diff --git a/DESCRIPTION b/DESCRIPTION
index 005b55868..96445f886 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.1.7
+Version: 4.1.9
 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,
@@ -35,7 +35,11 @@ Authors@R: c(
 	   person(given = "Philippine", family = "Louail",
 	   email = "philippine.louail@eurac.edu",
 	   role = "aut",
-	   comment = c(ORCID = "0009-0007-5429-6846"))
+	   comment = c(ORCID = "0009-0007-5429-6846")),
+	   person(given = "Pablo", family = "Vangeenderhuysen",
+	   email = "pablo.vangeenderhuysen@ugent.be",
+	   role = "ctb",
+	   comment = c(ORCID = "0000-0002-5492-6904"))
 	   )
 Depends:
     R (>= 4.0.0),
diff --git a/R/XcmsExperiment.R b/R/XcmsExperiment.R
index fdb94eddc..7b3672046 100644
--- a/R/XcmsExperiment.R
+++ b/R/XcmsExperiment.R
@@ -702,7 +702,7 @@
 NULL
 
 .empty_chrom_peaks <- function(sample = TRUE) {
-    cols <- c(.REQ_PEAKS_COLS, "maxo")
+    cols <- c(.REQ_PEAKS_COLS, "maxo","sn")
     if (!sample)
         cols <- cols[cols != "sample"]
     matrix(numeric(), ncol = length(cols), nrow = 0,
diff --git a/R/method-filterFeatures.R b/R/method-filterFeatures.R
index 8c708680b..9ef97ac0e 100644
--- a/R/method-filterFeatures.R
+++ b/R/method-filterFeatures.R
@@ -455,7 +455,7 @@ setMethod("filterFeatures",
                   vals <- rowPercentMissing(featureValues(object, ...)[, spl_idx])
                   fts_idx <- c(fts_idx, which(vals <= filter@threshold))
               }
-              fts_idx <- order(unique(fts_idx))
+              fts_idx <- sort(unique(fts_idx))
               message(length(vals) - length(fts_idx), " features were removed")
               ph <- XProcessHistory(param = filter,
                                     date. = date(),
@@ -479,7 +479,7 @@ setMethod("filterFeatures",
                   vals <- rowPercentMissing(assay(object, assay)[, spl_idx])
                   fts_idx <- c(fts_idx, which(vals <= filter@threshold))
               }
-              fts_idx <- order(unique(fts_idx))
+              fts_idx <- sort(unique(fts_idx))
               message(length(vals) - length(fts_idx), " features were removed")
               object[fts_idx]
           }
diff --git a/inst/NEWS b/inst/NEWS
index 5fc15922b..b61d17766 100644
--- a/inst/NEWS
+++ b/inst/NEWS
@@ -1,3 +1,14 @@
+Changes in version 4.1.9
+----------------------
+
+- Fix bug in `filterFeatures,PercentMissingFilter`.
+
+Changes in version 4.1.8
+----------------------
+
+- Fixing issue #716: edit of `.empty_chrom_peaks` function so an `sn` column is
+  returned. Fixes extracting and plotting of peaks after using `manualChromPeaks`
+
 Changes in version 4.1.7
 ----------------------
 
diff --git a/tests/testthat/test_XcmsExperiment.R b/tests/testthat/test_XcmsExperiment.R
index 4aa26f58e..f2b0e6303 100644
--- a/tests/testthat/test_XcmsExperiment.R
+++ b/tests/testthat/test_XcmsExperiment.R
@@ -4,7 +4,7 @@ mse_dia <- readMsExperiment(fl)
 test_that(".empty_chrom_peaks works", {
     res <- .empty_chrom_peaks()
     expect_true(nrow(res) == 0)
-    expect_equal(colnames(res), c(.REQ_PEAKS_COLS, "maxo"))
+    expect_equal(colnames(res), c(.REQ_PEAKS_COLS, "maxo","sn"))
 
     res <- .empty_chrom_peaks(sample = FALSE)
     expect_true(nrow(res) == 0)
@@ -995,8 +995,13 @@ test_that("manualChromPeaks,XcmsExperiment works", {
     expect_equal(unname(pks[, c("mz", "into", "maxo")]),
                  unname(pks_2[, c("mz", "into", "maxo")]))
 
+    chr_pks <- chromPeaks(res)
+    expect_true("sn" %in% colnames(chr_pks))
+
     res2 <- manualChromPeaks(tmp, pks, samples = 2)
     expect_equal(unname(chromPeaks(res2)), unname(pks_2))
+
+    
 })
 
 test_that("filterChromPeaks,XcmsExperiment works", {