New MS Amanda version for PD 2.X available!

Skip to first unread message

Viktoria Dorfer

Jul 24, 2015, 6:46:00 PM7/24/15
to MS Amanda
Dear MS Amanda users,

a new version of MS Amanda for Proteome Discoverer 2.X is available. You can download version from the MS Amanda homepage.
To use the new version of MS Amanda with Proteome Discoverer, please install first the Thermo ThirdParty Components, then follow the instructions on the homepage.
For PD 2.X, "AmandaInst.exe" is no longer available but was replaced by "UpdateMSAmandaInstallation.exe" which is also provided in the .zip file. Please execute that instead.

The latest version of MS Amanda for PD 2.X includes the following bug fixes and improvements:
  • Bugfix for n-terminal modifications targeting a specific amino acid (no matches)
  • Bugfix for database digestion (minor inaccuracies for different computers for peptides masses after the fourth decimal place)
  • Bugfix for neutral losses in the considered fragment ions (crash)
  • Feature Extension in Configuration Settings: Low RAM Mode
    • 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 the previous MS Amanda version for PD 2.0 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 the previous version:
      First Scan     Sequence                                             Amanda Score    Search Engine Rank
      7443             KGDTVVIYmPMIPQAMYTmLAcAR    82.95                   1
      7443             LLSNPETLAVDADVSFYYTcRSDR     79.86                   2
      7443             FLNEEFISLLDSQFNmDITAAMAR      62.50                   3
      7443             YQHSVEWAAELmRRQGQDESTVR   49.50                  4
      7443             LFTEFmHVRTEmEEVLQKSDYK        48.73                  5
    • The corresponding result from the latest version would look like:
      First Scan    Sequence                                              Amanda Score    Search Engine Rank
      7443            KGDTVVIYmPMIPQAMYTmLAcAR     82.95                   1
      7443            LLSNPETLAVDADVSFYYTcRSDR      79.86                   2
      7443            KGDTVVIYMPmIPQAMYTmLAcAR     67.90                   3
      7443            KGDTVVIYmPMIPQAmYTMLAcAR     67.77                   4
      7443            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,

Chia-wei Lin

Jan 4, 2019, 6:05:12 AM1/4/19
to MS Amanda
Dear Viktoria, 

Does MS Amanda also work on PD2.3? Thanks.


Viktoria Dorfer

Feb 1, 2019, 8:22:05 AM2/1/19
to MS Amanda
Hi Chia-wei,

in principle yes. There is a version of MS Amanda for PD 2.3, but that will not work with the latest version of PD 2.3 but was compiled for PD 2.3.339 and will not work with the latest version. We will release a new version in the next weeks!

Best regards,
Reply all
Reply to author
0 new messages