diff --git a/DESCRIPTION b/DESCRIPTION
index b1a33c7d..bda18ab1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Spectra
 Title: Spectra Infrastructure for Mass Spectrometry Data
-Version: 1.17.2
+Version: 1.17.3
 Description: The Spectra package defines an efficient infrastructure
    for storing and handling mass spectrometry spectra and functionality to
    subset, process, visualize and compare spectra data. It provides different
diff --git a/NEWS.md b/NEWS.md
index 40622b24..6fd58890 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,9 +1,14 @@
 # Spectra 1.17
 
+## Change in 1.17.3
+
+- Fix `cbind2()` unit test for backends that fails if the number of spectra in
+  the tested backend is (by chance) equal to 4.
+
 ## Change in 1.17.2
 
-- Add `cbind2()` method to easily add multiple `spectraVariables` and their 
-  content to the `spectraData` of a `Spectra` object. 
+- Add `cbind2()` method to easily add multiple `spectraVariables` and their
+  content to the `spectraData` of a `Spectra` object.
   See also [issue #342](https://github.com/rformassspectrometry/Spectra/issues/342)
 
 ## Changes in 1.17.1
diff --git a/R/MsBackend.R b/R/MsBackend.R
index 6bd97749..6b66fef1 100644
--- a/R/MsBackend.R
+++ b/R/MsBackend.R
@@ -9,6 +9,7 @@
 #' @aliases supportsSetBackend
 #' @aliases backendBpparam
 #' @aliases backendInitialize
+#' @aliases backendParallelFactor
 #' @aliases backendParallelFactor,MsBackendMzR-method
 #' @aliases backendParallelFactor,MsBackendHdf5Peaks-method
 #' @aliases dataStorageBasePath
@@ -64,8 +65,8 @@
 #'
 #' @param BPPARAM for `backendBpparam()`: parameter object from the
 #'     `BiocParallel` package defining the parallel processing setup.
-#'     Defaults to `BPPARAM = bpparam()`. See [bpparam()] for more
-#'     information.
+#'     Defaults to `BPPARAM = bpparam()`. See [BiocParallel::bpparam()]
+#'     for more information.
 #'
 #' @param columns For `spectraData()` accessor: optional `character` with
 #'     column names (spectra variables) that should be included in the
@@ -133,7 +134,7 @@
 #'
 #' @param ppm For `filterPrecursorMzValues()`: `numeric(1)` with the
 #'     m/z-relative maximal acceptable difference for a m/z to be considered
-#'     matching. See [closest()] for details.
+#'     matching. See [MsCoreUtils::closest()] for details.
 #'     For `filterValues()`: `numeric` of any length allowing to define
 #'     a maximal accepted difference between user input `values` and the
 #'     `spectraVariables` values.  If it is not equal to the length of the
@@ -171,7 +172,8 @@
 #'
 #' @param tolerance For `filterPrecursorMzValues()`: `numeric(1)` with the
 #'     maximal absolute acceptable difference for a m/z value to be considered
-#'     matching. See [closest()] for details. For `filterValues()`: `numeric`
+#'     matching. See [MsCoreUtils::closest()] for details.
+#'     For `filterValues()`: `numeric`
 #'     accepted tolerance between the `values` and the spectra variables.
 #'     Defaults to `tolerance = 0`. If it is not equal to the length of the
 #'     value provided with parameter `spectraVariables`, `tolerance[1]` will
@@ -358,9 +360,9 @@
 #'   support `logical` and eventually `character`). While being apparently
 #'   redundant to `[`, this methods avoids package namespace errors/problems
 #'   that can result in implementations of `[` being not found by R (which
-#'   can happen sometimes in parallel processing using the [SnowParam()]). This
-#'   method is used internally by `Spectra` to extract/subset its backend.
-#'   Implementation of this method is mandatory.
+#'   can happen sometimes in parallel processing using the
+#'   [BiocParallel::SnowParam()]). This method is used internally by `Spectra`
+#'   to extract/subset its backend. Implementation of this method is mandatory.
 #'
 #' - `filterAcquisitionNum()`: filters the object keeping only spectra matching
 #'   the provided acquisition numbers (argument `n`). If `dataOrigin` or
@@ -462,14 +464,14 @@
 #'    for `MsBackend` is available.
 #'
 #' - `intensity()`: gets the intensity values from the spectra. Returns
-#'   a [NumericList()] of `numeric` vectors (intensity values for each
+#'   a [IRanges::NumericList()] of `numeric` vectors (intensity values for each
 #'   spectrum). The length of the `list` is equal to the number of
 #'   `spectra` in `object`.
 #'
 #' - `intensity<-`: replaces the intensity values. `value` has to be a `list`
-#'   (or [NumericList()]) of length equal to the number of spectra and the
-#'   number of values within each list element identical to the number of
-#'   peaks in each spectrum (i.e. the `lengths(x)`). Note that just
+#'   (or [IRanges::NumericList()]) of length equal to the number of spectra
+#'   and the number of values within each list element identical to the
+#'   number of peaks in each spectrum (i.e. the `lengths(x)`). Note that just
 #'   writeable backends support this method.
 #'
 #' - `ionCount()`: returns a `numeric` with the sum of intensities for
@@ -512,8 +514,8 @@
 #' - `msLevel<-`: replaces the spectra's MS level.
 #'
 #' - `mz()`: gets the mass-to-charge ratios (m/z) from the
-#'   spectra. Returns a [NumericList()] or length equal to the number of
-#'   spectra, each element a `numeric` vector with the m/z values of
+#'   spectra. Returns a [IRanges::NumericList()] or length equal to the
+#'   number of spectra, each element a `numeric` vector with the m/z values of
 #'   one spectrum.
 #'
 #' - `mz<-`: replaces the m/z values. `value` has to be a `list` of length equal
@@ -700,10 +702,10 @@
 #'   precursor.
 #' - `"precursorCharge"`: `integer` with the charge of the precursor.
 #' - `"collisionEnergy"`: `numeric` with the collision energy.
-#' - `"mz"`: [NumericList()] of `numeric` vectors representing the m/z values
-#'   for each spectrum.
-#' - `"intensity"`: [NumericList()] of `numeric` vectors representing the
-#'   intensity values for each spectrum.
+#' - `"mz"`: [IRanges::NumericList()] of `numeric` vectors representing the
+#'   m/z values for each spectrum.
+#' - `"intensity"`: [IRanges::NumericList()] of `numeric` vectors
+#'   representing the intensity values for each spectrum.
 #'
 #' Additional columns are allowed too.
 #'
diff --git a/R/MsBackendCached.R b/R/MsBackendCached.R
index e2f4d4d2..bc1db97a 100644
--- a/R/MsBackendCached.R
+++ b/R/MsBackendCached.R
@@ -104,7 +104,7 @@ setClassUnion("characterOrInteger", c("character", "integer"))
 #'   the mzML file from which the data was read.
 #'
 #' - `intensity()`: gets the intensity values from the spectra. Returns
-#'   a [NumericList()] of `numeric` vectors (intensity values for each
+#'   a [IRanges::NumericList()] of `numeric` vectors (intensity values for each
