clipscros.blogg.se - Spectra 1 part

[ and split, a set of filter functions areĭefined for Spectra objects (for detailed help please see Levels and retention times for the spectra in sps.Īpart from classical subsetting operations such as We use msLevel and rtime to access the MS These are part of the core variablesĭefining a spectrum and for all of these accessor methods exist. Spectra object sps, it contains more variables "id" and "name", that were specified for the The two Spectra contain a different set of variables: SpectraVariables ( sps_sciex ) # "msLevel" "rtime" # "acquisitionNum" "scanIndex" # "dataStorage" "dataOrigin" # "centroided" "smoothed" # "polarity" "precScanNum" # "precursorMz" "precursorIntensity" # "precursorCharge" "collisionEnergy" # "isolationWindowLowerMz" "isolationWindowTargetMz" # "isolationWindowUpperMz" "peaksCount" # "totIonCurrent" "basePeakMZ" # "basePeakIntensity" "ionisationEnergy" # "lowMZ" "highMZ" # "mergedScan" "mergedResultScanNum" # "mergedResultStartScanNum" "mergedResultEndScanNum" # "injectionTime" "filterString" # "spectrumId" "ionMobilityDriftTime" # "scanWindowLowerLimit" "scanWindowUpperLimit" Section Backends for more details on backends Keeps only a subset of spectra variables in memory while reading the m/zĪnd intensity values from the original data files only on demand. This backend, specifically designed for raw MS data, MsBackendMzR backend to store the data (note that Spectra object from two mzML files and define to use a Spectrometry raw files in mzML/mzXML or CDF format. 18 more variables/columns.Īlternatively, it is possible to import spectra data from mass Library ( Spectra ) spd # 1 2 NA NA # 2 2 NA NA # 3 2 NA NA #. Also, some only make sense for MSn, but not for smoothed logical(1): whether the spectrum wasįor details on the individual variables and their getter/setterįunction see the help for Spectra ( ?Spectra).Īlso note that these variables are suggested, but not required toĬharacterize a spectrum.

scanIndex integer(1): the index of a spectrum.

rtime numeric(1): the retention time of a.

precursorIntensity numeric(1): the intensity.

precursorCharge integer(1): the charge of the.

Number of the precursor for an MSn spectrum.

precScanNum integer(1): the scan (acquisition).

Spectrum ( 0 and 1 representing negative and

polarity integer(1): the polarity of the.

mz numeric: the m/z values for the spectrum’s.

msLevel integer(1): the MS level of the.

isolationWindowUpperMz numeric(1): upper m/z.

M/z for the isolation window in which the (MSn) spectrum was

isolationWindowTargetMz numeric(1): the target.

isolationWindowLowerMz numeric(1): lower m/zįor the isolation window in which the (MSn) spectrum was measured.

intensity numeric: intensity values for the.

Where the spectrum’s peak data is stored. MsBackendHdf5Peaks it will be the name of the HDF5 file

dataStorage character(1): the (current).

Of the spectrum’s data, e.g. the mzML file from which it was read.

collisionEnergy numeric(1): collision energy.

centroided logical(1): whether the spectrum is.

acquisitionNum integer(1): the index ofĪcquisition of a spectrum during a MS run.

The core variables and their data type are (alphabetically ordered): Returned by it (or NA if the information is not available). Have their own accessor method and it is guaranteed that a value is (such as MS level or retention time) an arbitrary number of optional Of as a list of individual spectra, with each spectrum having a set of

Mass spectrometry data in Spectra objects can be thought