@@ -45,9 +45,13 @@

  peaksCount(object, scans, ...)

- peaks(object, ...) 

+ \S4method{peaks}{mzRpwiz}(object, scans)

+ \S4method{peaks}{mzRramp}(object, scans)

+ \S4method{peaks}{mzRnetCDF}(object, scans)

- spectra(object, ...) ## same as peaks

+ \S4method{spectra}{mzRpwiz}(object, scans)   ## same as peaks

+ \S4method{spectra}{mzRramp}(object, scans)

+ \S4method{spectra}{mzRnetCDF}(object, scans)

  get3Dmap(object, scans, lowMz, highMz, resMz, ...)

@@ -66,7 +70,7 @@

   \item{object}{An instantiated \code{mzR} object.}

   \item{scans}{A \code{numeric} specifying which scans to

-    return. Optional for the \code{header}, \code{peaks}, \code{scans}

+    return. Optional for the \code{header}, \code{peaks}, \code{spectra}

     and \code{peaksCount} methods. If ommited, the requested data for

     all peaks is returned. }

@@ -177,7 +181,7 @@

  colnames(header(mz))

  close(mz)

- ## A shortgun LCMSMS experiment 

+ ## A shotgun LCMSMS experiment

  f <- proteomics(full.names = TRUE,

                  pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")

  x <- openMSfile(f, backend = "pwiz")

@@ -187,7 +191,10 @@

  head(chromatogram(x, 1L)) ## same as tic(x)

  str(chromatogram(x)) ## as a list

- ## An MRM experiment 

+ peaks(x) ## extract all peak information

+ peaks(x, scan=4) ## extract just peaks from the 4th scan

+

+ ## An MRM experiment

  f <- proteomics(full.names = TRUE, pattern = "MRM")

  x <- openMSfile(f, backend = "pwiz")

  x