 #'   spectrum). The length of the `list` is equal to the number of
 #'   `spectra` in `object`.
 #'
@@ -136,8 +136,8 @@ setClassUnion("characterOrInteger", c("character", "integer"))
 #'   level for each spectrum (or `NA_integer_` if not available).
 #'
 #' - `mz()`: gets the mass-to-charge ratios (m/z) from the
-#'   spectra. Returns a [NumericList()] or length equal to the number of
-#'   spectra, each element a `numeric` vector with the m/z values of
+#'   spectra. Returns a [IRanges::NumericList()] or length equal to the
+#'   number of spectra, each element a `numeric` vector with the m/z values of
 #'   one spectrum.
 #'
 #' - `polarity()`, `polarity<-`: gets or sets the polarity for each
diff --git a/R/Spectra-estimatePrecursorMz.R b/R/Spectra-estimatePrecursorMz.R
index ad6ff630..b82dd750 100644
--- a/R/Spectra-estimatePrecursorMz.R
+++ b/R/Spectra-estimatePrecursorMz.R
@@ -46,7 +46,8 @@
 #'     m/z. See documentation of parameter `tolerance` for more information.
 #'
 #' @param BPPARAM parallel processing setup. Defaults to
-#'     `BPPARAM = SerialParam()`. See [SerialParam()] for more information.
+#'     `BPPARAM = SerialParam()`. See [BiocParallel::SerialParam()] for
+#'     more information.
 #'
 #' @return `numeric` of length equal to the number of spectra in `object` with
 #'     the fragment spectra's estimated precursor m/z values. For MS1 spectra
diff --git a/R/Spectra-functions.R b/R/Spectra-functions.R
index 93d9f2db..48ede719 100644
--- a/R/Spectra-functions.R
+++ b/R/Spectra-functions.R
@@ -198,7 +198,8 @@ NULL
 #' @param ... Additional parameters for `FUN`.
 #'
 #' @param BPPARAM Optional settings for `BiocParallel`-based parallel
-#'     processing. See [bpparam()] for more informations and options.
+#'     processing. See [BiocParallel::bpparam()] for more informations and
+#'     options.
 #'
 #' @return A `list` with the result of `FUN`.
 #'
@@ -959,8 +960,8 @@ filterPrecursorPeaks <- function(object, tolerance = 0, ppm = 20,
 #'   per file parallel processing if `f` or `chunkSize` is not defined.
 #'   Other on-disk backends: only if requested by the user.
 #'
-#' @param BPPARAM Parallel setup configuration. See [bpparam()] for more
-#'     information.
+#' @param BPPARAM Parallel setup configuration. See [BiocParallel::bpparam()]
+#'     for more information.
 #'
 #' @param object `Spectra` object.
 #'
@@ -1039,8 +1040,8 @@ filterPrecursorPeaks <- function(object, tolerance = 0, ppm = 20,
 #' For these, the `backendBpparam()` function will always return a
 #' `SerialParam()` independently on how parallel processing was defined.
 #'
-#' @param BPPARAM Parallel setup configuration. See [bpparam()] for more
-#'     information.
+#' @param BPPARAM Parallel setup configuration. See [BiocParallel::bpparam()]
+#'     for more information.
 #'
 #' @param object `Spectra` object.
 #'
diff --git a/R/Spectra.R b/R/Spectra.R
index 2502db4a..86fa6c8e 100644
--- a/R/Spectra.R
+++ b/R/Spectra.R
@@ -49,9 +49,9 @@ NULL
 #'     creation of `Spectra` objects for details.
 #'     For `export()`: [MsBackend-class] to be used to export the data.
 #'
-#' @param BPPARAM Parallel setup configuration. See [bpparam()] for more
-#'     information. This is passed directly to the [backendInitialize()] method
-#'     of the [MsBackend-class].
+#' @param BPPARAM Parallel setup configuration. See [BiocParallel::bpparam()]
+#'     for more information. This is passed directly to the
+#'     [backendInitialize()] method of the [MsBackend-class].
 #'
 #' @param f For `setBackend()`: factor defining how to split the data
 #'     for parallelized copying of the spectra data to the new backend. For
@@ -65,7 +65,7 @@ NULL
 #'     `Spectra` objects for details. For all other methods a `Spectra` object.
 #'
 #' @param processingQueue For `Spectra()`: optional `list` of
-#'     [ProcessingStep-class] objects.
+#'     [ProtGenerics::ProcessingStep-class] objects.
 #'
 #' @param source For `Spectra()`: instance of [MsBackend-class] that can be
 #'     used to import spectrum data from the provided files. See section
@@ -180,8 +180,8 @@ NULL
 #' - `...`: optional additional arguments passed to the [backendInitialize()]
 #'   method of the new `backend`.
 #'
-#' - `BPPARAM`: setup for the parallel processing. See [bpparam()] for
-#'   details.
+#' - `BPPARAM`: setup for the parallel processing. See
+#'   [BiocParallel::bpparam()] for details.
 #'
 #'
 #' @section Exporting data from a `Spectra` object:
@@ -608,9 +608,9 @@ setReplaceMethod("dataStorageBasePath", "Spectra", function(object, value) {
 #' replaced (again, using dedicated functions or using `$<-`).
 #'
 #'
-#' @param BPPARAM Parallel setup configuration. See [bpparam()] for more
-#'     information. See also [processingChunkSize()] for more information
-#'     on parallel processing.
+#' @param BPPARAM Parallel setup configuration. See [BiocParallel::bpparam()]
+#'     for more information. See also [processingChunkSize()] for more
+#'     information on parallel processing.
 #'
 #' @param columns For `spectraData()` accessor: optional `character` with
 #'     column names (spectra variables) that should be included in the
@@ -779,7 +779,7 @@ setReplaceMethod("dataStorageBasePath", "Spectra", function(object, value) {
 #'   with the data storage location of each spectrum.
 #'
 #' - `intensity()`: gets the intensity values from the spectra. Returns
-#'   a [NumericList()] of `numeric` vectors (intensity values for each
+#'   a [IRanges::NumericList()] of `numeric` vectors (intensity values for each
 #'   spectrum). The length of the list is equal to the number of
 #'   `spectra` in `object`.
 #'
@@ -818,19 +818,19 @@ setReplaceMethod("dataStorageBasePath", "Spectra", function(object, value) {
 #'   level for each spectrum.
 #'
 #' - `mz()`: gets the mass-to-charge ratios (m/z) from the
-#'   spectra. Returns a [NumericList()] or length equal to the number of
-#'   spectra, each element a `numeric` vector with the m/z values of
+#'   spectra. Returns a [IRanges::NumericList()] or length equal to the number
+#'   of spectra, each element a `numeric` vector with the m/z values of
 #'   one spectrum.
 #'
 #' - `peaksData()`: gets the *peaks* data for all spectra in `object`. Peaks
 #'   data consist of the m/z and intensity values as well as possible additional
 #'   annotations (variables) of all peaks of each spectrum. The function
-#'   returns a [SimpleList()] of two dimensional arrays (either `matrix` or
-#'   `data.frame`), with each array providing the values for the requested
-#'   *peak variables* (by default `"mz"` and `"intensity"`). Optional parameter
-#'   `columns` is passed to the backend's `peaksData()` function to allow
