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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 (by default: 0.01 i.e. 1% of the base peak). This is recommended to remove noise peaks from the spectrum. Filtering takes place after the initial precursor m/z removal.

Parameters

  • rel_int_from: specifies the minimum relative intensity to retain fragments. 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.