diff --git a/R/clean_Spectronaut.R b/R/clean_Spectronaut.R
index ebf7cc98..48b4287d 100644
--- a/R/clean_Spectronaut.R
+++ b/R/clean_Spectronaut.R
@@ -8,7 +8,7 @@
                                 anomalyModelFeatures,
                                 peptideSequenceColumn = "EG.ModifiedSequence",
                                 heavyLabels = NULL) {
-  FFrgLossType = FExcludedFromQuantification = NULL
+  FFrgLossType = FExcludedFromQuantification = Fraction = NULL
 
   spec_input = getInputFile(msstats_object, "input")
   .validateSpectronautInput(spec_input, peptideSequenceColumn)
@@ -29,8 +29,8 @@
 
   cols = c(protein_col, peptide_col, "FGCharge", "FFrgIon",
            f_charge_col, "RFileName", "RCondition", "RReplicate",
-           "EGQvalue", pg_qval_col, interference_col, exclude_col,
-           intensity_col)
+           "RFraction", "EGQvalue", pg_qval_col, interference_col,
+           exclude_col, intensity_col)
   if (calculateAnomalyScores){
     cols = c(cols, anomalyModelFeatures)
   }
@@ -41,11 +41,24 @@
     spec_input,
     c(protein_col, peptide_col, "FGCharge", "FFrgIon",
       f_charge_col, "RFileName", intensity_col,
-      "RCondition", "RReplicate"),
+      "RCondition", "RReplicate", "RFraction"),
     c("ProteinName", "PeptideSequence", "PrecursorCharge", "FragmentIon",
-      "ProductCharge", "Run", "Intensity", "Condition", "BioReplicate"),
+      "ProductCharge", "Run", "Intensity", "Condition", "BioReplicate",
+      "Fraction"),
     skip_absent = TRUE)
 
+  if ("Fraction" %in% colnames(spec_input)) {
+    n_missing_fraction = sum(is.na(spec_input$Fraction))
+    if (n_missing_fraction > 0) {
+      msg = paste("**", n_missing_fraction,
+                  "row(s) have missing (NA) values in the Fraction column.",
+                  "These will be assigned to Fraction 1.")
+      getOption("MSstatsLog")("WARN", msg)
+      getOption("MSstatsMsg")("WARN", msg)
+      spec_input[is.na(Fraction), Fraction := 1]
+    }
+  }
+
   spec_input = .assignSpectronautIsotopeLabelType(
     spec_input, heavyLabels)
 
diff --git a/inst/tinytest/test_clean_Spectronaut.R b/inst/tinytest/test_clean_Spectronaut.R
index be05e5fd..a4a581a7 100644
--- a/inst/tinytest/test_clean_Spectronaut.R
+++ b/inst/tinytest/test_clean_Spectronaut.R
@@ -9,6 +9,29 @@ output = MSstatsConvert:::.cleanRawSpectronaut(msstats_input, intensity = 'FG.MS
                                     calculateAnomalyScores = FALSE, 
                                     anomalyModelFeatures = c())
 expect_true(all(output$Intensity == 100000))
+expect_false("Fraction" %in% colnames(output))
+
+spectronaut_frac = data.table::copy(spectronaut_raw)
+spectronaut_frac$R.Fraction = 2L
+msstats_frac = MSstatsConvert::MSstatsImport(
+    list(input = spectronaut_frac), "MSstats", "Spectronaut")
+output_frac = MSstatsConvert:::.cleanRawSpectronaut(msstats_frac, intensity = 'FG.MS1Quantity',
+                                    calculateAnomalyScores = FALSE,
+                                    anomalyModelFeatures = c())
+expect_true("Fraction" %in% colnames(output_frac))
+expect_false("RFraction" %in% colnames(output_frac))
+expect_true(all(output_frac$Fraction == 2L))
+
+spectronaut_frac_na = data.table::copy(spectronaut_raw)
+spectronaut_frac_na$R.Fraction = NA_integer_
+msstats_frac_na = MSstatsConvert::MSstatsImport(
+    list(input = spectronaut_frac_na), "MSstats", "Spectronaut")
+output_frac_na = MSstatsConvert:::.cleanRawSpectronaut(msstats_frac_na, intensity = 'FG.MS1Quantity',
+                                    calculateAnomalyScores = FALSE,
+                                    anomalyModelFeatures = c())
+expect_true("Fraction" %in% colnames(output_frac_na))
+expect_false(any(is.na(output_frac_na$Fraction)))
+expect_true(all(output_frac_na$Fraction == 1))
 
 expect_error(MSstatsConvert:::.cleanRawSpectronaut(msstats_input, intensity = 'invalid',
                                                    calculateAnomalyScores = FALSE,