-#'   the selection of specific (or additional) peaks variables (columns) that
-#'   should be extracted (if available). Importantly,
+#'   returns a [S4Vectors::SimpleList()] of two dimensional arrays (either
+#'   `matrix` or `data.frame`), with each array providing the values for the
+#'   requested *peak variables* (by default `"mz"` and `"intensity"`).
+#'   Optional parameter `columns` is passed to the backend's `peaksData()`
+#'   function to allow the selection of specific (or additional) peaks
+#'   variables (columns) that should be extracted (if available). Importantly,
 #'   it is **not** guaranteed that each backend supports this parameter (while
 #'   each backend must support extraction of `"mz"` and `"intensity"` columns).
 #'   Parameter `columns` defaults to `c("mz", "intensity")` but any value
@@ -1522,9 +1522,9 @@ setReplaceMethod("[[", "Spectra", function(x, i, j, ..., value) {
 #' - `split()`: splits the `Spectra` object based on parameter `f` into a `list`
 #'   of `Spectra` objects.
 #'
-#' @param BPPARAM Parallel setup configuration. See [bpparam()] for more
-#'     information. This is passed directly to the [backendInitialize()] method
-#'     of the [MsBackend-class].
+#' @param BPPARAM Parallel setup configuration. See [BiocParallel::bpparam()]
+#'     for more information. This is passed directly to the
+#'     [backendInitialize()] method of the [MsBackend-class].
 #'
 #' @param by.x A `character(1)` specifying the spectra variable used
 #'     for merging. Default is `"spectrumId"`.
@@ -2028,12 +2028,13 @@ setMethod("combinePeaks", "Spectra", function(object, tolerance = 0, ppm = 20,
 #'
 #' - `deisotopeSpectra()`: *deisotopes* each spectrum keeping only the
 #'   monoisotopic peak for groups of isotopologues. Isotopologues are
-#'   estimated using the [isotopologues()] function from the
+#'   estimated using the [MetaboCoreUtils::isotopologues()] function from the
 #'   *MetaboCoreUtils* package. Note that
 #'   the default parameters for isotope prediction/detection have been
 #'   determined using data from the Human Metabolome Database (HMDB) and
 #'   isotopes for elements other than CHNOPS might not be detected. See
-#'   parameter `substDefinition` in the documentation of [isotopologues()] for
+#'   parameter `substDefinition` in the documentation of
+#'   [MetaboCoreUtils::isotopologues()] for
 #'   more information. The approach and code to define the parameters for
 #'   isotope prediction is described
 #'   [here](https://github.com/EuracBiomedicalResearch/isotopologues).
@@ -2105,7 +2106,7 @@ setMethod("combinePeaks", "Spectra", function(object, tolerance = 0, ppm = 20,
 #'     subsetted.
 #'
 #' @param charge For `deisotopeSpectra()`: expected charge of the ionized
-#'     compounds. See [isotopologues()] for details.
+#'     compounds. See [MetaboCoreUtils::isotopologues()] for details.
 #'
 #' @param dataOrigin For `filterDataOrigin()`: `character` to define which
 #'     spectra to keep.
@@ -2187,7 +2188,7 @@ setMethod("combinePeaks", "Spectra", function(object, tolerance = 0, ppm = 20,
 #'     For `filterPrecursorMaxIntensity()`: `numeric(1)` defining the relative
 #'     maximal accepted difference of precursor m/z values of spectra for
 #'     grouping them into *precursor groups*. For `filterPrecursorIsotopes()`:
-#'     passed directly to the [isotopologues()] function.
+#'     passed directly to the [MetaboCoreUtils::isotopologues()] function.
 #'     For `filterValues()`: `numeric` of any length allowing to define
 #'     a maximal accepted difference between user input `values` and the
 #'     `spectraVariables` values. If it is not equal to the length of the
@@ -2213,7 +2214,8 @@ setMethod("combinePeaks", "Spectra", function(object, tolerance = 0, ppm = 20,
 #'     `filterPrecursorIsotopes()`: `matrix` or `data.frame` with definitions
 #'     of isotopic substitutions. Uses by default isotopic substitutions
 #'     defined from all compounds in the Human Metabolome Database (HMDB). See
-#'     [isotopologues()] or [isotopicSubstitutionMatrix()] in the
+#'     [MetaboCoreUtils::isotopologues()] or
+#'     [MetaboCoreUtils::isotopicSubstitutionMatrix()] in the
 #'     *MetaboCoreUtils* for details.
 #'
 #' @param threshold For `filterFourierTransformArtefacts()`: the relative
@@ -2230,7 +2232,8 @@ setMethod("combinePeaks", "Spectra", function(object, tolerance = 0, ppm = 20,
 #'     For `filterPrecursorMaxIntensity()`: `numeric(1)` defining the
 #'     (constant) maximal accepted difference of precursor m/z values of
 #'     spectra for grouping them into *precursor groups*. For
-#'     `filterPrecursorIsotopes()`: passed directly to the [isotopologues()]
+#'     `filterPrecursorIsotopes()`: passed directly to the
+#'     [MetaboCoreUtils::isotopologues()]
 #'     function. For `filterValues()`: `numeric` of any length allowing to
 #'     define a maximal accepted difference between user input `values` and the
 #'     `spectraVariables` values. If it is not equal to the length of the
@@ -2906,7 +2909,8 @@ setMethod("filterValues", "Spectra",
 #'
 #' - `containsMz()`: checks for each of the spectra whether they contain mass
 #'   peaks with an m/z equal to `mz` (given acceptable difference as defined by
-#'   parameters `tolerance` and `ppm` - see [common()] for details). Parameter
+#'   parameters `tolerance` and `ppm` - see [MsCoreUtils::common()] for
+#'   details). Parameter
 #'   `which` allows to define whether any (`which = "any"`, the default) or
 #'   all (`which = "all"`) of the `mz` have to match. The function returns
 #'   `NA` if `mz` is of length 0 or is `NA`.
@@ -2918,7 +2922,8 @@ setMethod("filterValues", "Spectra",
 #'
 #' - `entropy()`: calculates the entropy of each spectra based on the metrics
 #'   suggested by Li et al. (https://doi.org/10.1038/s41592-021-01331-z).
-#'   See also [nentropy()] in the *MsCoreUtils* package for details.
+#'   See also [MsCoreUtils::nentropy()] in the *MsCoreUtils* package for
+#'   details.
 #'
 #' - `estimatePrecursorIntensity()`: defines the precursor intensities for MS2
 #'   spectra using the intensity of the matching MS1 peak from the
@@ -2992,10 +2997,11 @@ setMethod("filterValues", "Spectra",
 #' @param binSize For `bin()`: `numeric(1)` defining the size for the m/z bins.
 #'     Defaults to `binSize = 1`.
 #'
-#' @param BPPARAM Parallel setup configuration. See [bpparam()] for more
-#'     information. This is passed directly to the [backendInitialize()] method
-#'     of the [MsBackend-class]. See also [processingChunkSize()] for
-#'     additional information on parallel processing.
+#' @param BPPARAM Parallel setup configuration. See [BiocParallel::bpparam()]
