diff --git a/R/merge_processed_spectra.R b/R/merge_processed_spectra.R
index 1dbdf38..acf439d 100644
--- a/R/merge_processed_spectra.R
+++ b/R/merge_processed_spectra.R
@@ -5,13 +5,18 @@
 #' Aggregate multiple processed spectra, their associated peaks and metadata into a feature matrix and a concatenated metadata table.
 #'
 #' @param processed_spectra A [list] of the processed spectra and associated peaks and metadata in two possible formats:
-#' * A list of **in-memory objects** (named `spectra`, `peaks`, `metadata`) produced by [process_spectra].
+#' * A list of **in-memory objects** (named `spectra`, `peaks`, `metadata`) produced by [process_spectra]. Named lists will have names dropped, see Note.
 #' * `r lifecycle::badge('deprecated')` A list of **paths** to RDS files produced by [process_spectra] when using the `rds_prefix` option.
 #' @param remove_peakless_spectra A logical indicating whether to discard the spectra without detected peaks.
 #' @param interpolate_missing A logical indicating if intensity values for missing peaks should be interpolated from the processed spectra signal or left NA which would then be converted to 0.
 #'
 #' @return A *n*×*p* matrix, with *n* spectra as rows and *p* features as columns that are the peaks found in all the processed spectra.
 #'
+#' @note When aggregating multiple runs of processed spectra, if a named list is
+#' provided, note that the names will be dropped, to prevent further downstream
+#' issues when these names were being appended to the rownames of the matrix
+#' thus preventing downstream metadata merge.
+#'
 #' @seealso [process_spectra], the "Value" section in [`MALDIquant::intensityMatrix`](https://rdrr.io/cran/MALDIquant/man/intensityMatrix-functions.html)
 #' @export
 #' @examples
@@ -43,6 +48,14 @@
 #' # The feature matrix has 3×6=18 spectra as rows and
 #' #  35 peaks as columns
 #' dim(fm_all)
+#'
+#' # If using a list, names will be dropped and are not propagated to the matrix.
+#' \dontrun{
+#' fm_all <- merge_processed_spectra(
+#'  list("A" = processed, "B" = processed, "C" = processed))
+#' any(grepl("A|B|C", rownames(fm_all))) # FALSE
+#'  }
+#' 
 merge_processed_spectra <- function(processed_spectra, remove_peakless_spectra = TRUE, interpolate_missing = TRUE) {
   if (any(
     is.null(processed_spectra),
@@ -68,6 +81,12 @@ merge_processed_spectra <- function(processed_spectra, remove_peakless_spectra =
     processed <- processed_spectra
   }
 
+  # Names at the upper level causes problems when aggregating multiple runs by
+  #  being appended to the rownames of matrix thus preventing downstream metadata
+  #  merge.
+  if(!is.null(names(processed))){
+    processed <- unname(processed)
+  }
   stopifnot(is_a_processed_spectra_list(processed))
 
   peakless <- list()
diff --git a/dev/dereplicate-spectra.Rmd b/dev/dereplicate-spectra.Rmd
index 12be27f..3172f05 100644
--- a/dev/dereplicate-spectra.Rmd
+++ b/dev/dereplicate-spectra.Rmd
@@ -217,13 +217,18 @@ The current function enables the analyst to decide whether to interpolate the va
 #' Aggregate multiple processed spectra, their associated peaks and metadata into a feature matrix and a concatenated metadata table.
 #'
 #' @param processed_spectra A [list] of the processed spectra and associated peaks and metadata in two possible formats:
-#' * A list of **in-memory objects** (named `spectra`, `peaks`, `metadata`) produced by [process_spectra].
+#' * A list of **in-memory objects** (named `spectra`, `peaks`, `metadata`) produced by [process_spectra]. Named lists will have names dropped, see Note.
 #' * `r lifecycle::badge('deprecated')` A list of **paths** to RDS files produced by [process_spectra] when using the `rds_prefix` option.
 #' @param remove_peakless_spectra A logical indicating whether to discard the spectra without detected peaks.
 #' @param interpolate_missing A logical indicating if intensity values for missing peaks should be interpolated from the processed spectra signal or left NA which would then be converted to 0.
 #'
 #' @return A *n*×*p* matrix, with *n* spectra as rows and *p* features as columns that are the peaks found in all the processed spectra.
 #'
+#' @note When aggregating multiple runs of processed spectra, if a named list is
+#' provided, note that the names will be dropped, to prevent further downstream
+#' issues when these names were being appended to the rownames of the matrix
+#' thus preventing downstream metadata merge.
+#'
 #' @seealso [process_spectra], the "Value" section in [`MALDIquant::intensityMatrix`](https://rdrr.io/cran/MALDIquant/man/intensityMatrix-functions.html)
 #' @export
 merge_processed_spectra <- function(processed_spectra, remove_peakless_spectra = TRUE, interpolate_missing = TRUE) {
@@ -251,6 +256,12 @@ merge_processed_spectra <- function(processed_spectra, remove_peakless_spectra =
     processed <- processed_spectra
   }
 
