metID.matchSpectralDB: match spectra to spectral databases in the .msp file format...

In WMBEdmands/compMS2Miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets

Description

match spectra to spectral databases in the .msp file format (NIST)

Usage

metID.matchSpectralDB(object, ...)

Arguments

object	A "compMS2" class object.
mspFile	character string to an online or local .msp spectrum database file. (default = NULL, dependendent on polarity either a positive or negative mode version of massbank hosted on github will be downloaded) See https://raw.githubusercontent.com/WMBEdmands/mspFiles/master/MassBank_MSMS_Pos_Rev173_vs1.msp and https://raw.githubusercontent.com/WMBEdmands/mspFiles/master/MassBank_MSMS_Neg_Rev173_vs1.msp. Additional .msp files can be downloaded from the massbank of North America website http://mona.fiehnlab.ucdavis.edu/downloads.
minDBDotProdThresh	minimum dot product spectral similarity score (default = 0.65).
ppmMS1	numeric minimum mass accuracy (ppm) between database (.msp) precursor masses and the CompMS2 composite spectrum MS1 m/z. Dot products will only be calculated for database entries within this mass accuracy threshold (default=10ppm).
binSizeMS2	numeric bin size for between database (.msp) fragment masses and the CompMS2 composite spectrum fragment ions (default = 0.1).
autoPossId	logical if TRUE and if the .msp file database entries contain at the very least a SMILES code (for downstream metabolite identification purposes) all msp file database entries will be added to the best annotations table. and the function will also automatically add the name of the best annotation (highest dot product score above the user defined threshold) to the comments table and a note ("metID.matchSpectralDB") added to the comments column. This represents a form of automated metabolite identification which can still be modified in the comments table upon visualization with compMS2Explorer.
verbose	logical if TRUE display progress bars.

Details

If the msp file contains smiles codes then any matches above the min dot prod or minimum proportion of the spectrum explained will be added to the best annotations table.

Value

"compMS2" class object with any database matches above the minimum dot product score.

WMBEdmands/compMS2Miner documentation built on May 9, 2019, 10:04 p.m.