+#'     for more information. This is passed directly to the
+#'     [backendInitialize()] method of the [MsBackend-class]. See also
+#'     [processingChunkSize()] for additional information on parallel
+#'     processing.
 #'
 #' @param breaks For `bin()`: `numeric` defining the m/z breakpoints between
 #'     bins.
@@ -3055,8 +3061,8 @@ setMethod("filterValues", "Spectra",
 #'     value which should be subtracted from the spectrum's precursor m/z.
 #'
 #' @param normalized for `entropy()`: `logical(1)` whether the normalized
-#'     entropy should be calculated (default). See also [nentropy()] for
-#'     details.
+#'     entropy should be calculated (default). See also
+#'     [MsCoreUtils::nentropy()] for details.
 #'
 #' @param object A `Spectra` object.
 #'
@@ -3530,9 +3536,9 @@ setMethod("spectrapply", "Spectra", function(object, FUN, ...,
 #'     spectra belong to the same original data file (sample).
 #'     Defaults to `f = dataOrigin(x)`.
 #'
-#' @param BPPARAM Parallel setup configuration. See [bpparam()] for more
-#'     information. This is passed directly to the [backendInitialize()] method
-#'     of the [MsBackend-class].
+#' @param BPPARAM Parallel setup configuration. See [BiocParallel::bpparam()]
+#'     for more information. This is passed directly to the
+#'     [backendInitialize()] method of the [MsBackend-class].
 #'
 #' @author Johannes Rainer with feedback and suggestions from Corey Broeckling
 #'
@@ -3591,9 +3597,9 @@ setMethod(
 #' @description
 #'
 #' `compareSpectra()` compares each spectrum in `x` with each spectrum in `y`
-#' using the function provided with `FUN` (defaults to [ndotproduct()]). If
-#' `y` is missing, each spectrum in `x` is compared with each other spectrum
-#' in `x`.
+#' using the function provided with `FUN` (defaults to
+#' [MsCoreUtils::ndotproduct()]). If `y` is missing, each spectrum in `x` is
+#' compared with each other spectrum in `x`.
 #' The matching/mapping of peaks between the compared spectra is done with the
 #' `MAPFUN` function. The default [joinPeaks()] matches peaks of both spectra
 #' and allows to keep all peaks from the first spectrum (`type = "left"`),
@@ -3628,7 +3634,7 @@ setMethod(
 #' similarity in the scoring.
 #'
 #' @param FUN function to compare intensities of peaks between two spectra.
-#'     Defaults to [ndotproduct()].
+#'     Defaults to [MsCoreUtils::ndotproduct()].
 #'
 #' @param MAPFUN For `compareSpectra()`: function to map/match peaks between
 #'     the two compared spectra. See [joinPeaks()] for more information and
diff --git a/R/peaks-functions.R b/R/peaks-functions.R
index dc19e353..4b239719 100644
--- a/R/peaks-functions.R
+++ b/R/peaks-functions.R
@@ -255,9 +255,9 @@ NULL
 #'   matrices might be reported multiple times. Note that if one of
 #'   `xPrecursorMz` or `yPrecursorMz` are `NA` or if both are the same, the
 #'   results are the same as with [joinPeaks()]. To calculate GNPS similarity
-#'   scores, [gnps()] should be called on the aligned peak matrices (i.e.
-#'   `compareSpectra` should be called with `MAPFUN = joinPeaksGnps` and
-#'   `FUN = MsCoreUtils::gnps`).
+#'   scores, [MsCoreUtils::gnps()] should be called on the aligned peak
+#'   matrices (i.e. `compareSpectra` should be called with
+#'   `MAPFUN = joinPeaksGnps` and `FUN = MsCoreUtils::gnps`).
 #'
 #' - `joinPeaksNone()`: does not perform any peak matching but simply returns
 #'   the peak matrices in a `list`. This function should be used with the
@@ -313,8 +313,8 @@ NULL
 #' - [compareSpectra()] for the function to calculate similarities between
 #'   spectra.
 #'
-#' - [gnps()] in the *MsCoreUtils* package for more information on the GNPS
-#'   similarity score.
+#' - [MsCoreUtils::gnps()] in the *MsCoreUtils* package for more information
+#'   on the GNPS similarity score.
 #'
 #' @importFrom MsCoreUtils join ppm
 #'
diff --git a/R/plotting-functions.R b/R/plotting-functions.R
index 285a02a6..c75687f9 100644
--- a/R/plotting-functions.R
+++ b/R/plotting-functions.R
@@ -14,10 +14,10 @@
 #'
 #' - `plotSpectraMirror()`: plots a pair of spectra as a *mirror plot*.
 #'   Parameters `x` and `y` both have to be a `Spectra` of length 1. Matching
-#'   peaks (considering `ppm` and `tolerance`) are highlighted. See [common()]
-#'   for details on peak matching. Parameters `matchCol`, `matchLty`,
-#'   `matchLwd` and `matchPch` allow to customize how matching peaks are
-#'   indicated.
+#'   peaks (considering `ppm` and `tolerance`) are highlighted. See
+#'   [MsCoreUtils::common()] for details on peak matching. Parameters
+#'   `matchCol`, `matchLty`, `matchLwd` and `matchPch` allow to customize
+#'   how matching peaks are indicated.
 #'
 #' @param x a [Spectra()] object. For `plotSpectraMirror()` it has to be an
 #'     object of length 2.
@@ -70,12 +70,12 @@
 #'     plotting area.
 #'
 #' @param ppm for `plotSpectraMirror()`: m/z relative acceptable difference (in
-#'     ppm) for peaks to be considered matching (see [common()] for more
-#'     details).
+#'     ppm) for peaks to be considered matching (see [MsCoreUtils::common()]
+#'     for more details).
 #'
 #' @param tolerance for `plotSpectraMirror()`: absolute acceptable difference of
-#'     m/z values for peaks to be considered matching (see [common()] for more
-#'     details).
+#'     m/z values for peaks to be considered matching (see
+#'     [MsCoreUtils::common()] for more details).
 #'
 #' @param matchCol for `plotSpectraMirror()`: color for matching peaks.
 #'
diff --git a/inst/test_backends/test_MsBackend/test_spectra_subsetting.R b/inst/test_backends/test_MsBackend/test_spectra_subsetting.R
index 76d676a4..e1beb93e 100644
--- a/inst/test_backends/test_MsBackend/test_spectra_subsetting.R
+++ b/inst/test_backends/test_MsBackend/test_spectra_subsetting.R
@@ -68,7 +68,7 @@ test_that("cbind2 works", {
     expect_equal(res$cola, seq_len(seql))
     expect_equal(res$colb, rep("b", seql))
     expect_equal(res$colz, rep("z", seql))
-    df2  <- data.frame(cola = 3:6, colb = "b", colz = "z")
+    df2  <- data.frame(cola = seq_len(length(be) / 2), colb = "b", colz = "z")
     expect_error(cbind2(be, df2), "does not match")
     ## with matrix
     m <- matrix(1:seql, ncol = 1, dimnames = list(NULL, "m"))
diff --git a/man/MsBackend.Rd b/man/MsBackend.Rd
index 8842343d..b920d692 100644
--- a/man/MsBackend.Rd
+++ b/man/MsBackend.Rd
@@ -15,6 +15,7 @@
 \alias{supportsSetBackend}
 \alias{backendBpparam}
 \alias{backendInitialize}
+\alias{backendParallelFactor}
 \alias{backendParallelFactor,MsBackendMzR-method}
 \alias{backendParallelFactor,MsBackendHdf5Peaks-method}
 \alias{dataStorageBasePath}
@@ -315,8 +316,8 @@ MsBackendMzR()
 
