Spectra database matching — spectraMatchingParam • RuSirius

This function is to set up the parameter for matching to spectra databases. This needs to be run first. Spectral library matching is performed using the cosine score with squared peak intensities, ignoring the precursor peak.

Note that spectral library matches are added as annotations to CSI:FingerID results and do not influence the ranking of structure candidates.

Usage

spectraMatchingParam(
  spectraSearchDBs = c("BIO", "massbank"),
  peakDeviationPpm = 10,
  precursorDeviationPpm = 10,
  scoring = c("MODIFIED_COSINE", "INTENSITY", "GAUSSIAN")
)

Arguments

spectraSearchDBs: character vector of the databases to search. The default is c("BIO", "massbank"). Other values can be found by running listDatabases().
peakDeviationPpm: numeric Maximum allowed mass deviation in ppm for matching peaks.
precursorDeviationPpm: numeric Maximum allowed mass deviation in ppm for matching the precursor. If not specified, the same value as for the peaks is used.
scoring: character The scoring function to use. Possible values are MODIFIED_COSINE, GAUSSIAN, INTENSITY. The default is MODIFIED_COSINE.

Value

An object of class spectraMatchingParam

Note

For more information, see the Sirius documentation.

Examples

# Example of setting up the parameters for spectra matching
param <- spectraMatchingParam(spectraSearchDBs = c("BIO", "massbank"),
                              peakDeviationPpm = 10,
                              precursorDeviationPpm = 10,
                              scoring = "MODIFIED_COSINE")