HRMF: High Resolution Mass Filtering (HRMF) for GC/LC HRMS data

In enviGCMS: GC/LC-MS Data Analysis for Environmental Science

High Resolution Mass Filtering (HRMF) for GC/LC HRMS data

Description

Performs high-resolution mass filtering by matching experimental mass spectral peaks against theoretical isotope patterns derived from one or more candidate chemical formulae. Calculates forward HRMF score, reverse (MSP) score, and Figure of Merit (FoM) for each candidate.

Usage

HRMF(
  msp,
  formula,
  charge = 1,
  adduct = NULL,
  mass_accuracy = 5,
  intensity_cutoff = 1,
  IR_RelAb_cutoff = 1,
  detailed = FALSE
)

Arguments

msp	list. A single compound entry as returned by getMSP, containing at least a spectra element with columns mz and intensity.
formula	character vector. One or more candidate chemical formulae to evaluate.
charge	integer. Charge state: 1 for positive, -1 for negative, 0 for neutral. Default 1 (radical cation in EI). Ignored when adduct is supplied.
adduct	character vector of adduct names for singly-charged ESI ions (e.g. "[M+H]+", c("[M+H]+", "[M+Na]+")), or a named numeric vector of custom mass deltas in Da with names ending in "+" or "-" (e.g. c("[M+MeOH]+" = 33.033491)). Default NULL keeps the legacy radical-ion/neutral behaviour governed by charge. Built-in adducts: "[M+H]+", "[M+Na]+", "[M+NH4]+", "[M+K]+", "[M+H-H2O]+", "[M-H]-", "[M+Cl]-", "[M+HCOO]-", "[M+CH3COO]-".
mass_accuracy	numeric. Mass accuracy in ppm. Default 5.
intensity_cutoff	numeric. Minimum absolute intensity to retain a peak. Default 1.
IR_RelAb_cutoff	numeric. Relative abundance cutoff (%) for theoretical isotopologues. Default 1.
detailed	logical. If TRUE, return detailed list with all_ions, compound, and HRMF_scores for each formula. If FALSE (default), return a summary data.frame.

Details

The method is based on Kwiecien et al. (2015) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/acs.analchem.5b01503")}.

Unlike the original MSxplorer implementation, this version uses Rdisop (already a dependency of enviGCMS) for both formula decomposition and isotope pattern calculation, instead of rcdk/rJava/enviPat, requiring no additional dependencies.

The input msp should be a single entry from the list returned by getMSP. For batch processing of entire MSP files, see getHRMF.

For EI (GC-MS) radical ions use the default charge argument. For ESI (LC-MS/MS) data with even-electron adduct ions such as [M+H]+ or [M-H]-, supply adduct so that fragment m/z values are converted internally; the adduct should describe how fragment ions are formed (usually the same as the precursor adduct for singly-charged fragmentation).

Value

If detailed = FALSE, a data.frame with one row per candidate formula (and per adduct, if supplied) and columns: Candidate, Adduct, peak_count_forw, df_theortomsp, HRMF_theor_score, peak_count_rev, df_msptotheor, HRMF_msp_score, FoM. If detailed = TRUE, a named list of detailed results per formula/adduct.

See Also

getHRMF for batch processing, getMSP for reading MSP files.

Examples

## Not run: 
# Read MSP file and run HRMF on the first compound (EI radical cation)
msp_data <- getMSP("spectrum.msp")
result <- HRMF(msp_data[[1]], formula = "C8H11NO")

# Compare multiple candidates
result <- HRMF(msp_data[[1]], formula = c("C8H11NO", "C7H9NO2"))

# LC-MS/MS with protonated fragments
result <- HRMF(msp_data[[1]], formula = "C8H10N4O2", adduct = "[M+H]+")

# Multiple candidate adducts are scored separately
result <- HRMF(msp_data[[1]], formula = "C8H10N4O2",
               adduct = c("[M+H]+", "[M+Na]+"))

## End(Not run)

enviGCMS documentation built on Oct. 7, 2026, 5:07 p.m.