msmsWorkflow {RMassBank} | R Documentation

## RMassBank mass spectrometry pipeline

### Description

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

### Usage

    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)

### Arguments

`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

### Details

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.

### Value

The processed `msmsWorkspace`.

### Author(s)

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

### See Also

`msmsWorkspace-class`

[Package RMassBank version 2.8.0 Index]