Quantitative values in iq

tvpham / iq

An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics

BSD 3-Clause "New" or "Revised" License

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Quantitative values in iq #17

Open ghost opened 6 months ago

ghost commented 6 months ago

Hi,

I noticed that the quantitative values used by iq are derived from F.PeakArea. Could you please clarify if the quantitative values outputted by iq are at the MS1 level or the MS2 level?

Thank you for your assistance.

tvpham commented 6 months ago

Hi, F.PeakArea contains MS2 fragment intensities. So by default iq uses MS2 level quantification.

Thang