 \item{BPPARAM}{for \code{backendBpparam()}: parameter object from the
 \code{BiocParallel} package defining the parallel processing setup.
-Defaults to \code{BPPARAM = bpparam()}. See \code{\link[=bpparam]{bpparam()}} for more
-information.}
+Defaults to \code{BPPARAM = bpparam()}. See \code{\link[BiocParallel:register]{BiocParallel::bpparam()}}
+for more information.}
 
 \item{...}{Additional arguments.}
 
@@ -371,7 +372,7 @@ to subset \code{object}.}
 
 \item{ppm}{For \code{filterPrecursorMzValues()}: \code{numeric(1)} with the
 m/z-relative maximal acceptable difference for a m/z to be considered
-matching. See \code{\link[=closest]{closest()}} for details.
+matching. See \code{\link[MsCoreUtils:matching]{MsCoreUtils::closest()}} for details.
 For \code{filterValues()}: \code{numeric} of any length allowing to define
 a maximal accepted difference between user input \code{values} and the
 \code{spectraVariables} values.  If it is not equal to the length of the
@@ -380,7 +381,8 @@ recycled.}
 
 \item{tolerance}{For \code{filterPrecursorMzValues()}: \code{numeric(1)} with the
 maximal absolute acceptable difference for a m/z value to be considered
-matching. See \code{\link[=closest]{closest()}} for details. For \code{filterValues()}: \code{numeric}
+matching. See \code{\link[MsCoreUtils:matching]{MsCoreUtils::closest()}} for details.
+For \code{filterValues()}: \code{numeric}
 accepted tolerance between the \code{values} and the spectra variables.
 Defaults to \code{tolerance = 0}. If it is not equal to the length of the
 value provided with parameter \code{spectraVariables}, \code{tolerance[1]} will
@@ -644,9 +646,9 @@ however, \code{i} is expected to be an \code{integer} (while \code{[} should als
 support \code{logical} and eventually \code{character}). While being apparently
 redundant to \code{[}, this methods avoids package namespace errors/problems
 that can result in implementations of \code{[} being not found by R (which
-can happen sometimes in parallel processing using the \code{\link[=SnowParam]{SnowParam()}}). This
-method is used internally by \code{Spectra} to extract/subset its backend.
-Implementation of this method is mandatory.
+can happen sometimes in parallel processing using the
+\code{\link[BiocParallel:SnowParam-class]{BiocParallel::SnowParam()}}). This method is used internally by \code{Spectra}
+to extract/subset its backend. Implementation of this method is mandatory.
 \item \code{filterAcquisitionNum()}: filters the object keeping only spectra matching
 the provided acquisition numbers (argument \code{n}). If \code{dataOrigin} or
 \code{dataStorage} is also provided, \code{object} is subsetted to the spectra with
@@ -732,13 +734,13 @@ values are within any of the provided ranges are retained).
 Implementation of this method is optional since a default implementation
 for \code{MsBackend} is available.
 \item \code{intensity()}: gets the intensity values from the spectra. Returns
-a \code{\link[=NumericList]{NumericList()}} of \code{numeric} vectors (intensity values for each
+a \code{\link[IRanges:AtomicList-class]{IRanges::NumericList()}} of \code{numeric} vectors (intensity values for each
 spectrum). The length of the \code{list} is equal to the number of
 \code{spectra} in \code{object}.
 \item \verb{intensity<-}: replaces the intensity values. \code{value} has to be a \code{list}
-(or \code{\link[=NumericList]{NumericList()}}) of length equal to the number of spectra and the
-number of values within each list element identical to the number of
-peaks in each spectrum (i.e. the \code{lengths(x)}). Note that just
+(or \code{\link[IRanges:AtomicList-class]{IRanges::NumericList()}}) of length equal to the number of spectra
+and the number of values within each list element identical to the
+number of peaks in each spectrum (i.e. the \code{lengths(x)}). Note that just
 writeable backends support this method.
 \item \code{ionCount()}: returns a \code{numeric} with the sum of intensities for
 each spectrum. If the spectrum is empty (see \code{isEmpty()}),
@@ -769,8 +771,8 @@ vector (of length equal to the number of spectra) with the MS
 level for each spectrum (or \code{NA_integer_} if not available).
 \item \verb{msLevel<-}: replaces the spectra's MS level.
 \item \code{mz()}: gets the mass-to-charge ratios (m/z) from the
-spectra. Returns a \code{\link[=NumericList]{NumericList()}} or length equal to the number of
-spectra, each element a \code{numeric} vector with the m/z values of
+spectra. Returns a \code{\link[IRanges:AtomicList-class]{IRanges::NumericList()}} or length equal to the
+number of spectra, each element a \code{numeric} vector with the m/z values of
 one spectrum.
 \item \verb{mz<-}: replaces the m/z values. \code{value} has to be a \code{list} of length equal
 to the number of spectra and the number of values within each list element
@@ -945,10 +947,10 @@ containing the precursor of a (MS2) spectrum.
 precursor.
 \item \code{"precursorCharge"}: \code{integer} with the charge of the precursor.
 \item \code{"collisionEnergy"}: \code{numeric} with the collision energy.
-\item \code{"mz"}: \code{\link[=NumericList]{NumericList()}} of \code{numeric} vectors representing the m/z values
-for each spectrum.
-\item \code{"intensity"}: \code{\link[=NumericList]{NumericList()}} of \code{numeric} vectors representing the
-intensity values for each spectrum.
+\item \code{"mz"}: \code{\link[IRanges:AtomicList-class]{IRanges::NumericList()}} of \code{numeric} vectors representing the
+m/z values for each spectrum.
+\item \code{"intensity"}: \code{\link[IRanges:AtomicList-class]{IRanges::NumericList()}} of \code{numeric} vectors
+representing the intensity values for each spectrum.
 }
 
 Additional columns are allowed too.
diff --git a/man/MsBackendCached.Rd b/man/MsBackendCached.Rd
index ae8c6687..1cc219a9 100644
--- a/man/MsBackendCached.Rd
+++ b/man/MsBackendCached.Rd
@@ -269,7 +269,7 @@ returns a \code{numeric} with length equal to the number of spectra
 in \code{object} with the \emph{data origin} of each spectrum. This could e.g. be
 the mzML file from which the data was read.
 \item \code{intensity()}: gets the intensity values from the spectra. Returns
-a \code{\link[=NumericList]{NumericList()}} of \code{numeric} vectors (intensity values for each
+a \code{\link[IRanges:AtomicList-class]{IRanges::NumericList()}} of \code{numeric} vectors (intensity values for each
 spectrum). The length of the \code{list} is equal to the number of
 \code{spectra} in \code{object}.
 \item \code{ionCount()}: returns a \code{numeric} with the sum of intensities for
@@ -292,8 +292,8 @@ number of spectra). For empty spectra, \code{0} is returned.
 vector (of length equal to the number of spectra) with the MS
 level for each spectrum (or \code{NA_integer_} if not available).
 \item \code{mz()}: gets the mass-to-charge ratios (m/z) from the
-spectra. Returns a \code{\link[=NumericList]{NumericList()}} or length equal to the number of
-spectra, each element a \code{numeric} vector with the m/z values of
+spectra. Returns a \code{\link[IRanges:AtomicList-class]{IRanges::NumericList()}} or length equal to the
+number of spectra, each element a \code{numeric} vector with the m/z values of
 one spectrum.
 \item \code{polarity()}, \verb{polarity<-}: gets or sets the polarity for each
 spectrum.  \code{polarity} returns an \code{integer} vector (length equal
diff --git a/man/Spectra.Rd b/man/Spectra.Rd
index 1116f60c..1d7efdf0 100644
--- a/man/Spectra.Rd
+++ b/man/Spectra.Rd
@@ -72,7 +72,7 @@ object and initialize the with data.. See section on creation of
 \code{Spectra} objects for details. For all other methods a \code{Spectra} object.}
 
 \item{processingQueue}{For \code{Spectra()}: optional \code{list} of
-\linkS4class{ProcessingStep} objects.}
+\link[ProtGenerics:ProcessingStep]{ProtGenerics::ProcessingStep} objects.}
 
 \item{metadata}{For \code{Spectra()}: optional \code{list} with metadata information.}
 
