Dear MS Amanda users,
we just released a new Standalone version of MS Amanda for Windows (version 2.0.0.9695) and Linux/Mac (version 2.0.0.9706). As for Proteome Discoverer we also developed a significantly faster version (MS Amanda 2.0) for the command line. Score calculation has not changed!
We also added some additional settings in the settings.xml file:
- <PerformDeisotoping>true</PerformDeisotoping>: Deisotope MS2 spectra
- <MaxNoModifs>3</MaxNoModifs>: Maximum number of occurrences of a specific modification on a peptide. (min 0, max 10)
- <MaxNoDynModifs>4</MaxNoDynModifs>: Maximum number of dynamic modifications per peptide (in total). (min 0, max 10)
- <MaxNumberModSites>6</MaxNumberModSites>: Maximum number of potential
modification sites for a specific modification per peptide. Peptides
with a higher number are discarded, due to a too high complexity. (min
0, max 20)
- <MaxNumberNeutralLoss>1</MaxNumberNeutralLoss>: Maximum number of same neutral losses per peptide regarding water and ammonia losses. (min 0, max 5)
- <MaxNumberNeutralLossModifications>2</MaxNumberNeutralLossModifications>: Maximum number of same neutral losses per peptide regarding modification specific losses. (min 0, max 5)
- <MinimumPepLength>0</MinimumPepLength>: Only peptides with a certain length are matched.
- <LoadedProteinsAtOnce>100000</LoadedProteinsAtOnce>: Maximal number of proteins loaded into memory; bigger values need more memory. If possible set it to a higher number than proteins in your database, as this will increase speed. (min 1000, max 500000)
- <LoadedSpectraAtOnce>2000</LoadedSpectraAtOnce>: The number of spectra that shall be processed at a time; bigger values need more memory. (min 1000, max 50000)
The new version of MS Amanda will still work with your old settings file, as all parameters have default values.
For a performance comparison and downloading the new version please have a look here.
If you have any further questions, issues, or suggestions, please do not hesitate to contact us!
Best regards,
Viktoria