Export of spectra

[zouboulk]

Thank you for developing Annotator — it's very helpful to annotate my glycoproteomics data!

Main issue:
When exporting spectra as PDF, I’ve noticed a few limitations that make figure preparation harder:

1. The export currently only allows printing a full page.

2. The text in the exported PDF (peak labels, proteoform names) is not editable in Illustrator — it comes in as outlined shapes. Could the font be embedded as TrueType?

3. Proteoform and peak labels sometimes overlap; having additional spacing or better automatic label placement would greatly improve clarity.

These improvements would make it much easier to produce publication‑quality annotated spectra.

Also the spectra scale while scrolling over them - could this be switched off?

Thank you again for all your work on this great tool!

[douweschulte]

Thanks for the interest in the Annotator.

For a bit of background. The way the Annotator currently works the spectra are displayed as HTML (a website) which allows me to make them interactive. This also means that it is surprisingly hard to convert them to images. So printing the full page to a PDF is the only real way of exporting vector graphics. I can look into hiding some more things during printing, or maybe providing some option to really only show the spectrum when printing which could solve your 1st issue. The second issue is related, because the PDF is generated by the operating system I have no control on how exactly the text is inserted. If you have multiple options for printing to PDF you could try them all and see if some give more workable output.

For the 3rd issue, I would love to fix this, but this involves a lot of computation that is both hard and will make the spectrum viewer considerably slower. I am not sure I am able to make something like this fast enough to make it possible to use it. My current solution is to export to PDF and then manually fix up the labels that overlap.

The scaling spectrum when scrolling the page is sort of intended behaviour. I have built the scaling deliberately but also recognise that it interferes with scrolling the page sometimes. I will have to think if I can detect this case and then suppress the spectrum scaling.