User Library

Description

This module compares molecular features against a user-provided (targeted) spectral library. The matching algorithm works as follows:

For each feature, its MS/MS fragmentation spectrum is matched pairwise with each library spectrum, using one or more different algorithms described below.
For the modified cosine algorithm, library matches are only retained if feature and library spectra share a minimum number of matched peaks within a certain fragment tolerance, reach a cutoff score, and are inside a maximum precursor mass difference.
For the MS2DeepScore algorithm, library matches are only retained if feature and library spectra reach a certain cutoff score and are inside a maximum precursor mass difference.

fragment_tol: the absolute tolerance for matching two MS/MS fragments, in m/z units.
min_nr_matched_peaks: minimum number of fragments that must be matched between two MS/MS fragmentation spectra.
score_cutoff: minimum score to consider a match
max_precursor_mass_diff: maximum allowed difference between precursor m/z of feature and library m/z.

score_cutoff: minimum score to consider a match
max_precursor_mass_diff: maximum allowed difference between precursor m/z of feature and library m/z.

Spectral library matching is relatively slow (especially using the MS2DeepScore algorithm). Ideally, a targeted spectral library should be provided. For a more general library, see MS2Query annotation.