Skip to contents

MassSpecSettings_LoadFeaturesMS2_StreamFind

Source: R/class_S3_MassSpecSettings.R
MassSpecSettings_LoadFeaturesMS2_StreamFind.Rd

Settings for loading MS2 spectra for features.

Usage

MassSpecSettings_LoadFeaturesMS2_StreamFind(
  isolationWindow = 1.3,
  mzClust = 0.005,
  presence = 0.8,
  minIntensity = 10,
  filtered = FALSE
)

Arguments

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 ProcessingSettings S3 class object with subclass MassSpecSettings_LoadFeaturesMS2_StreamFind.