New MS Amanda Standalone Version available!

[Viktoria Dorfer]

Dear MS Amanda users,

we are proud to announce that there is now a new standalone version of MS Amanda available for download at the MS Amanda homepage (versions 1.0.0.5242 (Windows) and 1.0.0.5243 (Linux & Mac))!

These versions include several bug fixes and improvements:

• Bugfix for n-terminal modifications targeting a specific amino acid causing MS Amanda to crash
• Bugfix for database digestion, minor inaccuracies for different computers for peptides masses after the fourth decimal place:
• MS Amanda generates files with digested peptides for re-usage. The default location of that files is "C:\ProgramData\MSAmanda\AmandaDB\" for the Windows version and "\.MSAmanda\AmandaDB\" in the user's home directory for the Linux and Mac version.
• Please remove all files and folders in your corresponding database folder, such that all digested databases can be re-created with the new MS Amanda version.
• Feature extension for database folder specification:
• We added a new parameter "<data_folder>DEFAULT</data_folder>" to the settings.xml. This folder specifies the location of digested database files and temporary files generated during the search process and can be changed when necessary.
• Windows version: DEFAULT points to "C:\ProgramData\MSAmanda\"
• Linux&Mac version: DEFAULT points to "\.MSAmanda\" in the user's home directory.
• Performance improvements:
• In addition to various improvements in terms of speed, a new parameter "<low_ram_mode>true</low_ram_mode>" was added to the settings.xml
• Low_ram_mode=true accounts for very low RAM availability and will save intermediate results to temporary files.
• Low_ram_mode=false keeps intermediate results in memory and will therefore be faster.
• Low_ram_mode=false should not be applied for work stations with less than 2GB RAM per core.
• Alternative modification site consideration:
• In previous MS Amanda versions only the highest scoring configuration has been reported for modified peptides with multiple potential modification sites, whereas now also other combinations are reported up to the specified peptide rank.
• Example for a result from previous versions:
  Sequence                                         Score    Rank
  KGDTVVIYmPMIPQAMYTmLAcAR    82.95    1
  LLSNPETLAVDADVSFYYTcRSDR      79.86     2
  FLNEEFISLLDSQFNmDITAAMAR       62.50     3
  YQHSVEWAAELmRRQGQDESTVR   49.50     4
  LFTEFmHVRTEmEEVLQKSDYK        48.73     5
• The corresponding result from the latest version would look like:
  Sequence                                         Score    Rank
  KGDTVVIYmPMIPQAMYTmLAcAR    82.95     1
  LLSNPETLAVDADVSFYYTcRSDR      79.86     2
  KGDTVVIYMPmIPQAMYTmLAcAR    67.90     3
  KGDTVVIYmPMIPQAmYTMLAcAR    67.77     4
  FLNEEFISLLDSQFNmDITAAMAR       62.50     5
  

If you have any questions or problems with the latest release please do not hesitate to contact me!
Any feedback on the latest version will be very much appreciated!

Best regards,
Viktoria