checkIsotopes: Checks for isotopes in a 'msmsWorkspace'

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

Checks for isotopes in a msmsWorkspace

Usage

checkIsotopes(
  w,
  mode = "pH",
  intensity_cutoff = 0,
  intensity_precision = "none",
  conflict = "strict",
  isolationWindow = 2,
  evalMode = "complete",
  plotSpectrum = TRUE,
  settings = getOption("RMassBank")
)

Arguments

w	A msmsWorkspace to work with.
mode	"pH", "pNa", "pM", "pNH4", "mH", "mM", "mFA" for different ions ([M+H]+, [M+Na]+, [M]+, [M+NH4]+, [M-H]-, [M]-, [M+FA]-).
intensity_cutoff	The cutoff (as an absolute intensity value) under which isotopic peaks shouldn't be checked for or accepted as valid. Please note: The cutoff is not hard in the sense that it interacts with the intensity_precision parameter.
intensity_precision	The difference that is accepted between the calculated and observed intensity of a possible isotopic peak. Further details down below.
conflict	Either "isotopic"(Peak formulas are always chosen if they fit the requirements for an isotopic peak) or "strict"(Peaks are only marked as isotopic when there hasn't been a formula assigned before.)
isolationWindow	Half of the width of the isolation window in Da
evalMode	Currently no function yet, but planned. Currently must be "complete"
plotSpectrum	A boolean specifiying whether the spectrumshould be plotted
settings	Options to be used for processing. Defaults to the options loaded via loadRmbSettings et al. Refer to there for specific settings.

Details

text describing parameter inputs in more detail.

• intensity_precisionThis parameter determines how strict the intensity values should adhere to the calculated intensity in relation to the parent peak. Options for this parameter are "none", where the intensity is irrelevant, "low", which has an error margin of 70% and "high", where the error margin is set to 35%. The recommended setting is "low", but can be changed to adjust to the intensity precision of the mass spectrometer.

Value

The msmsWorkspace with annotated isolation peaks

Author(s)

Michael Stravs, Eawag <[e-mail]>

Erik Mueller, UFZ

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.