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XCMS MS1 annotation helpers

xcms_extension_annotation.Rd

Matches features in an XCMSnExp object to compounds in a CompoundDb database using m/z and retention time tolerance. Calculates adduct masses for each compound and finds matches within specified ppm error. Results are stored as candidate lists in featureDefinitions.

Match xcms features to compound databases by MS1 m/z and retention time.

Usage

xcms_get_feature_ms1_candidate(
  xcms.xcms,
  cpdb,
  mz.ppm = 10,
  rt.tol = Inf,
  selected_adduct = MSCC::adduct.table$Adduct,
  ...
)

Arguments

xcms.xcms

XCMSnExp object with feature definitions.

cpdb

CompoundDb object containing compound database.

mz.ppm

Numeric. Mass accuracy tolerance in parts per million (default 10).

rt.tol

Numeric. Retention time tolerance in seconds (default Inf, no RT filtering).

selected_adduct

Character vector of adducts to consider (default from MSCC::adduct.table$Adduct).

...

Additional arguments passed to internal functions.

Value

XCMSnExp object with featureDefinitions updated with candidate.id, candidate.formula, candidate.adduct, and candidate.mz columns.

Functions

  • xcms_get_feature_ms1_candidate(): match features to compound database