build.lcms.library: lib.search

View source: R/build.lcms.library.R

build.lcms.libraryR Documentation

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 May 21, 2024, 1:26 a.m.