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@@ -90,14 +90,15 @@
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will return a numeric of length \code{n}.
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The \code{\link{header}} function returns a list containing
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- \code{seqNum}, \code{acquisitionNum} , \code{msLevel},
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+ \code{seqNum}, \code{acquisitionNum}, \code{msLevel},
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\code{peaksCount}, \code{totIonCurrent}, \code{retentionTime} (in
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seconds), \code{basePeakMZ}, \code{basePeakIntensity},
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\code{collisionEnergy}, \code{ionisationEnergy}, \code{lowM},
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\code{highMZ}, \code{precursorScanNum}, \code{precursorMZ},
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\code{precursorCharge}, \code{precursorIntensity},
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\code{mergedScan}, \code{mergedResultScanNum},
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- \code{mergedResultStartScanNum} and \code{mergedResultEndScanNum},
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+ \code{mergedResultStartScanNum}, \code{mergedResultEndScanNum},
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+ \code{spectrumId} and
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\code{injectionTime} (ion injection time, in seconds) when available
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in the original file. If multiple scans are queried, a
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\code{data.frame} is returned with the scans reported along the
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@@ -128,6 +129,16 @@
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}
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+\note{
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+ Spectrum identifiers are only specified in \emph{mzML} files, thus,
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+ for all other file types the column \code{"spectrumId"} of the result
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+ \code{data.frame} returned by \code{header} contains \code{"scan="}
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+ followed by the acquisition number of the spectrum. Also, only the
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+ \code{pwiz} backend supports extraction of the spectras' IDs from
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+ \emph{mzML} files. Thus, only \emph{mzML} files read with
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+ \code{backend = "pwiz"} provide the spectrum IDs defined in the file.
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+}
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+
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\seealso{
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\code{\link{instrumentInfo}} for metadata access and the
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\code{"\linkS4class{mzR}"} class.
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