Fragment Ion Matches

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Simon Perkins

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Apr 15, 2019, 11:44:35 AM4/15/19
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Hi,

Is there a way to extract information about the matching fragment ions for a given PSM using MS Amanda?

Thanks,

Simon

Viktoria Dorfer

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Apr 17, 2019, 6:07:38 AM4/17/19
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Hi Simon,

unfortunately not. Are you using Proteome Discoverer or the standalone version/SearchGUI&PeptideShaker?

In PD there is a column "Matched Ions", telling you how many ions have been matched by MS Amanda and if you click on a PSM the spectrum viewer opens and you can see the ions that match the spectrum (but this is recalculated by PD, so this may not perfectly overlap with MS Amanda).

We are currently including the matched ions output in the mzIdentMl result, that will be available in the next release. Also, if you are using PeptideShaker to have a look at your results, you can have a look at the matched ions for your spectrum in the "Spectrumd IDs" tab.

Hope that helped!
Best regards,
Viktoria

Simon Perkins

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Apr 17, 2019, 12:14:40 PM4/17/19
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Hi Viktoria,

Thank you for replying quickly. I am using the standalone version of MS Amanda.
Is the matched ions output in the current mzIdentML export of the standalone version? Is it planned for the next release in the PD version and the standalone version?

I may try through searchGUI next.

Thanks,

Simon

Viktoria Dorfer

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Apr 18, 2019, 4:42:43 AM4/18/19
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Hi Simon,

the matched ions output is in the current release in the PD version and will be in the next release of the standalone version. Sorry for the confusion!

Best regards,
Viktoria
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