docs: address Mar's comments and fix documentation

DESCRIPTION

@@ -72,6 +72,7 @@ VignetteBuilder: knitr
 BugReports: https://github.com/RforMassSpectrometry/Spectra/issues
 URL: https://github.com/RforMassSpectrometry/Spectra
 biocViews: Infrastructure, Proteomics, MassSpectrometry, Metabolomics
+Encoding: UTF-8
 RoxygenNote: 7.3.1
 Roxygen: list(markdown=TRUE)
 Collate:

R/Spectra-estimatePrecursorMz.R

@@ -14,11 +14,12 @@
 #' m/z of a fragment spectrum using the following approach: in data dependent
 #' acquisition (DDA) mode, the MS instrument will select ions with the highest
 #' intensities in one MS scan for fragmentation. Thus, for each fragment
-#' spectrum, this method identifies the peak with the highest intensity and
-#' an m/z value similar to the fragment spectrum's reported precursor m/z
-#' (given parameters `tolerance` and `ppm`). This m/z value is then reported.
-#' Since the fragment spectrum's potential MS1 mass peak is selected based on
-#' its intensity, this method should **only be used for DDA data**.
+#' spectrum, this method identifies in the previous MS1 spectrum the peak with
+#' the highest intensity and an m/z value similar to the fragment spectrum's
+#' reported precursor m/z (given parameters `tolerance` and `ppm`). This m/z
+#' value is then reported. Since the fragment spectrum's potential MS1 mass
+#' peak is selected based on its intensity, this method should **only be used
+#' for DDA data**.
 #'
 #' @note
 #'
@@ -73,6 +74,10 @@
 #' identical(precursorMz(s), pmz)
 #' all.equal(precursorMz(s), pmz)
 #'
+#' ## Plot also the difference of m/z values against the m/z value
+#' plot(precursorMz(s), precursorMz(s) - pmz, xlab = "precursor m/z",
+#'     ylab = "difference reported - estimated precursor m/z")
+#'
 #' ## we could then replace the reported precursor m/z values
 #' s$precursorMz <- pmz
 estimatePrecursorMz <- function(object, tolerance = 0.3, ppm = 10,