diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index 6372778e..09338ee6 100644
--- a/.github/workflows/check-bioc.yml
+++ b/.github/workflows/check-bioc.yml
@@ -54,8 +54,8 @@ jobs:
       matrix:
         config:
           - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'next', bioc: '3.19'}
-          - { os: windows-latest, r: 'next', bioc: '3.19'}
+          - { os: macOS-latest, r: '4.4', bioc: 'devel'}
+          - { os: windows-latest, r: '4.4', bioc: 'devel'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -141,15 +141,15 @@ jobs:
           ## required for ncdf4
           ## brew install netcdf ## Does not work as it is compiled with gcc
           ## Use pre-compiled libraries from https://mac.r-project.org/libs-4/
-          curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz
-          tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C /
-          rm netcdf-4.7.4-darwin.17-x86_64.tar.gz
-          curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz
-          tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C /
-          rm hdf5-1.12.0-darwin.17-x86_64.tar.gz
-          curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz
-          tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C /
-          rm szip-2.1.1-darwin.17-x86_64.tar.gz
+          # curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz
+          # tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C /
+          # rm netcdf-4.7.4-darwin.17-x86_64.tar.gz
+          # curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz
+          # tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C /
+          # rm hdf5-1.12.0-darwin.17-x86_64.tar.gz
+          # curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz
+          # tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C /
+          # rm szip-2.1.1-darwin.17-x86_64.tar.gz
 
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
diff --git a/DESCRIPTION b/DESCRIPTION
index e700676d..e370ec7e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.3.0
+Version: 4.3.1
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,
diff --git a/NAMESPACE b/NAMESPACE
index 1592c843..3b122388 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -580,6 +580,7 @@ importFrom("MsExperiment", "sampleData<-")
 importFrom("MsExperiment", "sampleData")
 importFrom("MsExperiment", "readMsExperiment")
 importMethodsFrom("MsExperiment", "spectra<-")
+export("plotPrecursorIons")
 
 importFrom("progress", "progress_bar")
 
diff --git a/NEWS.md b/NEWS.md
index 6d0da0e0..ecb3f7b3 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,10 +1,20 @@
+# xcms 4.3
+
+## Changes in version 4.3.1
+
+- Support excluding samples or sample groups from defining features with
+  *PeakDensity* correspondence analysis (issue #742).
+- Add `plotPrecursorIons()` function.
+- Fix in `dropFeatureDefinitions()` that was not correctly removing additional
+  metadata from gap-filled chromatographic peaks.
+
+
 # xcms 4.1
 
 ## Changes in version 4.1.14
 
 - Fix for issue #734. XIC plot is is now working with MS2 Data.
 
