cleanMGF: Clean an MGF file by keeping only formula-explainable peaks

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

Clean an MGF file by keeping only formula-explainable peaks

Description

For each MS2 spectrum, the precursor neutral mass is derived from PEPMASS, CHARGE and the supplied adduct, candidate parent formulae are enumerated with Rdisop, and fragment peaks that can be explained as sub-formulae of the best candidate (the one explaining the most peaks) are kept. Spectra without PEPMASS or without any candidate formula are written back unchanged.

Usage

cleanMGF(
  file,
  out_file = NULL,
  adduct = "[M+H]+",
  charge = NULL,
  mass_accuracy = 5,
  elements = "CHNOPS",
  max_candidates = 3,
  intensity_cutoff = 0,
  min_peaks = 2
)

Arguments

file	character. Path to an MGF file.
out_file	character. Output MGF path. Default NULL writes <file stem>_clean.mgf next to the input file.
adduct	character. Single adduct name (see HRMF), e.g. "[M+H]+". Fragments are assumed singly-charged with this adduct.
charge	integer. Precursor charge state used when the CHARGE header is missing. Default NULL uses 1 (from the adduct sign).
mass_accuracy	numeric. Mass accuracy in ppm for both precursor decomposition and fragment matching. Default 5.
elements	character. Elements allowed in precursor formula enumeration, e.g. "CHNOPS". Default "CHNOPS".
max_candidates	integer. Maximum number of precursor formula candidates to evaluate per spectrum. Default 3.
intensity_cutoff	numeric. Discard peaks below this absolute intensity before annotation. Default 0 (keep all).
min_peaks	integer. Drop spectra left with fewer than this many peaks after cleaning. Default 2.

Details

The cleaned file preserves the original header lines and peak line formatting; the chosen parent formula is appended as a FORMULA= header when a candidate is found.

Value

Invisibly, a data.frame with one row per spectrum: title, pepmass, charge, chosen formula, peak counts before/after, kept fraction and status ("cleaned", "kept" = unchanged, or "dropped").

See Also

HRMF, getMSP

Examples

## Not run: 
summary <- cleanMGF("ms2.mgf", adduct = "[M+H]+")
summary[, c("title", "formula", "n_before", "n_kept", "status")]

## End(Not run)

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