Prediction model with a different instrument

compomics / ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.

https://ms2pip.readthedocs.io

Apache License 2.0

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Prediction model with a different instrument #204

Closed tretyacv closed 9 months ago

tretyacv commented 10 months ago

Hello, would you consider the TTOF5600 model applicable to TTOF6600 spectra prediction?

JB91451 commented 10 months ago

Hi,

I am not a developer of ms2pip but a (former) user of TTof instruments. Fragmentation in both instruments is essentially the same. There are only some differences in the ion path etc. but ms2 spectra should behave the same. So I would guess that there are no issues in applying the TTof5600 model to TTof6600.

Best, Juergen

RalfG commented 9 months ago

Hi @tretyacv,

I second Juergen's comment. I assume they will be extremely similar. You could also try the latest HCD model, as we have seen that Orbitrap and Sciex TOF fragmentation patterns are quite similar too (https://pubmed.ncbi.nlm.nih.gov/31028400/#&gid=article-figures&pid=figure-1-uid-0), and the latest HCD model is a bit more performant in general than our older models.

Best, Ralf