Dear MS Amanda users,
a new version of MS Amanda for Proteome Discoverer 2.X is available. You can download version 2.1.5.5262 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,
Viktoria