-
 ## Changes in version 4.1.13
 
 - Add parameter `rtimeDifferenceThreshold` to `ObiwarpParam` allowing to
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index ec2cb71d..fbf47a96 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -1319,7 +1319,15 @@ setGeneric("group", function(object, ...) standardGeneric("group"))
 #'   representing the m/z dependent measurement error of some MS instruments).
 #'   All peaks (from the same or from different samples) with their apex
 #'   position being close on the retention time axis are grouped into a LC-MS
-#'   feature. See in addition [do_groupChromPeaks_density()] for the core API
+#'   feature. Only samples with non-missing sample group assignment (i.e. for
+#'   which the value provided with parameter `sampleGroups` is different than
+#'   `NA`) are considered and counted for the feature definition. This allows
+#'   to exclude certain samples or groups (e.g. blanks) from the feature
+#'   definition avoiding thus features with only detected peaks in these. Note
+#'   that this affects only the **definition** of **new** features.
+#'   Chromatographic peaks in these samples will still be assigned to features
+#'   which were defined based on the other samples.
+#'   See in addition [do_groupChromPeaks_density()] for the core API
 #'   function.
 #'
 #' - `NearestPeaksParam`: performs peak grouping based on the proximity of
@@ -1399,11 +1407,13 @@ setGeneric("group", function(object, ...) standardGeneric("group"))
 #'
 #' @param sampleGroups For `PeakDensityParam`: A vector of the same length than
 #'     samples defining the sample group assignments (i.e. which samples
-#'     belong to which sample
-#'     group). This parameter is mandatory for the `PeakDensityParam`
-#'     and has to be provided also if there is no sample grouping in the
-#'     experiment (in which case all samples should be assigned to the
-#'     same group).
+#'     belong to which sample group). This parameter is mandatory for
+#'     `PeakDensityParam` and has to be defined also if there is no sample
+#'     grouping in the experiment (in which case all samples should be
+#'     assigned to the same group). Samples for which a `NA` is provided will
+#'     not be considered in the feature definitions step. Providing `NA` for
+#'     all blanks in an experiment will for example avoid features to be
+#'     defined for signals (chrom peaks) present only in blank samples.
 #'
 #' @param value Replacement value for `<-` methods.
 #'
diff --git a/R/XcmsExperiment-plotting.R b/R/XcmsExperiment-plotting.R
index e657f751..ed16537b 100644
--- a/R/XcmsExperiment-plotting.R
+++ b/R/XcmsExperiment-plotting.R
@@ -406,3 +406,73 @@ setMethod(
         }
     }
 }
+
+#' @title General visualization of precursor ions of LC-MS/MS data
+#'
+#' @description
+#'
+#' Simple visualization of the position of fragment spectra's precursor ion
+#' in the MS1 retention time by m/z area.
+#'
+#' @param x `MsExperiment` of LC-MS/MS data.
+#'
+#' @param pch `integer(1)` defining the symbol/point type to be used to draw
+#'     points. See [points()] for details. Defaults to `pch = 21` which allows
+#'     defining the background and border color for points.
+#'
+#' @param col the color to be used for all data points. Defines the border
+#'     color if `pch = 21`.
+#'
+#' @param bg the background color (if `pch = 21`).
+#'
+#' @param xlab `character(1)` defining the x-axis label.
+#'
+#' @param ylab `character(1)` defining the y-axis label.
+#'
+#' @param main Optional `character(1)` with the title for **every** plot. If
+#'     not provided (the default) the base file name will be used for each
+#'     sample.
+#'
+#' @param ... additional parameters to be passed to the `plot` calls.
+#'
+#' @importFrom grDevices n2mfrow
+#'
+#' @export
+#'
+#' @author Johannes Rainer
+#'
+#' @md
+#'
+#' @examples
+#'
+#' ## Load a test data file with DDA LC-MS/MS data
+#' library(MsExperiment)
+#' fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
+#' pest_dda <- readMsExperiment(fl)
+#'
+#' plotPrecursorIons(pest_dda)
+#' grid()
+#'
+#' ## Subset the data object to plot the data specifically for one or
+#' ## selected file/sample:
+#' plotPrecursorIons(pest_dda[1L])
+plotPrecursorIons <- function(x, pch = 21, col = "#00000080",
+                              bg = "#00000020", xlab = "retention time",
+                              ylab = "m/z", main = character(), ...) {
+    if (!inherits(x, "MsExperiment"))
+        stop("'x' should be a 'MsExperiment' object or an object of a ",
+             "class extending it.")
+    par(mfrow = n2mfrow(length(x)))
+    for (i in seq_along(x)) {
+        x_sub <- x[i]
+        rtr <- range(rtime(spectra(x_sub)))
+        mzr <- range(range(mz(filterEmptySpectra(spectra(x_sub)))))
+        pmz <- precursorMz(spectra(x_sub))
+        prt <- rtime(spectra(x_sub)[!is.na(pmz)])
+        pmz <- pmz[!is.na(pmz)]
+        if (!length(main))
+            main <- basename(dataOrigin(spectra(x_sub)[1L]))
+        plot(prt, pmz, xlim = rtr, ylim = mzr, pch = pch, col = col, bg = bg,
+             xlab = xlab, ylab = ylab, main = main[1L], ...)
+    }
+}
diff --git a/R/XcmsExperiment.R b/R/XcmsExperiment.R
index 1c86f049..356edbce 100644
--- a/R/XcmsExperiment.R
+++ b/R/XcmsExperiment.R
@@ -206,6 +206,9 @@
 #' - `plotChromPeaks`: indicate identified chromatographic peaks from one
 #'   sample in the RT-m/z space. See [plotChromPeaks()] for details.
 #'
+#' - `plotPrecursorIons`: general visualization of precursor ions of
+#'   LC-MS/MS data. See [plotPrecursorIons()] for details.
+#'
 #' - `refineChromPeaks`: *refines* identified chromatographic peaks in `object`.
 #'   See [refineChromPeaks()] for details.
 #'
@@ -1553,9 +1556,8 @@ setMethod(
             object@processHistory, type = .PROCSTEP.PEAK.GROUPING, num = 1L)
         object@featureDefinitions <- .empty_feature_definitions()
         if (.hasFilledPeaks(object)) {
-            object@chromPeaks <- object@chromPeaks[
-                                            !object@chromPeakData$is_filled, ,
-                                            drop = FALSE]
+            object <- .filter_chrom_peaks(
+                object, which(!.chromPeakData(object)$is_filled))
             object@processHistory <- dropProcessHistoriesList(
                 object@processHistory, type = .PROCSTEP.PEAK.FILLING)
         }
diff --git a/R/do_groupChromPeaks-functions.R b/R/do_groupChromPeaks-functions.R
index 1170ef44..85087eab 100644
--- a/R/do_groupChromPeaks-functions.R
+++ b/R/do_groupChromPeaks-functions.R
@@ -113,8 +113,11 @@ do_groupChromPeaks_density <- function(peaks, sampleGroups,
              paste0("'", .reqCols[!.reqCols %in% colnames(peaks)],"'",
                     collapse = ", "), " not found in 'peaks' parameter")
 
