MassSpecSettings_SuspectScreening_StreamFind — MassSpecSettings_SuspectScreening

Settings for performing suspect screening using a data.frame with target compounds.

Usage

MassSpecSettings_SuspectScreening_StreamFind(
  database = data.table::data.table(name = character(), formula = character(), mass =
    numeric()),
  ppm = 5,
  sec = 10,
  ppmMS2 = 10,
  minFragments = 3,
  isolationWindow = 1.3,
  mzClust = 0.003,
  presence = 0.8,
  minIntensity = 0,
  filtered = FALSE
)

Arguments

database: A data.frame with at least the columns name and mass, indicating the name and neutral monoisotopic mass of the suspect targets.
ppm: Numeric of length one with the mass deviation, in ppm.
sec: Numeric of length one with the time deviation, in seconds.
ppmMS2: Numeric (length 1) with the mass deviation for MS2, in ppm.
minFragments: Integer (length 1) with the minimum number of fragments.
isolationWindow: Numeric value with the isolation window (in Da) applied for ion isolation and fragmentation during acquisition of tandem data (i.e., MS2 data).
mzClust: Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.
presence: Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.
minIntensity: Numeric (length 1) with the minimum intensity.
filtered: Logical (length 1). When TRUE, filtered features/groups are considered.

Value

A MassSpecSettings_SuspectScreening_StreamFind object.