Filter MSP entries — filter_msp

Should be used after parseMSP_to_list() to filter entries and MS2 spectra based on a set of parameters.#'

Usage

filter_msp_entries(
  msp_entries,
  minimumIntensityOfMaximalMS2peak = 2000,
  minimumProportionOfMS2peaks = 0.05,
  neutralLossesPrecursorToFragments = T,
  neutralLossesFragmentsToFragments = F,
  mz_tol = 0.17,
  min_frag_nb = 2,
  min_intensity = 500
)

Arguments

msp_entries: list of MSP entries created with parseMSP_to_list()
minimumIntensityOfMaximalMS2peak: numeric(1) Spectra entries with a maximum intensity below this value are removed.
minimumProportionOfMS2peaks: numeric(1) Between 0 and 1. Within a spectra, fragments with an intensity below this proportion of the maximum intensity fragment are removed.
neutralLossesPrecursorToFragments: boolean Should neutral losses to precursor be calculated.
neutralLossesFragmentsToFragments: boolean Should neutral losses for each fragment pair be calculated.
mz_tol: numeric(1) tolerance used for matching precursor fragment.
min_frag_nb: numeric(1) minimum number of fragments needed to include spectrum
min_intensity: numeric(1) minimum intensity to include fragment

Value

list of spectra object, and stats