findMsMsHR: Extract MS/MS spectra for specified precursor
In RMassBank: Workflow to process tandem MS files and build MassBank records

Description Usage Arguments Details Value Functions Note Author(s) See Also Examples

Extracts MS/MS spectra from LC-MS raw data for a specified precursor, specified either via the RMassBank compound list (see loadList) or via a mass.

findMsMsHR(
  fileName = NULL,
  msRaw = NULL,
  cpdID,
  mode = "pH",
  confirmMode = 0,
  useRtLimit = TRUE,
  ppmFine = getOption("RMassBank")$findMsMsRawSettings$ppmFine,
  mzCoarse = getOption("RMassBank")$findMsMsRawSettings$mzCoarse,
  fillPrecursorScan = getOption("RMassBank")$findMsMsRawSettings$fillPrecursorScan,
  rtMargin = getOption("RMassBank")$rtMargin,
  deprofile = getOption("RMassBank")$deprofile,
  headerCache = NULL,
  peaksCache = NULL,
  enforcePolarity = getOption("RMassBank")$enforcePolarity,
  diaWindows = getOption("RMassBank")$findMsMsRawSettings$diaWindows
)

findMsMsHR.mass(
  msRaw,
  mz,
  limit.coarse,
  limit.fine,
  rtLimits = NA,
  maxCount = NA,
  headerCache = NULL,
  fillPrecursorScan = FALSE,
  deprofile = getOption("RMassBank")$deprofile,
  peaksCache = NULL,
  cpdID = NA,
  polarity = NA,
  diaWindows = getOption("RMassBank")$findMsMsRawSettings$diaWindows
)

`fileName`	The file to open and search the MS2 spectrum in.
`msRaw`	The opened raw file (mzR file handle) to search the MS2 spectrum in. Specify either this or `fileName`.
`cpdID`	The compound ID in the compound list (see `loadList`) to use for formula lookup. Note: In \codefindMsMsHR.mass, this is entirely optional and used only in case a warning must be displayed; compound lookup is done via mass only.
`mode`	The processing mode (determines which ion/adduct is searched): `"pH", "pNa", "pM", "pNH4", "mH", "mM", "mFA"` for different ions ([M+H]+, [M+Na]+, [M]+, [M+NH4]+, [M-H]-, [M]-, [M+FA]-).
`confirmMode`	Whether to use the highest-intensity precursor (=0), second- highest (=1), third-highest (=2)...
`useRtLimit`	Whether to respect retention time limits from the compound list.
`ppmFine`	The limit in ppm to use for fine limit (see below) calculation.
`mzCoarse`	The coarse limit to use for locating potential MS2 scans: this tolerance is used when finding scans with a suitable precursor ion value.
`fillPrecursorScan`	If `TRUE`, the precursor scan will be filled from MS1 data. To be used for data where the precursor scan is not stored in the raw data.
`rtMargin`	The retention time tolerance to use.
`deprofile`	Whether deprofiling should take place, and what method should be used (cf. `deprofile`)
`headerCache`	If present, the complete `mzR::header(msRaw)`. Passing this value is useful if spectra for multiple compounds should be extracted from the same mzML file, since it avoids getting the data freshly from `msRaw` for every compound.
`peaksCache`	If present, the complete output of `mzR::peaks(msRaw)`. This speeds up the lookup if multiple compounds should be searched in the same file.
`diaWindows`	A data frame with columns `precursorMz`, `mzMin`, `mzMax` which specifies the precursor and window size of each window for DIA acquisition.
`mz`	The mass to use for spectrum search.
`limit.coarse`	Parameter in `findMsMsHR.mass` corresponding to `mzCoarse`. (The parameters are distinct to clearly conceptually distinguish findMsMsHR.mass (a standalone useful function) from the cpdID based functions (workflow functions).)
`limit.fine`	The fine limit to use for locating MS2 scans: this tolerance is used when locating an appropriate analyte peak in the MS1 precursor spectrum.
`rtLimits`	`c(min, max)`: Minimum and maximum retention time to use when locating the MS2 scans.
`maxCount`	The maximal number of spectra groups to return. One spectra group consists of all data-dependent scans from the same precursor whose precursor mass matches the specified search mass.

Different versions of the function get the data from different sources. Note that findMsMsHR and findMsMsHR.direct differ mainly in that findMsMsHR opens a file whereas findMsMs.direct uses an open file handle - both are intended to be used in a full process which involves compound lists etc. In contrast, findMsMsHR.mass is a low-level function which uses the mass directly for lookup and is intended for use as a standalone function in unrelated applications.

An RmbSpectraSet (for findMsMsHR). Contains parent MS1 spectrum (@parent), a block of dependent MS2 spectra ((@children) and some metadata (id,mz,name,mode in which the spectrum was acquired.

For findMsMsHR.mass: a list of RmbSpectraSets as defined above, sorted by decreasing precursor intensity.

findMsMsHR.mass: A submethod of find MsMsHR that retrieves basic spectrum data

findMsMs.direct is deactivated

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

findEIC

## Not run: 
			loadList("mycompoundlist.csv")
			# if Atrazine has compound ID 1:
			msms_atrazine <- findMsMsHR(fileName = "Atrazine_0001_pos.mzML", cpdID = 1, mode = "pH")
			# Or alternatively:
			msRaw <- openMSfile("Atrazine_0001_pos.mzML")
			msms_atrazine <- findMsMsHR(msRaw=msRaw, cpdID = 1, mode = "pH")
			# Or directly by mass (this will return a list of spectra sets):
			mz <- findMz(1)$mzCenter
			msms_atrazine_all <- findMsMsHR.mass(msRaw, mz, 1, ppm(msRaw, 10, p=TRUE))
			msms_atrazine <- msms_atrazine_all[[1]]

## End(Not run)