@@ -87,9 +87,9 @@ passing the full spectra data to the initialize method. See section on
 creation of \code{Spectra} objects for details.
 For \code{export()}: \linkS4class{MsBackend} to be used to export the data.}
 
-\item{BPPARAM}{Parallel setup configuration. See \code{\link[=bpparam]{bpparam()}} for more
-information. This is passed directly to the \code{\link[=backendInitialize]{backendInitialize()}} method
-of the \linkS4class{MsBackend}.}
+\item{BPPARAM}{Parallel setup configuration. See \code{\link[BiocParallel:register]{BiocParallel::bpparam()}}
+for more information. This is passed directly to the
+\code{\link[=backendInitialize]{backendInitialize()}} method of the \linkS4class{MsBackend}.}
 
 \item{source}{For \code{Spectra()}: instance of \linkS4class{MsBackend} that can be
 used to import spectrum data from the provided files. See section
@@ -254,8 +254,8 @@ new backend is performed separately (and in parallel) for each file. Users
 are advised to use the default setting.
 \item \code{...}: optional additional arguments passed to the \code{\link[=backendInitialize]{backendInitialize()}}
 method of the new \code{backend}.
-\item \code{BPPARAM}: setup for the parallel processing. See \code{\link[=bpparam]{bpparam()}} for
-details.
+\item \code{BPPARAM}: setup for the parallel processing. See
+\code{\link[BiocParallel:register]{BiocParallel::bpparam()}} for details.
 }
 }
 
diff --git a/man/addProcessing.Rd b/man/addProcessing.Rd
index 787aeabe..e431bb21 100644
--- a/man/addProcessing.Rd
+++ b/man/addProcessing.Rd
@@ -118,10 +118,11 @@ splitted while it defaults to \code{f = processingChunkSize(object)} for
 \code{applyProcessing()} splitting thus the object by default into chunks
 depending on \code{\link[=processingChunkSize]{processingChunkSize()}}.}
 
-\item{BPPARAM}{Parallel setup configuration. See \code{\link[=bpparam]{bpparam()}} for more
-information. This is passed directly to the \code{\link[=backendInitialize]{backendInitialize()}} method
-of the \linkS4class{MsBackend}. See also \code{\link[=processingChunkSize]{processingChunkSize()}} for
-additional information on parallel processing.}
+\item{BPPARAM}{Parallel setup configuration. See \code{\link[BiocParallel:register]{BiocParallel::bpparam()}}
+for more information. This is passed directly to the
+\code{\link[=backendInitialize]{backendInitialize()}} method of the \linkS4class{MsBackend}. See also
+\code{\link[=processingChunkSize]{processingChunkSize()}} for additional information on parallel
+processing.}
 
 \item{...}{Additional arguments passed to internal and downstream functions.}
 
@@ -177,8 +178,8 @@ spectrum.}
 value which should be subtracted from the spectrum's precursor m/z.}
 
 \item{normalized}{for \code{entropy()}: \code{logical(1)} whether the normalized
-entropy should be calculated (default). See also \code{\link[=nentropy]{nentropy()}} for
-details.}
+entropy should be calculated (default). See also
+\code{\link[MsCoreUtils:entropy]{MsCoreUtils::nentropy()}} for details.}
 
 \item{halfWindowSize}{For \code{pickPeaks()}: \code{integer(1)}, used in the
 identification of the mass peaks: a local maximum has to be the
@@ -330,7 +331,8 @@ calculations a chunk-wise processing is generally performed.
 \code{\link[=chunkapply]{chunkapply()}} for details and examples.
 \item \code{containsMz()}: checks for each of the spectra whether they contain mass
 peaks with an m/z equal to \code{mz} (given acceptable difference as defined by
-parameters \code{tolerance} and \code{ppm} - see \code{\link[=common]{common()}} for details). Parameter
+parameters \code{tolerance} and \code{ppm} - see \code{\link[MsCoreUtils:matching]{MsCoreUtils::common()}} for
+details). Parameter
 \code{which} allows to define whether any (\code{which = "any"}, the default) or
 all (\code{which = "all"}) of the \code{mz} have to match. The function returns
 \code{NA} if \code{mz} is of length 0 or is \code{NA}.
@@ -340,7 +342,8 @@ acceptable difference as defined by parameters \code{tolerance} and \code{ppm}).
 Returns \code{NA} for MS1 spectra (or spectra without a precursor m/z).
 \item \code{entropy()}: calculates the entropy of each spectra based on the metrics
 suggested by Li et al. (https://doi.org/10.1038/s41592-021-01331-z).
-See also \code{\link[=nentropy]{nentropy()}} in the \emph{MsCoreUtils} package for details.
+See also \code{\link[MsCoreUtils:entropy]{MsCoreUtils::nentropy()}} in the \emph{MsCoreUtils} package for
+details.
 \item \code{estimatePrecursorIntensity()}: defines the precursor intensities for MS2
 spectra using the intensity of the matching MS1 peak from the
 closest MS1 spectrum (i.e. the last MS1 spectrum measured before the
diff --git a/man/combineSpectra.Rd b/man/combineSpectra.Rd
index 87cbed0d..921dfcdc 100644
--- a/man/combineSpectra.Rd
+++ b/man/combineSpectra.Rd
@@ -48,9 +48,9 @@ performed.}
 \item{FUN}{For \code{combineSpectra()}: function to combine the (peak matrices)
 of the spectra. Defaults to \code{\link[=combinePeaksData]{combinePeaksData()}}.}
 
-\item{BPPARAM}{Parallel setup configuration. See \code{\link[=bpparam]{bpparam()}} for more
-information. This is passed directly to the \code{\link[=backendInitialize]{backendInitialize()}} method
-of the \linkS4class{MsBackend}.}
+\item{BPPARAM}{Parallel setup configuration. See \code{\link[BiocParallel:register]{BiocParallel::bpparam()}}
+for more information. This is passed directly to the
+\code{\link[=backendInitialize]{backendInitialize()}} method of the \linkS4class{MsBackend}.}
 
 \item{y}{For \code{joinSpectraData()}: \code{DataFrame} with the spectra variables
 to join/add. For \code{cbind2()}: a \code{data.frame}, \code{DataFrame} or
diff --git a/man/compareSpectra.Rd b/man/compareSpectra.Rd
index 375671c4..e621af58 100644
--- a/man/compareSpectra.Rd
+++ b/man/compareSpectra.Rd
@@ -46,7 +46,7 @@ accepted difference between m/z values for peaks to be matched. This
 parameter is directly passed to \code{MAPFUN}.}
 
 \item{FUN}{function to compare intensities of peaks between two spectra.
-Defaults to \code{\link[=ndotproduct]{ndotproduct()}}.}
+Defaults to \code{\link[MsCoreUtils:distance]{MsCoreUtils::ndotproduct()}}.}
 