-    sampleGroups <- as.character(sampleGroups)
-    sampleGroupNames <- unique(sampleGroups)
+    ## With a `factor` we also support excluding samples/groups, i.e. samples
+    ## with an NA are not considered in the feature definition.
+    if (!is.factor(sampleGroups))
+        sampleGroups <- factor(sampleGroups)
+    sampleGroupNames <- levels(sampleGroups)
     sampleGroupTable <- table(sampleGroups)
     nSampleGroups <- length(sampleGroupTable)
 
@@ -160,15 +163,12 @@ do_groupChromPeaks_density <- function(peaks, sampleGroups,
             pb$tick()
         if (endIdx - startIdx < 0)
             next
-        resL[[i]] <- .group_peaks_density(peaks[startIdx:endIdx, , drop = FALSE],
-                                          bw = bw, densFrom = densFrom,
-                                          densTo = densTo, densN = densN,
-                                          sampleGroups = sampleGroups,
-                                          sampleGroupTable = sampleGroupTable,
-                                          minFraction = minFraction,
-                                          minSamples = minSamples,
-                                          maxFeatures = maxFeatures,
-                                          sleep = sleep)
+        resL[[i]] <- .group_peaks_density(
+            peaks[startIdx:endIdx, , drop = FALSE], bw = bw,
+            densFrom = densFrom, densTo = densTo, densN = densN,
+            sampleGroups = sampleGroups, sampleGroupTable = sampleGroupTable,
+            minFraction = minFraction, minSamples = minSamples,
+            maxFeatures = maxFeatures, sleep = sleep)
     }
     res <- do.call(rbind, resL)
     if (nrow(res)) {
diff --git a/R/functions-Params.R b/R/functions-Params.R
index cbf00d36..d790162c 100644
--- a/R/functions-Params.R
+++ b/R/functions-Params.R
@@ -236,9 +236,8 @@ CentWavePredIsoParam <- function(ppm = 25, peakwidth = c(20, 50), snthresh = 10,
 PeakDensityParam <- function(sampleGroups = numeric(), bw = 30,
                              minFraction = 0.5, minSamples = 1,
                              binSize = 0.25, ppm = 0, maxFeatures = 50) {
-    if (length(sampleGroups) == 0 | any(is.na(sampleGroups)))
-        stop("Argument 'sampleGroups' has to be defined. It should not ",
-             "contain 'NA's")
+    if (length(sampleGroups) == 0)
+        stop("Argument 'sampleGroups' has to be defined.")
     new("PeakDensityParam", sampleGroups = sampleGroups, bw = bw,
         minFraction = minFraction, minSamples = minSamples,
         binSize = binSize, ppm = ppm, maxFeatures = maxFeatures)
diff --git a/man/XcmsExperiment.Rd b/man/XcmsExperiment.Rd
index de7e1c35..f7676365 100644
--- a/man/XcmsExperiment.Rd
+++ b/man/XcmsExperiment.Rd
@@ -580,6 +580,8 @@ peaks per file along the retention time. See \code{\link[=plotChromPeakImage]{pl
 details.
 \item \code{plotChromPeaks}: indicate identified chromatographic peaks from one
 sample in the RT-m/z space. See \code{\link[=plotChromPeaks]{plotChromPeaks()}} for details.
+\item \code{plotPrecursorIons}: general visualization of precursor ions of
+LC-MS/MS data. See \code{\link[=plotPrecursorIons]{plotPrecursorIons()}} for details.
 \item \code{refineChromPeaks}: \emph{refines} identified chromatographic peaks in \code{object}.
 See \code{\link[=refineChromPeaks]{refineChromPeaks()}} for details.
 }
diff --git a/man/do_groupChromPeaks_density.Rd b/man/do_groupChromPeaks_density.Rd
index 739e915c..6befbddd 100644
--- a/man/do_groupChromPeaks_density.Rd
+++ b/man/do_groupChromPeaks_density.Rd
@@ -27,11 +27,13 @@ the index of the sample in which the peak was found.}
 
