Spectral DB search

Description

Run on any feature list to match all rows against a local spectral library (formats: MoNA json, NIST msp, GNPS json (internal library submission format), JCAMP-DX jdx).

Method parameters

Peaklist
Select any peaklist
Masslist
Masslist of scans
Spectral libraries
json/msp from MoNA (MassBank of North America)
msp NIST format
JCAMP-DX jdx
mgf format from GNPS
json GNPS (format from the spectral DB submission module)
MS level
Set MS level to "1" to compare MS1 spectra (e.g. GC-EI-MS data) or set it to "2" or higher for MS/MS scans
Check all scans (only for MS2)
Either use all MS2 scans or only the most intense MS2 scan. This only applies to MS2 spectral matching.
Precursor m/z tolerance
Only used for MS level > 1. Filter all library entries by precursor m/z.
13C deisotoping
Deletes 13C isotope signals in the query and library mass spectra
Monotonic shape: Especially, for small molecules. 13C isotope pattern with first signal as the most abundant
Min matched isotope signals
Minimum number of "isotope" signals that need to be matched in the query and library scan. Searches for putative:
13C signals
-H (M+ to M+H+) and -2H signals
Cl isotope signals
Crop spectra to m/z overlap
Only match signals that fall within the overlapping m/z range of both spectra (bounds are expanded by spectral m/z tolerance))
Spectral m/z tolerance
Tolerance to match signals in the two spectra (library and query)
Retention time tolerance
Optional: Only used if the DB entry has a retention time
Noise level
An additional noise level for masslists (masslists are typically already thresholded)
Minimum matched signals
Minimum number of signals within m/z tolerance in a masslist and the spectral library entry
Similarity
Different similarity functions to match query and library spectra