MassSpecSettings_AnnotateFeatures_StreamFind

Settings for annotation of isotopic and adduct 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 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. Adducts are annotated by the mass difference of the monoisotopic ion and the adduct ion. Elements considered for annotation of isotopes are C, H, N, O, S, Cl, Br and Si, which are the most relevent for organic molecules. The adducts considered are Na+, K+, NH4+, CH3OH+, DMSO+, CH3CN+ for positive ionization and Cl-,Br-, -2H+Na, -2H+K, CHO2- and CH3COO- for negative ionization. In-source fragments are not yet annotated in the current version but planned.

Usage

MassSpecSettings_AnnotateFeatures_StreamFind(
  rtWindowAlignment = 0.3,
  maxIsotopes = 8,
  maxCharge = 1,
  maxGaps = 1
)

Arguments

rtWindowAlignment

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

maxIsotopes

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

maxCharge

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

maxGaps

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

Value

A MassSpecSettings_AnnotateFeatures_StreamFind object.