 \item{sampleGroups}{For \code{PeakDensityParam}: A vector of the same length than
 samples defining the sample group assignments (i.e. which samples
-belong to which sample
-group). This parameter is mandatory for the \code{PeakDensityParam}
-and has to be provided also if there is no sample grouping in the
-experiment (in which case all samples should be assigned to the
-same group).}
+belong to which sample group). This parameter is mandatory for
+\code{PeakDensityParam} and has to be defined also if there is no sample
+grouping in the experiment (in which case all samples should be
+assigned to the same group). Samples for which a \code{NA} is provided will
+not be considered in the feature definitions step. Providing \code{NA} for
+all blanks in an experiment will for example avoid features to be
+defined for signals (chrom peaks) present only in blank samples.}
 
 \item{bw}{For \code{PeakDensityParam}: \code{numeric(1)} defining the bandwidth
 (standard deviation ot the smoothing kernel) to be used. This argument
diff --git a/man/do_groupChromPeaks_nearest.Rd b/man/do_groupChromPeaks_nearest.Rd
index 085f1bc1..92c29185 100644
--- a/man/do_groupChromPeaks_nearest.Rd
+++ b/man/do_groupChromPeaks_nearest.Rd
@@ -23,11 +23,13 @@ the index of the sample in which the peak was found.}
 
 \item{sampleGroups}{For \code{PeakDensityParam}: A vector of the same length than
 samples defining the sample group assignments (i.e. which samples
-belong to which sample
-group). This parameter is mandatory for the \code{PeakDensityParam}
-and has to be provided also if there is no sample grouping in the
-experiment (in which case all samples should be assigned to the
-same group).}
+belong to which sample group). This parameter is mandatory for
+\code{PeakDensityParam} and has to be defined also if there is no sample
+grouping in the experiment (in which case all samples should be
+assigned to the same group). Samples for which a \code{NA} is provided will
+not be considered in the feature definitions step. Providing \code{NA} for
+all blanks in an experiment will for example avoid features to be
+defined for signals (chrom peaks) present only in blank samples.}
 
 \item{mzVsRtBalance}{For \code{NearestPeaksParam}: \code{numeric(1)} representing the
 factor by which m/z values are multiplied before calculating the
diff --git a/man/do_groupPeaks_mzClust.Rd b/man/do_groupPeaks_mzClust.Rd
index dba42f79..48eb6d9c 100644
--- a/man/do_groupPeaks_mzClust.Rd
+++ b/man/do_groupPeaks_mzClust.Rd
@@ -22,11 +22,13 @@ the index of the sample in which the peak was found.}
 
 \item{sampleGroups}{For \code{PeakDensityParam}: A vector of the same length than
 samples defining the sample group assignments (i.e. which samples
-belong to which sample
-group). This parameter is mandatory for the \code{PeakDensityParam}
-and has to be provided also if there is no sample grouping in the
-experiment (in which case all samples should be assigned to the
-same group).}
+belong to which sample group). This parameter is mandatory for
+\code{PeakDensityParam} and has to be defined also if there is no sample
+grouping in the experiment (in which case all samples should be
+assigned to the same group). Samples for which a \code{NA} is provided will
+not be considered in the feature definitions step. Providing \code{NA} for
+all blanks in an experiment will for example avoid features to be
+defined for signals (chrom peaks) present only in blank samples.}
 
