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Batch High Resolution Mass Filtering for all compounds in an MSP file

Source: R/hrmf.R
getHRMF.Rd

Applies HRMF to every compound in an MSP file that has a chemical formula annotation.

Usage

getHRMF(
  file,
  charge = 1,
  adduct = NULL,
  mass_accuracy = 5,
  intensity_cutoff = 1,
  IR_RelAb_cutoff = 1
)

Arguments

file

character. Path to an MSP file.

charge

integer. Charge state (see HRMF). Default 1. Ignored when adduct is supplied.

adduct

character vector of adduct names or named numeric vector of custom mass deltas (see HRMF). Default NULL.

mass_accuracy

numeric. Mass accuracy in ppm. Default 5.

intensity_cutoff

numeric. Minimum absolute intensity. Default 1.

IR_RelAb_cutoff

numeric. Relative abundance cutoff (%) for theoretical isotopologues. Default 1.

Value

A named list where each element contains the HRMF results for one compound (with a valid formula) from the MSP file.

See also

HRMF, getMSP

Examples

if (FALSE) { # \dontrun{
results <- getHRMF("library.msp")

# LC-MS/MS library with protonated ions
results <- getHRMF("library.msp", adduct = "[M+H]+")
} # }