New Standalone Version for MS Amanda

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Viktoria Dorfer

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Aug 2, 2019, 8:16:45 AM8/2/19
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Dear MS Amanda users,

a new standalone version of MS Amanda (v. 2.0.0.13723) for all operating systems is available and can be downloaded from the MS Amanda webpage or directly following this link.

Here is the changelog compared to the previous version:

general changes

  • output for number of matched ions

  • additional setting 'maximum peptide length'

  • maxRank maximum value set to 999

  • additional setting reportBothBestHitsForTD:

     true -> ranking of target and decoy as before
     false -> target and decoy share the ranking
  • Core & Utils are .NET Standard 2.0

  • fasta files can have the same name if they are in different folders

mzid output

  • now generates a zip (.mzid.gz)
  • corrected spectrumId attribute
  • SpectrumIdentificationItem includes element for calculatedMassToCharge
  • settings included in SpectrumIdentificationProtocol
Please let us know if anything does not work for you!
Happy searching!
Best regards,
Viktoria

Harald Barsnes

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Sep 4, 2019, 6:07:11 AM9/4/19
to MS Amanda

Hi Viktoria,

There seems to be a minor bug in the output option for mzIdentML where ".mzid.gz" is always added to the name provided via the -o option. In other words, if using -o "C:\qExactive01819.ms-amanda.mzid.gz" the output file will rather be called "C:\qExactive01819.ms-amanda.mzid.gz.mzid.gz". (The same does not happen when using the csv output option.)

Would be great if this could be fixed as it would make it easier to control the name of the mzid output file and to check whether the file was created or not.

Best regards,
Harald

Viktoria Dorfer

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Sep 13, 2019, 2:48:13 PM9/13/19
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Hi Harald,

sorry for the late reply and thanks for reporting this! We will fix that asap!

Thanks!
Best regards,
Viktoria

Viktoria Dorfer

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Sep 18, 2019, 1:02:53 PM9/18/19
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Hi Harald,

we fixed this issue, the new version is available here: MSAmanda 2.0 Standalone v2.0.0.14078

Thanks for reporting this!
Cheers,
Viktoria

Harald Barsnes

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Sep 19, 2019, 9:43:02 AM9/19/19
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Hi Viktoria,

Thanks! I can confirm that it now works as expected. :)

Best regards,
Harald
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