 \item{ppm}{For \code{MzClustParam}: \code{numeric(1)} representing the relative m/z
 error for the clustering/grouping (in parts per million).
diff --git a/man/groupChromPeaks.Rd b/man/groupChromPeaks.Rd
index 5a404952..7be3bf18 100644
--- a/man/groupChromPeaks.Rd
+++ b/man/groupChromPeaks.Rd
@@ -190,11 +190,13 @@ object will remove previous results.}
 
 \item{sampleGroups}{For \code{PeakDensityParam}: A vector of the same length than
 samples defining the sample group assignments (i.e. which samples
-belong to which sample
-group). This parameter is mandatory for the \code{PeakDensityParam}
-and has to be provided also if there is no sample grouping in the
-experiment (in which case all samples should be assigned to the
-same group).}
+belong to which sample group). This parameter is mandatory for
+\code{PeakDensityParam} and has to be defined also if there is no sample
+grouping in the experiment (in which case all samples should be
+assigned to the same group). Samples for which a \code{NA} is provided will
+not be considered in the feature definitions step. Providing \code{NA} for
+all blanks in an experiment will for example avoid features to be
+defined for signals (chrom peaks) present only in blank samples.}
 
 \item{bw}{For \code{PeakDensityParam}: \code{numeric(1)} defining the bandwidth
 (standard deviation ot the smoothing kernel) to be used. This argument
@@ -271,7 +273,15 @@ larger than 0, m/z dependent bin sizes can be used instead (better
 representing the m/z dependent measurement error of some MS instruments).
 All peaks (from the same or from different samples) with their apex
 position being close on the retention time axis are grouped into a LC-MS
-feature. See in addition \code{\link[=do_groupChromPeaks_density]{do_groupChromPeaks_density()}} for the core API
+feature. Only samples with non-missing sample group assignment (i.e. for
+which the value provided with parameter \code{sampleGroups} is different than
+\code{NA}) are considered and counted for the feature definition. This allows
+to exclude certain samples or groups (e.g. blanks) from the feature
+definition avoiding thus features with only detected peaks in these. Note
+that this affects only the \strong{definition} of \strong{new} features.
+Chromatographic peaks in these samples will still be assigned to features
+which were defined based on the other samples.
+See in addition \code{\link[=do_groupChromPeaks_density]{do_groupChromPeaks_density()}} for the core API
 function.
 \item \code{NearestPeaksParam}: performs peak grouping based on the proximity of
 chromatographic peaks from different samples in the m/z - rt space similar
diff --git a/man/plotPrecursorIons.Rd b/man/plotPrecursorIons.Rd
new file mode 100644
index 00000000..aaf7f7fe
--- /dev/null
+++ b/man/plotPrecursorIons.Rd
@@ -0,0 +1,60 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/XcmsExperiment-plotting.R
+\name{plotPrecursorIons}
+\alias{plotPrecursorIons}
+\title{General visualization of precursor ions of LC-MS/MS data}
+\usage{
+plotPrecursorIons(
+  x,
+  pch = 21,
+  col = "#00000080",
+  bg = "#00000020",
+  xlab = "retention time",
+  ylab = "m/z",
+  main = character(),
+  ...
+)
+}
+\arguments{
+\item{x}{\code{MsExperiment} of LC-MS/MS data.}
+
+\item{pch}{\code{integer(1)} defining the symbol/point type to be used to draw
+points. See \code{\link[=points]{points()}} for details. Defaults to \code{pch = 21} which allows
+defining the background and border color for points.}
+
+\item{col}{the color to be used for all data points. Defines the border
+color if \code{pch = 21}.}
+
+\item{bg}{the background color (if \code{pch = 21}).}
+
+\item{xlab}{\code{character(1)} defining the x-axis label.}
+
+\item{ylab}{\code{character(1)} defining the y-axis label.}
+
+\item{main}{Optional \code{character(1)} with the title for \strong{every} plot. If
+not provided (the default) the base file name will be used for each
+sample.}
+
+\item{...}{additional parameters to be passed to the \code{plot} calls.}
+}
+\description{
+Simple visualization of the position of fragment spectra's precursor ion
+in the MS1 retention time by m/z area.
+}
+\examples{
+
+## Load a test data file with DDA LC-MS/MS data
+library(MsExperiment)
+fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
+pest_dda <- readMsExperiment(fl)
+
+plotPrecursorIons(pest_dda)
+grid()
+
+## Subset the data object to plot the data specifically for one or
+## selected file/sample:
+plotPrecursorIons(pest_dda[1L])
+}
+\author{
+Johannes Rainer
+}
diff --git a/tests/testthat/test_Param_classes.R b/tests/testthat/test_Param_classes.R
index 5a3eb6f8..4281d56f 100644
--- a/tests/testthat/test_Param_classes.R
+++ b/tests/testthat/test_Param_classes.R
@@ -500,7 +500,6 @@ test_that("PeakDensityParam works", {
     expect_error(sampleGroups(p) <- NULL)
     expect_error(sampleGroups(p) <- c(2, 2, NA))
     expect_error(PeakDensityParam())
-    expect_error(PeakDensityParam(sampleGroups = c(1, 1, NA)))
 
