Last chance! 50% off unlimited learning
Sale ends in
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, retrieval = "standard")
findMsMsHR.mass(msRaw, mz, limit.coarse, limit.fine, rtLimits = NA, maxCount = NA, headerCache = NULL, fillPrecursorScan = FALSE, deprofile = getOption("RMassBank")$deprofile, peaksCache = NULL, cpdID = NA)fileName.loadList)
to use for formula lookup. Note: In \codefindMsMsHR.mass, this is entirely optional and
used only in case a warning must be displayed; compound lookup is done via mass only."pH", "pNa", "pM", "pNH4", "mH", "mM", "mFA" for different ions
([M+H]+, [M+Na]+, [M]+, [M+NH4]+, [M-H]-, [M]-, [M+FA]-).TRUE, the precursor scan will be filled from MS1 data.
To be used for data where the precursor scan is not stored in the raw data.deprofile)mzR::header(msRaw). Passing
this value is useful if spectra for multiple compounds should be
extracted from the same mzML file, since it avoids getting the data
freshly from msRaw for every compound.mzR::peaks(msRaw). This speeds up the lookup
if multiple compounds should be searched in the same file.findMsMsHR.mass corresponding to mzCoarse.
(The parameters are distinct to clearly conceptually distinguish findMsMsHR.mass
(a standalone useful function) from the cpdID based functions (workflow functions).)c(min, max): Minimum and maximum retention time to use
when locating the MS2 scans.RmbSpectraSet (for findMsMsHR). Contains parent MS1 spectrum (@parent), a block of dependent MS2 spectra ((@children)
and some metadata (id,mz,name,mode in which the spectrum was acquired.For findMsMsHR.mass: a list of RmbSpectraSets as defined above, sorted
by decreasing precursor intensity.
findMsMsHR.mass: A submethod of find MsMsHR that retrieves basic spectrum data
## Not run:
# loadList("mycompoundlist.csv")
# # if Atrazine has compound ID 1:
# msms_atrazine <- findMsMsHR(fileName = "Atrazine_0001_pos.mzML", cpdID = 1, mode = "pH")
# # Or alternatively:
# msRaw <- openMSfile("Atrazine_0001_pos.mzML")
# msms_atrazine <- findMsMsHR(msRaw=msRaw, cpdID = 1, mode = "pH")
# # Or directly by mass (this will return a list of spectra sets):
# mz <- findMz(1)$mzCenter
# msms_atrazine_all <- findMsMsHR.mass(msRaw, mz, 1, ppm(msRaw, 10, p=TRUE))
# msms_atrazine <- msms_atrazine_all[[1]]
# ## End(Not run)
Run the code above in your browser using DataLab