Export matched fragments (and batch spectra export) not reporting c- and z-ions

[iahendriks]

Hi all,

First of all, thank you for providing this fantastic piece of software. :)

I'm analyzing some EThcD data and inspecting the matched fragments/ions using the "Export matched fragments" feature, through the psm.tsv. It appears that this feature writes b- and y-ions along with some other types like precursor. However, c- and z-ions are missing. This leads to some hits being reported as having no matched fragments at all, e.g. []. Or only precursor ions. See also the screenshot.

(The issue is more pronounced in data dominated by c- and z-ions, here I just analyzed an old EThcD HeLa run for the example.)

Is there some way to have c- and z-ions reported in the psm.tsv file? (Or all supported ion types that were searched.) Or would this be a feature request rather than a bug report?

Another related issue is with FragPipe-PDV. By default spectra are shown with b- and y-ions only. It is straightforward to visualize other ion types like c- and z-ions, and manually exporting a single spectrum works fine. However, the batch export feature seems to default to only exporting spectra with b- and y-ions annotated. It would be convenient if the batch export followed the visualized ion settings defined in FragPipe-PDV (as it does for the single spectrum export).

Kind regards,
Ivo

log_2026-01-26_13-55-02.zip

[KaiLiCn]

Hi Ivo,

We currently only support b and y ions in that function. We could add an option to select ion types in the future.

Best,
Kai