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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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Modifications view: mirrored spectrum #491

Closed szabzola closed 1 year ago

szabzola commented 1 year ago

Hi, thanks for great software! In the modifications view for a number releases, the mirrored spectrum (selecting modified and related peptide) shows really mirrored spectrum (the same spectrum on top/bottom) just labels are different. Regards,

hbarsnes commented 1 year ago

Do you have an example screenshot that you can share here? Please note that these peptide-spectrum-matches can be very similar and thus look almost the same.

szabzola commented 1 year ago

Hi, at the moment I found only this. In mirrored spectra beacuse of label on y2 (even if y labels ar off) all other peaks look small, I have found no way to change scaling (feature request?). But I have chosen a different charge state for related PSM (unmodified peptide), which is completely different. Also, if I change selection in related PSM list, mirrored spectrum is not changed (peak labels may change). Mirrored MS/MS spectra: image Modified peptide MS/MS (+2) image Unmodified peptide MS/MS (+3) image

hbarsnes commented 1 year ago

You are correct. There was indeed a bug that resulted in the mirrored spectrum not always updating correctly. I've just released a new version (v2.2.14) which should solve the problem. Please give it a go and let me know.

As to the scaling, you can always zoom in on a wanted area by using the mouse. Simply click and drag to the right for the given area you want to zoom in on. Right-clicking will reset the zoom to the entire spectrum.

szabzola commented 1 year ago

Thanks, a lot, I will try it. About zooming: in mirrored view if I zoom in on the m/z axis (which is the only zoom option) the intensity scale remains the same (unlike in singe spectrum view, when it autoscales).

hbarsnes commented 1 year ago

About zooming: in mirrored view if I zoom in on the m/z axis (which is the only zoom option) the intensity scale remains the same (unlike in singe spectrum view, when it autoscales).

I think it is due to the rescaling required to make spectra comparable even if the max intensity levels are very different, as otherwise one would risk one of the spectra not being visible at all. I will look into making the scaling an option that can be turned off, as there are clearly also cases were seeing the actual intensities are preferred.

hbarsnes commented 1 year ago

Just released yet another new version (v2.2.15) which improves the zooming when looking at mirrored spectra. I think this is the best I can do without making larger changes. See what you think.

szabzola commented 1 year ago

Everything is just perfect, including scaling in 2.2.15. Thank you for the really quick solutions.