     p <- new("PeakDensityParam", bw = 3)
     expect_equal(bw(p), 3)
diff --git a/tests/testthat/test_XcmsExperiment-plotting.R b/tests/testthat/test_XcmsExperiment-plotting.R
index 312d0a87..a4ab590a 100644
--- a/tests/testthat/test_XcmsExperiment-plotting.R
+++ b/tests/testthat/test_XcmsExperiment-plotting.R
@@ -53,6 +53,19 @@ test_that("plot,XcmsExperiment and .xmse_plot_xic works", {
     plot(tmp)
 })
 
+test_that("plotPrecursorIons works", {
+    expect_error(plotPrecursorIons(3), "MsExperiment")
+    fl <- system.file("TripleTOF-SWATH", "PestMix1_SWATH.mzML",
+                      package = "msdata")
+    a <- readMsExperiment(fl)
+    plotPrecursorIons(a, main = "SWATH")
+
+    fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML",
+                      package = "msdata")
+    a <- readMsExperiment(fl)
+    plotPrecursorIons(a)
+})
+
 test_that(".xmse_plot_xic works with ms2 data", {
   tmp <-  filterMz(filterRt(mse_ms2, rt= c(2160, 2190)), mz = c(990,1000))
   plot(tmp)
diff --git a/tests/testthat/test_do_groupChromPeaks-functions.R b/tests/testthat/test_do_groupChromPeaks-functions.R
index f01f3617..56e49e96 100644
--- a/tests/testthat/test_do_groupChromPeaks-functions.R
+++ b/tests/testthat/test_do_groupChromPeaks-functions.R
@@ -85,3 +85,37 @@ test_that(".group_peaks_density works", {
     expect_true(nrow(res) == 0)
     expect_true(is(res, "data.frame"))
 })
+
+test_that("do_groupChromPeaks_density works with skipping samples", {
+    x <- loadXcmsData("xmse")
+    pks <- chromPeaks(x)
+    ## Errors
+    expect_error(do_groupChromPeaks_density(pks), "sampleGroups")
+    expect_error(do_groupChromPeaks_density(3, sampleGroups = 3), "matrix")
+    expect_error(do_groupChromPeaks_density(pks[, 1:3], sampleGroups = 1),
+                 "not found")
+    expect_error(do_groupChromPeaks_density(pks, sampleGroups = 1:3),
+                 "Sample indices")
+
+    ## groups for all samples.
+    grps <- sampleData(x)$sample_group
+    res <- do_groupChromPeaks_density(pks, sampleGroups = grps,
+                                      minFraction = 1, bw = 30)
+    expect_true(all(res$WT == 4 | res$KO == 4))
+    expect_true(all(res$WT <= 4))
+    expect_true(all(res$KO <= 4))
+
+    res_2 <- do_groupChromPeaks_density(
+        pks, sampleGroups = rep(1, length(grps)), minFraction = 1)
+    expect_true(nrow(res_2) < nrow(res))
+    expect_true(all(res_2$`1` == 8))
+
+    ## using only one sample group
+    grps[grps == "KO"] <- NA
+    res_3 <- do_groupChromPeaks_density(pks, sampleGroups = grps,
+                                        minFraction = 1)
+    expect_true(nrow(res_3) < nrow(res))
+    expect_true(all(res_3$WT == 4))
+    expect_equal(nrow(res_3), sum(res$WT == 4))
+    tmp <- res[res$WT == 4, ]
+})