MS/MS Filtering

Description

This module performs filtering of MS/MS fragmentation spectra of features. MS/MS spectra regularly contain fragments caused by instrument noise, which obfuscate and prolongate the analysis.

By default, FERMO will quality-filter MS/MS fragments and remove the fragment corresponding to the precursor m/z and all fragments +- 10 m/z units around the precursor m/z. These fragments are usually artifacts and do not correspond to any meaningful neutral losses.

Additionally, FERMO can remove fragments with a relative intensity lower than a user-specified value. This is recommended to remove noise peaks from the spectrum. Filtering takes place after the initial precursor m/z removal.

Parameters

Key	Possible Values	Default
filepath	(the filepath)	N/A
format	mgf	N/A
rel_int_from	0.0-1.0	0.01

Explanation

• rel_int_from: specifies the minimum relative intensity to retain fragments in an MS/MS spectrum. If 0.0, all fragments are retained. A value of 0.01 would remove all fragments with an intensity of less than 1% of the most intense fragment.