+  # Names at the upper level causes problems when aggregating multiple runs by
+  #  being appended to the rownames of matrix thus preventing downstream metadata
+  #  merge.
+  if(!is.null(names(processed))){
+    processed <- unname(processed)
+  }
   stopifnot(is_a_processed_spectra_list(processed))
 
   peakless <- list()
@@ -335,6 +346,14 @@ fm_all <- merge_processed_spectra(list(processed, processed, processed))
 # The feature matrix has 3×6=18 spectra as rows and
 #  35 peaks as columns
 dim(fm_all)
+
+# If using a list, names will be dropped and are not propagated to the matrix.
+#' \dontrun{
+#' fm_all <- merge_processed_spectra(
+#'  list("A" = processed, "B" = processed, "C" = processed))
+#' any(grepl("A|B|C", rownames(fm_all))) # FALSE
+#'  }
+#' 
 ```
   
 ```{r tests-merge_processed_spectra}
@@ -351,6 +370,14 @@ test_that("merge_processed_spectra works", {
   expect_identical(
     sum(fm == 0), 0L
   )
+  expect_no_error(
+    fm_multiple <- merge_processed_spectra(
+      list("with_name_bar" = processed_test, "with_name_foo" = processed_test)
+    )
+  )
+  expect_equal(
+    dim(fm_multiple), c(4, 26)
+  )
 })
 test_that("merge_processed_spectra works without interpolation", {
   expect_no_error(
diff --git a/man/merge_processed_spectra.Rd b/man/merge_processed_spectra.Rd
index 0344ac4..8c64334 100644
--- a/man/merge_processed_spectra.Rd
+++ b/man/merge_processed_spectra.Rd
@@ -13,7 +13,7 @@ merge_processed_spectra(
 \arguments{
 \item{processed_spectra}{A \link{list} of the processed spectra and associated peaks and metadata in two possible formats:
 \itemize{
-\item A list of \strong{in-memory objects} (named \code{spectra}, \code{peaks}, \code{metadata}) produced by \link{process_spectra}.
+\item A list of \strong{in-memory objects} (named \code{spectra}, \code{peaks}, \code{metadata}) produced by \link{process_spectra}. Named lists will have names dropped, see Note.
 \item \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} A list of \strong{paths} to RDS files produced by \link{process_spectra} when using the \code{rds_prefix} option.
 }}
 
@@ -27,6 +27,12 @@ A \emph{n}×\emph{p} matrix, with \emph{n} spectra as rows and \emph{p} features
 \description{
 Aggregate multiple processed spectra, their associated peaks and metadata into a feature matrix and a concatenated metadata table.
 }
+\note{
+When aggregating multiple runs of processed spectra, if a named list is
+provided, note that the names will be dropped, to prevent further downstream
+issues when these names were being appended to the rownames of the matrix
+thus preventing downstream metadata merge.
+}
 \examples{
 # Get an example directory of six Bruker MALDI Biotyper spectra
 directory_biotyper_spectra <- system.file(
@@ -56,6 +62,14 @@ fm_all <- merge_processed_spectra(list(processed, processed, processed))
 # The feature matrix has 3×6=18 spectra as rows and
 #  35 peaks as columns
 dim(fm_all)
+
+# If using a list, names will be dropped and are not propagated to the matrix.
+\dontrun{
+fm_all <- merge_processed_spectra(
+ list("A" = processed, "B" = processed, "C" = processed))
+any(grepl("A|B|C", rownames(fm_all))) # FALSE
+ }
+
 }
 \seealso{
 \link{process_spectra}, the "Value" section in \href{https://rdrr.io/cran/MALDIquant/man/intensityMatrix-functions.html}{\code{MALDIquant::intensityMatrix}}
diff --git a/tests/testthat/test-merge_processed_spectra.R b/tests/testthat/test-merge_processed_spectra.R
index d9e9817..9dafefb 100644
--- a/tests/testthat/test-merge_processed_spectra.R
+++ b/tests/testthat/test-merge_processed_spectra.R
@@ -13,6 +13,14 @@ test_that("merge_processed_spectra works", {
   expect_identical(
     sum(fm == 0), 0L
   )
+  expect_no_error(
+    fm_multiple <- merge_processed_spectra(
+      list("with_name_bar" = processed_test, "with_name_foo" = processed_test)
+    )
+  )
+  expect_equal(
+    dim(fm_multiple), c(4, 26)
+  )
 })
 test_that("merge_processed_spectra works without interpolation", {
   expect_no_error(
diff --git a/vignettes/dereplicate-bruker-maldi-biotyper-spectra.Rmd b/vignettes/dereplicate-bruker-maldi-biotyper-spectra.Rmd
index b5343fa..41e3438 100644
--- a/vignettes/dereplicate-bruker-maldi-biotyper-spectra.Rmd
+++ b/vignettes/dereplicate-bruker-maldi-biotyper-spectra.Rmd
@@ -109,6 +109,14 @@ fm_all <- merge_processed_spectra(list(processed, processed, processed))
 # The feature matrix has 3×6=18 spectra as rows and
 #  35 peaks as columns
 dim(fm_all)
+
+# If using a list, names will be dropped and are not propagated to the matrix.
+#' \dontrun{
+#' fm_all <- merge_processed_spectra(
+#'  list("A" = processed, "B" = processed, "C" = processed))
+#' any(grepl("A|B|C", rownames(fm_all))) # FALSE
+#'  }
+#' 
 ```