checkIsotopes: Checks for isotopes in a 'msmsWorkspace'
In RMassBank: Workflow to process tandem MS files and build MassBank records

Description Usage Arguments Details Value Author(s)

Checks for isotopes in a msmsWorkspace

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

`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.

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.

The msmsWorkspace with annotated isolation peaks

Michael Stravs, Eawag <michael.stravs@eawag.ch>

Erik Mueller, UFZ

RMassBank documentation built on Nov. 8, 2020, 6:06 p.m.