analyzeMsMs {RMassBank} | R Documentation |
Analyze MSMS spectra
Description
Analyzes MSMS spectra of a compound by fitting formulas to each subpeak.
Usage
analyzeMsMs(msmsPeaks, mode = "pH", detail = FALSE, run = "preliminary",
filterSettings = getOption("RMassBank")$filterSettings,
spectraList = getOption("RMassBank")$spectraList, method = "formula")
analyzeMsMs.formula(msmsPeaks, mode = "pH", detail = FALSE,
run = "preliminary",
filterSettings = getOption("RMassBank")$filterSettings)
analyzeMsMs.intensity(msmsPeaks, mode = "pH", detail = FALSE,
run = "preliminary",
filterSettings = getOption("RMassBank")$filterSettings)
Arguments
msmsPeaks |
A RmbSpectraSet object.
Corresponds to a parent spectrum and children MSMS spectra of one compound (plus some metadata).
The objects are typically generated with findMsMsHR , and populate the @spectrum slot
in a msmsWorkspace (refer to the corresponding
documentation for the precise format specifications).
|
mode |
Specifies the processing mode, i.e. which molecule species the
spectra contain. pH (positive H) specifies [M+H]+,
pNa specifies [M+Na]+, pM specifies [M]+,
mH and mNa specify [M-H]- and [M-Na]-,
respectively. (I apologize for the naming of pH which has
absolutely nothing to do with chemical pH values.)
|
detail |
Whether detailed return information should be provided
(defaults to FALSE ). See below.
|
run |
"preliminary" or "recalibrated" . In the
preliminary run, mass tolerance is set to 10 ppm (above m/z 120) and
15 ppm (below m/z 120), the default intensity cutoff is $10^4$ for positive
mode (no default cutoff in negative mode), and the column "mz" from
the spectra is used as data source. In the recalibrated run, the
mass tolerance is set to 5 ppm over the whole mass range, the default cutoff
is 0 and the column "mzRecal" is used as source for the m/z values.
Defaults to "preliminary" .
|
filterSettings |
Settings for the filter parameters, by default loaded from the RMassBank settings
set with e.g. loadRmbSettings . Must contain:
-
ppmHighMass , allowed ppm deviation before recalibration
for high mass range
-
ppmLowMass , allowed ppm deviation before recalibration
for low mass range
-
massRangeDivision , division point between high and low mass
range (before recalibration)
-
ppmFine , allowed ppm deviation overall after recalibration
-
prelimCut , intensity cutoff for peaks in preliminary run
-
prelimCutRatio , relative intensity cutoff for peaks in
preliminary run, e.g. 0.01 = 1
-
fineCut , intensity cutoff for peaks in second run
-
fineCutRatio , relative intensity cutoff for peaks in
second run
-
specOkLimit , minimum intensity of base peak for spectrum
to be accepted for processing
-
dbeMinLimit , minimum double bond equivalent for accepted
molecular subformula.
-
satelliteMzLimit , for satellite peak filtering
(filterPeakSatellites : mass window to use for satellite
removal
-
satelliteIntLimit , the relative intensity below which to
discard "satellites". (refer to filterPeakSatellites ).
|
spectraList |
The list of MS/MS spectra present in each data block. As also
defined in the settings file.
|
method |
Selects which function to actually use for data evaluation. The default
"formula" runs a full analysis via formula assignment to fragment peaks. The
alternative setting "intensity" calls a "mock" implementation which circumvents
formula assignment and filters peaks purely based on intensity cutoffs and the
satellite filtering. (In this case, the ppm and dbe related settings in filterSettings
are ignored.)
|
Details
The analysis function uses Rcdk. Note
that in this step, satellite peaks are removed by a simple heuristic
rule (refer to the documentation of filterPeakSatellites
for details.)
Value
The processed RmbSpectraSet
object.
Added (or filled, respectively, since the slots are present before) data include
list("complete") |
whether all spectra have useful value
|
list("empty") |
whether there are no useful spectra
|
list("children") |
The processed RmbSpectrum2 objects (in a RmbSpectrum2List ).
-
ok if the spectrum was successfully processed with at least one resulting peak
-
mz , intensity : note that mz/int pairs can be duplicated when multiple matches
are found for one mz value, therefore the two slots are not necessarily unchanged from before
-
rawOK (logical) whether the m/z peak passes satellite/low removal
-
low , satellite if TRUE , the peak failed cutoff (low ) or was removed as satellite
-
formula , mzCalc , dppm , dbe Formula, calculated mass, ppm deviation and dbe assigned to a peak
-
formulaCount , dppmBest Number of formulae matched for this m/z value and ppm deviation of the best match
-
info Spectrum identifying information (collision energy, resolution, collision mode) from
the spectraList
All other entries are retained from the original RmbSpectrum2 .
|
Functions
Author(s)
Michael Stravs
See Also
msmsWorkflow
, filterLowaccResults
,
filterPeakSatellites
, reanalyzeFailpeaks
Examples
## Not run: analyzed <- analyzeMsMs(spec, "pH", TRUE)
[Package
RMassBank version 2.8.0
Index]