Expand theoretical spectrum generation tutorial

[timosachsenberg]

• introduce b and y ions and how they are formed
• talk about add prefix ions and precursor ions option (e.g., to explain how many ions are generated)

[timosachsenberg]

this issue is based on requests from users...

[JeeH-K]

Is it going to be included on readthedocs? @timosachsenberg

[timosachsenberg]

Hi. Yeah it would be great to look for the appropriate section in the readthedocs documentation (I think we already cover spectrum generation) and expand that a bit.

[JeeH-K]

https://openms.readthedocs.io/en/latest/openms-applications-and-tools/visualize-with-openms/views-in-toppview.html#d-view Here's the only place that talks about the theoretical spectrum generation. I'll try to add an extra page for this.

[timosachsenberg]

ah no this is pyopenms

[timosachsenberg]

https://pyopenms.readthedocs.io/en/latest/search.html?q=TheoreticalSpectrumGenerator&check_keywords=yes&area=default

[JeeH-K]

I'll expand here https://pyopenms.readthedocs.io/en/latest/hyperscore.html?highlight=theoretical%20spectrum#generate-a-theoretical-spectrum

Or do you mean the TheoreticalSpectrumGenerator itself?

[timosachsenberg]

e.g. or here https://pyopenms.readthedocs.io/en/latest/theoreticalspectrumgenerator.html?highlight=TheoreticalSpectrumGenerator#y-ion-spectrum but please decide for yourself

[JeeH-K]

A little bit off-topic maybe, but curious: https://pyopenms.readthedocs.io/en/latest/theoreticalspectrumgenerator.html?highlight=TheoreticalSpectrumGenerator#y-ion-spectrum "plot_spectrum" is implemented in pyopenms? It doesn't work with me

[JeeH-K]

https://github.com/OpenMS/pyopenms-docs/issues/338 I guess it doesn't correspond to the released pyopenms

[timosachsenberg]

@matteopilz

[JeeH-K]

Maybe it's worth mentioning in the document since we have got an issue opened lately. https://github.com/OpenMS/pyopenms-docs/pull/341

[jpfeuffer]

I think instead it should go into the changelog and one should just use the documentation that is corresponding to the version that they are using. Unfortunately, this selection is not very visible -> #342 should be fixed first

[JeeH-K]

Cannot agree more. I'd prefer the doc to correspond to the released version, not the nightly/develop version.

[JeeH-K]

Trying to solve this issue before working on doc: https://github.com/OpenMS/OpenMS/issues/6701

[jpfeuffer]

What to display as default is a different issue which should be discussed separately. The linked issue is about the visibility of the version switch.

[jpfeuffer]

By default I mean where pyopenms.readthedocs.io redirects to.