Variable peak width distributions using FeatureFinderIdentification for Bruker Impact data

Hi everyone,

I am trying to obtain the FWHM of identified peptides from Bruker Impact data using the FeatureFinderIdentification module (attached workflow image and FFID settings) but I obtain very different FWHM distributions from very similar samples. Attached is a excel file containing the FWHM values of the identified peptides on each sample and a histogram of the distributions.
For sample 1 we have a nice distribution with apex in 15s, but for sample 2 we have a lot of noise and the distribution is centered around 4s . Any ideas on what could it be the cause?

Thanks a lot,

Edu

FWHM values.xlsx (120.0 KB)