug causing incorrect manual labeling of low-intensity peaks has been fixed.
  • The bug causing a source application window to freeze while dragging documents onto mMass has been fixed.
  • Various bugs in the Sequence Search tool have been fixed.

New in mMass 3.2.0 (Mar 15, 2010)

  • Isotopic pattern calculator is now collapsible, which can be useful while overlaying theoretical and acquired pattern on a small monitor.
  • Hidden modifications can now be used in the Mascot tools.
  • Modified documents are marked with '*' in the documents panel.
  • Relative intensities for annotations and sequence matches are not stored within documents but calculated from a peak list instead.
  • Recent Mascot issue fixed.

New in mMass 3.1.0 (Mar 4, 2010)

  • 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".

New in mMass 3.0.0 RC2 (Jan 21, 2010)

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

New in mMass 3.0.0 RC1 (Jan 21, 2010)

  • 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

New in mMass 3.0.0 Beta 1 (Dec 15, 2009)

  • 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

New in mMass 3.0.0 Alpha 1 (Oct 27, 2009)

  • Everything has changed and mMass is completely new.