build.lcms.library: lib.search

In cbroeckl/csu.pmf.tools: a collection of features used internally at CSU PMF for non-targeted metabolomics data processing

lib.search

Description

spectral searching using Spectra::compare function(s)

Usage

build.lcms.library(
  lib.directory = NULL,
  ri.file.name = NULL,
  column = "T3",
  lib.name = "cannabinoids-t3",
  trim.to.precursor = TRUE,
  intensity.filter = NULL
)

Arguments

lib.directory	allowable product ion mass error in spectral matching in parts per million. generally, use ~ 15 for TOF, 500 for quad.
ri.file.name	allowable precursor ion mass error in spectral matching in parts per million. generally, use ~ 15 for TOF, 500 for quad. Note though that quad isolation is NOT accurate mass, so you could consider using a larger window to account for potential chimeric spectra.
column	retention time (or index) sigma for adjusting spectral match scores when retention similarity is used. use similarly to RAMClustR retention time similarity calculation.
lib.name	experimental spectra, as an R object of class 'Spectra' produced from the Spectra package
trim.to.precursor	logical. should MS/MS mass range be trimmed to below the precursor mass? If TRUE, values above the precursor mass + 4 m/z are discarded
get.pubchem	logical. should pubchem parameters be retrieved for inclusion in spectrum output? If TRUE, INCHIKEY, Smiles, formula, and a few other paramaters are added to the msp format. while NIST cannot use all these, R Spectra can import them.

Details

function for building an LC-MS precursor (or not) MS/MS library in msp format for convervion to NIST format or searching within R.

Value

nothing - exports an msp formatted file named lib.name.msp

Author(s)

Corey Broeckling

cbroeckl/csu.pmf.tools documentation built on Jan. 26, 2024, 6:27 p.m.