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Published 20 hours ago • verified publisher icon vdemichev

meaning of pMs1Ratio

Open wenronchen opened this issue 1 year ago • 2 comments

Dear Vadim,

I'm seeking clarification on the calculated scores for potential elution peaks. Could you explain the meaning of the 'pMs1Ratio' parameter? I noticed it doesn't appear among the 73 scores discussed in the supplemental of the DIA-NN paper.

Additionally, I'm curious about the 'bool' parameter 'AAS'. Is this parameter always set to true? Under what circumstances would it be false?

Thank you for your assistance.

Wenrong

wenronchen avatar Dec 13 '23 15:12 wenronchen

Hi Wenrong,

I think it's the ratio of MS1/MS2 signals for the precursor. All the undocumented (i.e. not explained here https://github.com/vdemichev/DiaNN) stuff might not be reliable, it is just there because at some point it was needed for some internal benchmark, so please only use the documented functionality /output.

Not sure what AAS refers to?

Best, Vadim

vdemichev avatar Dec 14 '23 10:12 vdemichev

Hi Vadim,

"AAS" is a parameter in your source code. And it seems to be related to modifications. I noticed that the default value of this parameter is "true" in your last open-source version 1.7.18.

Thank you for your clarification!

Wenrong

wenronchen avatar Dec 14 '23 14:12 wenronchen