Intact Native spectra provide unique challenges compared to denatured deconvolution. The challenges come primarily from the low number of charge states and the altered spacing in the charge envelope. The following settings are recommended to correct for this:
The primary parameter to adjust is 'Charge vectors spacing' for native data 3 is recommended though in more complex data sets 5 and 10 may also be appropriate.
The following advanced commands are also recommended for all Native projects:
ChargeEnvelopeWeights=0.1, 0.8, 0.1
These settings will adjust the expected spacing of the charge envelopes and help maintain mass accuracy at higher m/z ranges.
Additionally, ChargeEnvelopeFilterPower2=true can also be utilized to improve sensitivity for low signal to noise species.