Match Ions by M/Z and Retention Time

Matches two lists of ions based on mass-to-charge ratio (m/z) and retention time (RT). Returns all matched pairs including multiple matches, with error values for each match.

Usage

match_mz_rt(
  mz1,
  rt1 = rep(NA, length(mz1)),
  mz2,
  rt2 = rep(NA, length(mz2)),
  mz.ppm = 10,
  rt.tol = Inf
)

Arguments

mz1

Numeric vector of m/z values for the first ion list.

rt1

Numeric vector of retention times for the first ion list. Default is NA values of same length as mz1.

mz2

Numeric vector of m/z values for the second ion list.

rt2

Numeric vector of retention times for the second ion list. Default is NA values of same length as mz2.

mz.ppm

Numeric tolerance for m/z matching in parts per million (ppm). Default is 10.

rt.tol

Numeric tolerance for retention time matching. Default is Inf (no RT filtering).

Value

A data.table with columns: ion1 (index in first list), ion2 (index in second list), mz.error (relative m/z error), and rt.error (absolute RT difference).

Details

Matching is done in two steps for efficiency:

1. match_mz_foverlaps finds m/z candidate pairs within mz.ppm using data.table::foverlaps() on ppm-expanded intervals (denominator mz1).

2. In data.table, absolute RT differences are computed and rows with rt.error < rt.tol (or NA RT error) are kept.

mz.error is the relative m/z error abs(mz1 - mz2) / mz1 (i.e. abs(mz.ppm) / 1e6 from match_mz_foverlaps), not ppm units. This function returns all surviving pairs; callers decide how to pick one match per ion (e.g. closest RT then m/z in get_Spectra_ms2_feature_id).

See also

match_mz_foverlaps, match_mz, get_Spectra_ms2_feature_id