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@@ -129,6 +129,19 @@
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}
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+\details{
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+ The column \code{acquisitionNum} in the \code{data.frame} returned by
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+ the \code{header} method contains the index during the scan in which
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+ the signal from the spectrum was measured. The \code{pwiz} backend
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+ extracts this number from the spectrum's ID provided in the mzML
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+ file. In contrast, column \code{seqNum} contains the index of each
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+ spectrum within the file and is thus consecutively numbered. Spectra
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+ from files with multiple MS levels are linked to each other \emp{via}
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+ their \code{acquisitionNum}: column \code{precursorScanNum} of an e.g. MS
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+ level 2 spectrum contains the \code{acquisitionNum} of the related MS
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+ level 1 spectrum.
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+}
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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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