New Standalone Version for MS Amanda (MS Amanda 2.0)

[Viktoria Dorfer]

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

[Nick Hartel]

Hi Viktoria,

Is it possible to configure user-specified neutral losses for certain post-translational modifications?

I have tried editing the MSAmanda configuration file but it doesn't seem to change my results.

Best,

Nick

[Viktoria Dorfer]

Hi Nick,

in the standalone version you can specify neutral losses for user-defined modifications by extending the unimod.xml or the unimod.obo file. It depends on which output file you want to generate: the .csv uses the .xml file, the .mzIdentMl uses the .obo file.

As an example on how this should you look like, I recommend looking at Phospho(S). You can just extend the modification where you want to add a neutral loss, MS Amanda is parsing the the unimod files for every run again.

One important thing however: if you add a neutral loss to a modification where there was none before, please also add the neutral loss of "0.0Da". If this is missing, MS Amanda is forcing the modification to have a neutral loss. If both neutral losses are present (your new one and "0.0Da"), MS Amanda is trying both options. Of course you can add more than one neutral loss.

Hope that helped!

Best regards,

Viktoria