MassSpecSettings_AnnotateFeatures_StreamFind

Settings for annotation of isotopic features. The method uses the maxIsotopes to define the maximum length of the isotopic chain. The list of candidate features is build with the rtWindowAlignment and the maximum mass increment to match the maximum chain length. Then, the mass difference of the natural isotopes defined by elements and a given monoisotopic ion (i.e., feature) are targeted. Each candidate is then evaluated according to the mass error and the expected relative intensity range as defined by the mode.

Usage

MassSpecSettings_AnnotateFeatures_StreamFind(
  maxIsotopes = 5,
  elements = c("C", "H", "N", "O", "S", "Cl", "Br"),
  mode = "small molecules",
  maxCharge = 1,
  rtWindowAlignment = 0.3,
  maxGaps = 1
)

Arguments

maxIsotopes

Numeric (length 1) with the maximum number of isotopic steps.

elements

Character vector with the elements to target the isotopic annotation. Possible elements are C, H, N, O, S, Cl, Br.

mode

Character (length 1) with the type of molecules to be targeted. For now, only "small molecules" are possible.

maxCharge

Numeric (length 1) with the maximum charge that ions can be ionized to find isotopes.

rtWindowAlignment

Numeric (length 1) with the proportion of the monoisotopic feature time window to be used for retrieving isotopic candidates.

maxGaps

Numeric (length 1) with the maximum of allowed gaps in isotopic chains.

Value

A ProcessingSettings S3 class object with subclass MassSpecSettings_AnnotateFeatures_StreamFind.