 \item{...}{Additional arguments passed to the internal functions.}
 
@@ -56,9 +56,9 @@ of length 1).}
 }
 \description{
 \code{compareSpectra()} compares each spectrum in \code{x} with each spectrum in \code{y}
-using the function provided with \code{FUN} (defaults to \code{\link[=ndotproduct]{ndotproduct()}}). If
-\code{y} is missing, each spectrum in \code{x} is compared with each other spectrum
-in \code{x}.
+using the function provided with \code{FUN} (defaults to
+\code{\link[MsCoreUtils:distance]{MsCoreUtils::ndotproduct()}}). If \code{y} is missing, each spectrum in \code{x} is
+compared with each other spectrum in \code{x}.
 The matching/mapping of peaks between the compared spectra is done with the
 \code{MAPFUN} function. The default \code{\link[=joinPeaks]{joinPeaks()}} matches peaks of both spectra
 and allows to keep all peaks from the first spectrum (\code{type = "left"}),
diff --git a/man/estimatePrecursorIntensity.Rd b/man/estimatePrecursorIntensity.Rd
index 8780aab4..672989a5 100644
--- a/man/estimatePrecursorIntensity.Rd
+++ b/man/estimatePrecursorIntensity.Rd
@@ -38,9 +38,9 @@ should be estimated. Defaults to \code{2L}.}
 spectra belong to the same original data file (sample).
 Defaults to \code{f = dataOrigin(x)}.}
 
-\item{BPPARAM}{Parallel setup configuration. See \code{\link[=bpparam]{bpparam()}} for more
-information. This is passed directly to the \code{\link[=backendInitialize]{backendInitialize()}} method
-of the \linkS4class{MsBackend}.}
+\item{BPPARAM}{Parallel setup configuration. See \code{\link[BiocParallel:register]{BiocParallel::bpparam()}}
+for more information. This is passed directly to the
+\code{\link[=backendInitialize]{backendInitialize()}} method of the \linkS4class{MsBackend}.}
 }
 \description{
 Some MS instrument manufacturers don't provide precursor intensities for
diff --git a/man/estimatePrecursorMz.Rd b/man/estimatePrecursorMz.Rd
index 7bc9e6cd..48400317 100644
--- a/man/estimatePrecursorMz.Rd
+++ b/man/estimatePrecursorMz.Rd
@@ -19,7 +19,8 @@ precursorMz +/- (tolerance + ppm(precursorMz, ppm)) are considered.}
 m/z. See documentation of parameter \code{tolerance} for more information.}
 
 \item{BPPARAM}{parallel processing setup. Defaults to
-\code{BPPARAM = SerialParam()}. See \code{\link[=SerialParam]{SerialParam()}} for more information.}
+\code{BPPARAM = SerialParam()}. See \code{\link[BiocParallel:SerialParam-class]{BiocParallel::SerialParam()}} for
+more information.}
 }
 \value{
 \code{numeric} of length equal to the number of spectra in \code{object} with
diff --git a/man/filterMsLevel.Rd b/man/filterMsLevel.Rd
index 0ea3698b..be29771d 100644
--- a/man/filterMsLevel.Rd
+++ b/man/filterMsLevel.Rd
@@ -171,7 +171,8 @@ filterPrecursorPeaks(
 \code{filterPrecursorIsotopes()}: \code{matrix} or \code{data.frame} with definitions
 of isotopic substitutions. Uses by default isotopic substitutions
 defined from all compounds in the Human Metabolome Database (HMDB). See
-\code{\link[=isotopologues]{isotopologues()}} or \code{\link[=isotopicSubstitutionMatrix]{isotopicSubstitutionMatrix()}} in the
+\code{\link[MetaboCoreUtils:isotopologues]{MetaboCoreUtils::isotopologues()}} or
+\code{\link[MetaboCoreUtils:isotopicSubstitutionMatrix]{MetaboCoreUtils::isotopicSubstitutionMatrix()}} in the
 \emph{MetaboCoreUtils} for details.}
 
 \item{tolerance}{For \code{filterMzValues()} and \code{reduceSpectra()}:
@@ -182,7 +183,8 @@ tolerance for each m/z value.
 For \code{filterPrecursorMaxIntensity()}: \code{numeric(1)} defining the
 (constant) maximal accepted difference of precursor m/z values of
 spectra for grouping them into \emph{precursor groups}. For
-\code{filterPrecursorIsotopes()}: passed directly to the \code{\link[=isotopologues]{isotopologues()}}
+\code{filterPrecursorIsotopes()}: passed directly to the
+\code{\link[MetaboCoreUtils:isotopologues]{MetaboCoreUtils::isotopologues()}}
 function. For \code{filterValues()}: \code{numeric} of any length allowing to
 define a maximal accepted difference between user input \code{values} and the
 \code{spectraVariables} values. If it is not equal to the length of the
@@ -195,7 +197,7 @@ m/z values for peaks to be matched (or grouped).
 For \code{filterPrecursorMaxIntensity()}: \code{numeric(1)} defining the relative
 maximal accepted difference of precursor m/z values of spectra for
 grouping them into \emph{precursor groups}. For \code{filterPrecursorIsotopes()}:
-passed directly to the \code{\link[=isotopologues]{isotopologues()}} function.
+passed directly to the \code{\link[MetaboCoreUtils:isotopologues]{MetaboCoreUtils::isotopologues()}} function.
 For \code{filterValues()}: \code{numeric} of any length allowing to define
 a maximal accepted difference between user input \code{values} and the
 \code{spectraVariables} values. If it is not equal to the length of the
@@ -203,7 +205,7 @@ value provided with parameter \code{spectraVariables}, \code{ppm[1]} will be
 recycled.}
 
 \item{charge}{For \code{deisotopeSpectra()}: expected charge of the ionized
-compounds. See \code{\link[=isotopologues]{isotopologues()}} for details.}
+compounds. See \code{\link[MetaboCoreUtils:isotopologues]{MetaboCoreUtils::isotopologues()}} for details.}
 
 \item{object}{\code{Spectra} object.}
 
@@ -453,12 +455,13 @@ These operations don't affect the number of spectra in the \code{Spectra} object
 \itemize{
 \item \code{deisotopeSpectra()}: \emph{deisotopes} each spectrum keeping only the
 monoisotopic peak for groups of isotopologues. Isotopologues are
-estimated using the \code{\link[=isotopologues]{isotopologues()}} function from the
+estimated using the \code{\link[MetaboCoreUtils:isotopologues]{MetaboCoreUtils::isotopologues()}} function from the
 \emph{MetaboCoreUtils} package. Note that
 the default parameters for isotope prediction/detection have been
 determined using data from the Human Metabolome Database (HMDB) and
 isotopes for elements other than CHNOPS might not be detected. See
-parameter \code{substDefinition} in the documentation of \code{\link[=isotopologues]{isotopologues()}} for
+parameter \code{substDefinition} in the documentation of
+\code{\link[MetaboCoreUtils:isotopologues]{MetaboCoreUtils::isotopologues()}} for
 more information. The approach and code to define the parameters for
 isotope prediction is described
 \href{https://github.com/EuracBiomedicalResearch/isotopologues}{here}.
diff --git a/man/joinPeaks.Rd b/man/joinPeaks.Rd
index bc1fa688..f420808d 100644
--- a/man/joinPeaks.Rd
+++ b/man/joinPeaks.Rd
@@ -79,9 +79,9 @@ peaks in \code{x} can match up to two peaks in \code{y} hence peaks in the retur
 matrices might be reported multiple times. Note that if one of
 \code{xPrecursorMz} or \code{yPrecursorMz} are \code{NA} or if both are the same, the
 results are the same as with \code{\link[=joinPeaks]{joinPeaks()}}. To calculate GNPS similarity
-scores, \code{\link[=gnps]{gnps()}} should be called on the aligned peak matrices (i.e.
-\code{compareSpectra} should be called with \code{MAPFUN = joinPeaksGnps} and
-\code{FUN = MsCoreUtils::gnps}).
+scores, \code{\link[MsCoreUtils:gnps]{MsCoreUtils::gnps()}} should be called on the aligned peak
+matrices (i.e. \code{compareSpectra} should be called with
+\code{MAPFUN = joinPeaksGnps} and \code{FUN = MsCoreUtils::gnps}).
 \item \code{joinPeaksNone()}: does not perform any peak matching but simply returns
 the peak matrices in a \code{list}. This function should be used with the
 \code{MAPFUN} parameter of \code{\link[=compareSpectra]{compareSpectra()}} if the spectra similarity
@@ -145,8 +145,8 @@ joinPeaksGnps(x, y, pmz_x, yPrecursorMz = NA)
 \itemize{
 \item \code{\link[=compareSpectra]{compareSpectra()}} for the function to calculate similarities between
 spectra.
-\item \code{\link[=gnps]{gnps()}} in the \emph{MsCoreUtils} package for more information on the GNPS
-similarity score.
+\item \code{\link[MsCoreUtils:gnps]{MsCoreUtils::gnps()}} in the \emph{MsCoreUtils} package for more information
+on the GNPS similarity score.
 }
 }
 \author{
diff --git a/man/processingChunkSize.Rd b/man/processingChunkSize.Rd
index a9382611..ce32edb0 100644
--- a/man/processingChunkSize.Rd
+++ b/man/processingChunkSize.Rd
@@ -22,8 +22,8 @@ processingChunkFactor(x)
 
