Build MS2 spectra target list (mz/rt windows) — get_MSdev_spectra_target

Extract MS2 spectra from object@spectra$MS2_Spectra and summarise them into a target table with mz, rt, rtmin, rtmax. If spectra are assigned to features (feature_id) and feature definitions contain MSIP annotations (compound_id, iso_form), targets can be grouped at compound or isotopologue level.

Usage

get_MSdev_spectra_target_list(
  object,
  prefer = c("assigned_feature", "all_ms2"),
  group_by = c("compound_iso", "compound", "feature", "none"),
  rt_expand = 0,
  mz_col = c("isolationWindowTargetMz", "precursorMz"),
  rt_col = c("rtime")
)

Arguments

object: MSdev object.
prefer: character, either "assigned_feature" (default; only MS2 with non-missing feature_id) or "all_ms2".
group_by: character, grouping strategy. One of "compound_iso", "compound", "feature", "none". When requested metadata are missing, it falls back to the next available level.
rt_expand: numeric, seconds added to both sides of the final RT window.
mz_col: candidate mz columns in spectraData; first match is used. Default prefers isolationWindowTargetMz, then precursorMz.
rt_col: candidate RT columns in spectraData; first match is used. Default is rtime (Spectra / XcmsExperiment naming).

Value

data.frame with columns mz, rt, rtmin, rtmax plus grouping columns when available.