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