News Archive
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.
Apr 09, 2010 - mMass 3.3 released
Version 3.3 of mMass software has been released. Important fixes have been made and some new features have been added.
- 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. Be sure to use the latest version of CompassXport (3.0.1).
- 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.
Apr 09, 2010 - RPM package for OpenSUSE available
Thanks to Sebastian Gibb the RPM package of mMass 3.2 is available for OpenSUSE Linux.
Mar 31, 2010 - Protein modification screencast
New video tutorial has been published, showing some basics of a protein modification and corresponding data interpretation using mMass. The data I am using in this video corresponds to Aldolase A from rabbit modified by p-chloromercury benzoate and digested by trypsin. Mass spectrum was acquired on a MALDI-TOF mass spectrometer. In this video you will learn how to perform the following tasks:
- how to define new modification,
- how to get a protein sequence from UniProt,
- how to apply variable modification,
- how to perform in-silico digestion,
- how to match theoretical data to acquired spectrum,
- how to annotate matched peptides,
- how to generate and save theoretical isotopic pattern,
- how to generate Analysis Report.
Mar 30, 2010 - Spectrum viewer screencast
New video tutorial has been published, showing some basics of spectrum manipulations in the mMass's spectrum viewer. In this video you will learn how to perform the following tasks:
- how to zoom spectrum,
- how to move within spectrum,
- how to scale spectrum.
Mar 29, 2010 - Lipids identification screencast
New video tutorial has been published, where I would like to show you some basics of a lipids identification using mMass and its Compounds Search tool. In this video you will learn how to perform the following tasks:
- how to label peaks,
- how to search for lipids using Compounds Search tool,
- how to match theoretical data to acquired spectrum,
- how to annotate matched peptides,
- how to generate theoretical isotopic pattern,
- how to generate Analysis Report.
Mar 22, 2010 - Protein identification screencast
Today I started with a serial of mMass's screencasts and in the first video I would like to show you some basics of protein identifications using mMass. In this episode you will learn how to perform the following tasks:
- how to label peaks,
- how to send data to Mascot's PMF tool,
- how to define a new protein sequence and apply modifications,
- how to perform in-silico digestion,
- how to match theoretical data to acquired spectrum,
- how to annotate matched peptides,
- how to search unmatched peaks by Mascot's PMF tool,
- how to search for non-specific peptides,
- how to generate theoretical isotopic pattern,
- how to generate Analysis Report.
Mar 14, 2010 - Version 3.2 released
New version of mMass is now available for download. Changes are as follows:
- 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.