Clean an MGF file by keeping only formula-explainable peaks

For each MS2 spectrum, the precursor neutral mass is derived from PEPMASS, CHARGE and the supplied adduct, candidate parent formulae are enumerated with the native HORIZON engine, 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.

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").

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.

Examples

if (FALSE) { # \dontrun{
summary <- cleanMGF("ms2.mgf", adduct = "[M+H]+")
summary[, c("title", "formula", "n_before", "n_kept", "status")]
} # }