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Published 20 hours ago • verified publisher icon MannLabs

Supported fragmentlosstype?

Open hxxhust163 opened this issue 10 months ago • 4 comments

Hi

Thanks for your work in Alphapeptdeep. I found a tsv_str your provided in the /nbdev_nbs/pipeline_api.ipynb containing 'noloss, H3PO4, 1(+H2+O)1(+H3+O4+P)' in the FragmentLossType column. I wonder whether peptdeep supports the fragmentlloss such as 'H2O, NH3' which means loss of 18 and 17 in mass?

Thanks very much!

Best wishes Xiaoxiang

hxxhust163 avatar Apr 15 '24 06:04 hxxhust163

No, we did not train model for H2O and NH3 losses

jalew188 avatar Apr 15 '24 07:04 jalew188

In principle, it is very easy to train a new model for H2O and NH3 losses, I am just not sure if it is very necessary

jalew188 avatar Apr 15 '24 07:04 jalew188

OK, thanks again!

hxxhust163 avatar Apr 15 '24 10:04 hxxhust163

I will write a comprehensive tutorial about alphabase/alpharaw/peptdeep

jalew188 avatar Apr 17 '24 18:04 jalew188