msmsWorkflow: RMassBank mass spectrometry pipeline
In RMassBank: Workflow to process tandem MS files and build MassBank records

Description Usage Arguments Details Value Author(s) See Also

Extracts and processes spectra from a specified file list, according to loaded options and given parameters.

msmsWorkflow(
  w,
  mode = "pH",
  steps = c(1:8),
  confirmMode = FALSE,
  newRecalibration = TRUE,
  useRtLimit = TRUE,
  archivename = NA,
  readMethod = "mzR",
  findPeaksArgs = NULL,
  plots = FALSE,
  precursorscan.cf = FALSE,
  settings = getOption("RMassBank"),
  analyzeMethod = "formula",
  progressbar = "progressBarHook",
  MSe = FALSE
)

`w`	A `msmsWorkspace` to work with.
`mode`	`"pH", "pNa", "pM", "mH", "mM", "mFA", "pNH4"` for different ions ([M+H]+, [M+Na]+, [M]+, [M-H]-, [M]-, [M+FA]-, [M+NH4]+).
`steps`	Which steps of the workflow to process. See the vignette `vignette("RMassBank")` for details.
`confirmMode`	Defaults to false (use most intense precursor). Value 1 uses the 2nd-most intense precursor for a chosen ion (and its data-dependent scans) , etc.
`newRecalibration`	Whether to generate a new recalibration curve (`TRUE`, default) or to reuse the currently stored curve (`FALSE`, useful e.g. for adduct-processing runs.)
`useRtLimit`	Whether to enforce the given retention time window.
`archivename`	The prefix under which to store the analyzed result files.
`readMethod`	Several methods are available to get peak lists from the files. Currently supported are "mzR", "xcms", "MassBank" and "peaklist". The first two read MS/MS raw data, and differ in the strategy used to extract peaks. MassBank will read existing records, so that e.g. a recalibration can be performed, and "peaklist" just requires a CSV with two columns and the column header "mz", "int".
`findPeaksArgs`	A list of arguments that will be handed to the xcms-method findPeaks via do.call
`plots`	A parameter that determines whether the spectra should be plotted or not (This parameter is only used for the xcms-method)
`precursorscan.cf`	Whether to fill precursor scans. To be used with files which for some reasons do not contain precursor scan IDs in the mzML, e.g. AB Sciex converted files.
`settings`	Options to be used for processing. Defaults to the options loaded via `loadRmbSettings` et al. Refer to there for specific settings.
`analyzeMethod`	The "method" parameter to pass to `analyzeMsMs`.
`progressbar`	The progress bar callback to use. Only needed for specialized applications. Cf. the documentation of `progressBarHook` for usage.
`MSe`	A boolean value that determines whether the spectra were recorded using MSe or not

The filenames of the raw LC-MS runs are read from the array files in the global enviroment. See the vignette vignette("RMassBank") for further details about the workflow.

The processed msmsWorkspace.

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

msmsWorkspace-class

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