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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Questions on MS1-subtract and mass-acc-quant Options #952

Open dong-gi-jang opened 7 months ago

dong-gi-jang commented 7 months ago

Hello,

I've been making great use of your program and it's been working wonderfully for me. I have a question though. I'm curious about what the MS1-subtract option and the mass-acc-quant option stand for.

Thank you, Dong-gi Jang

vdemichev commented 7 months ago

Hi Dong-gi,

ms1-subtract signficantly reduces the degree of MS1 interference between isotopic channels when using --channels. mass-acc-quant specifies which mass tolerance threshold should be used for chromatogram extraction for quantification

Best, Vadim

dong-gi-jang commented 7 months ago

Thank you for the quick response! Can I understand that MS1 interference in the ms1-subtract option is calculated using something like averagine?

Thank you again, Dong-gi Jang

vdemichev commented 7 months ago

No, it's more simple, just subtracts whatever signal there is at the peptide mass minus C13/C12 delta mass.