 \item{object}{\code{Spectra} object.}
 
-\item{BPPARAM}{Parallel setup configuration. See \code{\link[=bpparam]{bpparam()}} for more
-information.}
+\item{BPPARAM}{Parallel setup configuration. See \code{\link[BiocParallel:register]{BiocParallel::bpparam()}}
+for more information.}
 }
 \value{
 \code{processingChunkSize()} returns the currently defined processing
diff --git a/man/spectra-plotting.Rd b/man/spectra-plotting.Rd
index 6d2ec22f..50c4865a 100644
--- a/man/spectra-plotting.Rd
+++ b/man/spectra-plotting.Rd
@@ -140,12 +140,12 @@ plotting area.}
 which \code{x} should be plotted against.}
 
 \item{ppm}{for \code{plotSpectraMirror()}: m/z relative acceptable difference (in
-ppm) for peaks to be considered matching (see \code{\link[=common]{common()}} for more
-details).}
+ppm) for peaks to be considered matching (see \code{\link[MsCoreUtils:matching]{MsCoreUtils::common()}}
+for more details).}
 
 \item{tolerance}{for \code{plotSpectraMirror()}: absolute acceptable difference of
-m/z values for peaks to be considered matching (see \code{\link[=common]{common()}} for more
-details).}
+m/z values for peaks to be considered matching (see
+\code{\link[MsCoreUtils:matching]{MsCoreUtils::common()}} for more details).}
 
 \item{matchCol}{for \code{plotSpectraMirror()}: color for matching peaks.}
 
@@ -171,10 +171,10 @@ the plot area into as many panels as there are spectra.
 an overlay).
 \item \code{plotSpectraMirror()}: plots a pair of spectra as a \emph{mirror plot}.
 Parameters \code{x} and \code{y} both have to be a \code{Spectra} of length 1. Matching
-peaks (considering \code{ppm} and \code{tolerance}) are highlighted. See \code{\link[=common]{common()}}
-for details on peak matching. Parameters \code{matchCol}, \code{matchLty},
-\code{matchLwd} and \code{matchPch} allow to customize how matching peaks are
-indicated.
+peaks (considering \code{ppm} and \code{tolerance}) are highlighted. See
+\code{\link[MsCoreUtils:matching]{MsCoreUtils::common()}} for details on peak matching. Parameters
+\code{matchCol}, \code{matchLty}, \code{matchLwd} and \code{matchPch} allow to customize
+how matching peaks are indicated.
 }
 }
 \examples{
diff --git a/man/spectraData.Rd b/man/spectraData.Rd
index 2aad735f..0f64f913 100644
--- a/man/spectraData.Rd
+++ b/man/spectraData.Rd
@@ -220,9 +220,9 @@ in the individual \code{matrix} of the returned \code{list}. Defaults to
 \code{c("mz", "value")} but any values returned by \code{peaksVariables(object)}
 with \code{object} being the \code{Spectra} object are supported.}
 
-\item{BPPARAM}{Parallel setup configuration. See \code{\link[=bpparam]{bpparam()}} for more
-information. See also \code{\link[=processingChunkSize]{processingChunkSize()}} for more information
-on parallel processing.}
+\item{BPPARAM}{Parallel setup configuration. See \code{\link[BiocParallel:register]{BiocParallel::bpparam()}}
+for more information. See also \code{\link[=processingChunkSize]{processingChunkSize()}} for more
+information on parallel processing.}
 
 \item{initial}{For \code{tic()}: \code{logical(1)} whether the initially
 reported total ion current should be reported, or whether the
@@ -370,7 +370,7 @@ values for the data origin of each spectrum.
 \item \code{dataStorage()}: returns a \code{character} vector (same length than \code{object})
 with the data storage location of each spectrum.
 \item \code{intensity()}: gets the intensity values from the spectra. Returns
-a \code{\link[=NumericList]{NumericList()}} of \code{numeric} vectors (intensity values for each
+a \code{\link[IRanges:AtomicList-class]{IRanges::NumericList()}} of \code{numeric} vectors (intensity values for each
 spectrum). The length of the list is equal to the number of
 \code{spectra} in \code{object}.
 \item \code{ionCount()}: returns a \code{numeric} with the sum of intensities for
@@ -399,18 +399,18 @@ number of spectra). For empty spectra, \code{0} is returned.
 being spectrum names, length equal to the number of spectra) with the MS
 level for each spectrum.
 \item \code{mz()}: gets the mass-to-charge ratios (m/z) from the
-spectra. Returns a \code{\link[=NumericList]{NumericList()}} or length equal to the number of
-spectra, each element a \code{numeric} vector with the m/z values of
+spectra. Returns a \code{\link[IRanges:AtomicList-class]{IRanges::NumericList()}} or length equal to the number
+of spectra, each element a \code{numeric} vector with the m/z values of
 one spectrum.
 \item \code{peaksData()}: gets the \emph{peaks} data for all spectra in \code{object}. Peaks
 data consist of the m/z and intensity values as well as possible additional
 annotations (variables) of all peaks of each spectrum. The function
-returns a \code{\link[=SimpleList]{SimpleList()}} of two dimensional arrays (either \code{matrix} or
-\code{data.frame}), with each array providing the values for the requested
-\emph{peak variables} (by default \code{"mz"} and \code{"intensity"}). Optional parameter
-\code{columns} is passed to the backend's \code{peaksData()} function to allow
-the selection of specific (or additional) peaks variables (columns) that
-should be extracted (if available). Importantly,
+returns a \code{\link[S4Vectors:SimpleList-class]{S4Vectors::SimpleList()}} of two dimensional arrays (either
+\code{matrix} or \code{data.frame}), with each array providing the values for the
+requested \emph{peak variables} (by default \code{"mz"} and \code{"intensity"}).
+Optional parameter \code{columns} is passed to the backend's \code{peaksData()}
+function to allow the selection of specific (or additional) peaks
+variables (columns) that should be extracted (if available). Importantly,
 it is \strong{not} guaranteed that each backend supports this parameter (while
 each backend must support extraction of \code{"mz"} and \code{"intensity"} columns).
 Parameter \code{columns} defaults to \code{c("mz", "intensity")} but any value