Oct 02, 2012 mMass in PLoS ONE

Together with Timo H.J. Niedermeyer we are proud to announce that our recent work on peptide fragmentation capabilities of mMass has been published in PLoS ONE journal. The paper is also a very nice review of current knowledge about fragmentation of natural linear and cyclic peptides. Since the journal is Open Access, feel free to download your copy of the paper without any fee.

Aug 27, 2012 mMass 5.3 released

Version 5.3 of mMass software has been released with additional new features and bug fixes. Go to the download page or see all the new features and changes in version history.

A simple new tool called Mass Defect Plot has been added to visualize peaks in selected document based on their fractional mass or various types of mass defect. In a generated plot, similar compounds tend to group into clusters. Standard mass defect is defined as the difference between a compound’s or peaks’s exact mass and its nominal mass. Kendrick mass defect can be utilized to group all the compounds differing just in the number of CH2 groups. In addition, custom Kendrick mass defect can be used to group compounds by user-specified formula.

Mass Defect Plot

Jul 01, 2012 mMass 5.2 released

Version 5.2 of mMass software has been released with some minor improvements and bug fixes. Go to the download page or see all the new features and changes in version history.

As one of the improvements, I have implemented support for direct file association via server-client approach. First instance of mMass creates a server listening on port 65456 for any file path to open. You might be asked by your system firewall to allow this connection. You can change the port number or even disable this feature in config.xml file. This feature can also be used as a base to implement possible API. Any ideas or requests for this API functionality? Just let me know in comments.

Jun 18, 2012 Correction of Natural Scrolling in OS X Lion

One of the new feature introduced to Apple's OS X Lion is "natural scroll", which somehow crippled mMass's mouse behavior in the spectrum viewer panel. Fortunately, there is a way to correct this issue.

  1. First, you'll need to make your Library folder visible. Open Terminal application and type:
    chflags nohidden ~/Library/
  2. In Finder locate the mMass's configurations folder:
    ~/Library/Application Support/mMass/
  3. Make a duplicate copy of "config.xml" file, just to be safe.
  4. Open the original "config.xml" file in TextEdit or other plain-text editor.
  5. Locate the following line:

    and change it to:
  6. Save the changes, close TextEdit and open mMass. It should be OK now.

Jun 15, 2012 List of mMass's Citations

Today, I have compiled a list of articles citing mMass. It is really nice to see how mMass is incorporated within totally different mass spec areas. Thank you very much for this kind of support!