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.
Limitations
- Spectral library matching is prohibitively slow with large spectral libraries (especially using the MS2DeepScore algorithm). Therefore, a targeted spectral library should be provided. For a more general library, see MS2Query annotation.
Parameters modified cosine
| Key |
Possible Values |
Default |
| activate_module |
true, false |
false |
| min_nr_matched_peaks |
>=1 |
5 |
| fragment_tol |
>0 |
0.1 |
| score_cutoff |
0.0-1.0 |
0.7 |
| max_precursor_mass_diff |
>=1 |
600 |
Explanation
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 matchmax_precursor_mass_diff: maximum allowed difference between precursor m/z of feature and library m/z.
Parameters ms2deepscore
| Key |
Possible Values |
Default |
| activate_module |
true, false |
false |
| score_cutoff |
0.0-1.0 |
0.8 |
| max_precursor_mass_diff |
>=1 |
600 |
Explanation
score_cutoff: minimum score to consider a matchmax_precursor_mass_diff: maximum allowed difference between precursor m/z of feature and library m/z.