diff --git a/.gitignore b/.gitignore
index 7c81cae0..ee6edbaa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@
 inst/doc
 *.Rproj
 *.DS_Store
+*.log
diff --git a/DESCRIPTION b/DESCRIPTION
index 365ec25c..89057915 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -29,6 +29,7 @@ Suggests:
     knitr,
     rmarkdown
 Collate: 
+    'clean_Metamorpheus.R'
     'clean_DIANN.R'
     'clean_Philosopher.R'
     'clean_Spectronaut.R'
diff --git a/R/MSstatsConvert_core_functions.R b/R/MSstatsConvert_core_functions.R
index 1bd59788..7141e231 100644
--- a/R/MSstatsConvert_core_functions.R
+++ b/R/MSstatsConvert_core_functions.R
@@ -271,6 +271,13 @@ setMethod("MSstatsClean", signature = "MSstatsPhilosopherFiles",
 #' @return data.table
 setMethod("MSstatsClean", signature = "MSstatsDIANNFiles", 
           .cleanRawDIANN)
+#' Clean Metamorpheus files
+#' @include clean_Metamorpheus.R
+#' @rdname MSstatsClean
+#' @inheritParams .cleanRawMetamorpheus
+#' @return data.table
+setMethod("MSstatsClean", signature = "MSstatsMetamorpheusFiles", 
+          .cleanRawMetamorpheus)
 
 
 #' Preprocess outputs from MS signal processing tools for analysis with MSstats
diff --git a/R/clean_Metamorpheus.R b/R/clean_Metamorpheus.R
new file mode 100644
index 00000000..1ebeb10d
--- /dev/null
+++ b/R/clean_Metamorpheus.R
@@ -0,0 +1,18 @@
+#' Clean raw Metamorpheus files
+#' @param msstats_object an object of class `MSstatsMetamorpheusFiles`.
+#' @return data.table
+#' @keywords internal
+.cleanRawMetamorpheus = function(msstats_object) {
+    metamorpheus_input = getInputFile(msstats_object, "input")
+    metamorpheus_input = data.table::as.data.table(metamorpheus_input)
+    req_cols = c('FileName', 'ProteinGroup', 'FullSequence', 
+                 'PrecursorCharge', 'Peakintensity')
+    metamorpheus_input = metamorpheus_input[, req_cols, with = FALSE]
+    data.table::setnames(
+        metamorpheus_input, 
+        c("ProteinGroup", "FullSequence", "PrecursorCharge", "FileName", "Peakintensity"),
+        c("ProteinName", "PeptideSequence", "PrecursorCharge", "Run", "Intensity"), 
+        skip_absent = TRUE)
+    .logSuccess("Metamorpheus", "clean")
+    metamorpheus_input
+}
\ No newline at end of file
diff --git a/inst/tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds b/inst/tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds
new file mode 100644
index 00000000..252a0912
Binary files /dev/null and b/inst/tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds differ
diff --git a/inst/tinytest/raw_data/Metamorpheus/Annotation.tsv b/inst/tinytest/raw_data/Metamorpheus/Annotation.tsv
new file mode 100644
index 00000000..3745fb78
--- /dev/null
+++ b/inst/tinytest/raw_data/Metamorpheus/Annotation.tsv
@@ -0,0 +1,5 @@
+Run	Condition	BioReplicate	Fraction
+NEG1-calib	neg	1	1
+NEG2-calib	neg	2	1
+POS1-calib	pos	3	1
+POS2-calib	pos	4	1
\ No newline at end of file
diff --git a/inst/tinytest/test_clean_Metamorpheus.R b/inst/tinytest/test_clean_Metamorpheus.R
new file mode 100644
index 00000000..5bbc2136
--- /dev/null
+++ b/inst/tinytest/test_clean_Metamorpheus.R
@@ -0,0 +1,12 @@
+# Test Metamorpheus .cleanRawMetamorpheus ---------------------------
+
+file_path = system.file("tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds", package="MSstatsConvert")
+input = readRDS(file_path)
+output = MSstatsConvert:::.cleanRawMetamorpheus(input)
+expect_equal(ncol(output), 5)
+expect_true(nrow(output) > 0)
+expect_true("Run" %in% colnames(output))
+expect_true("ProteinName" %in% colnames(output))
+expect_true("PeptideSequence" %in% colnames(output))
+expect_true("PrecursorCharge" %in% colnames(output))
+expect_true("Intensity" %in% colnames(output))
\ No newline at end of file
diff --git a/man/MSstatsClean.Rd b/man/MSstatsClean.Rd
index 5568bd5a..bca5ce16 100644
--- a/man/MSstatsClean.Rd
+++ b/man/MSstatsClean.Rd
@@ -13,6 +13,7 @@
 \alias{MSstatsClean,MSstatsSpectronautFiles-method}
 \alias{MSstatsClean,MSstatsPhilosopherFiles-method}
 \alias{MSstatsClean,MSstatsDIANNFiles-method}
+\alias{MSstatsClean,MSstatsMetamorpheusFiles-method}
 \title{Clean files generated by a signal processing tools.}
 \usage{
 MSstatsClean(msstats_object, ...)
@@ -57,6 +58,8 @@ MSstatsClean(msstats_object, ...)
 )
 
 \S4method{MSstatsClean}{MSstatsDIANNFiles}(msstats_object, MBR = TRUE)
+
+\S4method{MSstatsClean}{MSstatsMetamorpheusFiles}(msstats_object)
 }
 \arguments{
 \item{msstats_object}{object that inherits from \code{MSstatsInputFiles} class.}
@@ -125,6 +128,8 @@ data.table
 
 data.table
 
+data.table
+
 data.table
 }
 \description{
@@ -151,6 +156,8 @@ Clean Spectronaut files
 Clean Philosopher files
 
 Clean DIA-NN files
+
+Clean Metamorpheus files
 }
 \examples{
 evidence_path = system.file("tinytest/raw_data/MaxQuant/mq_ev.csv", 
diff --git a/man/dot-cleanRawMetamorpheus.Rd b/man/dot-cleanRawMetamorpheus.Rd
new file mode 100644
index 00000000..b977802d
--- /dev/null
+++ b/man/dot-cleanRawMetamorpheus.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_Metamorpheus.R
+\name{.cleanRawMetamorpheus}
+\alias{.cleanRawMetamorpheus}
+\title{Clean raw Metamorpheus files}
+\usage{
+.cleanRawMetamorpheus(msstats_object)
+}
+\arguments{
+\item{msstats_object}{an object of class \code{MSstatsMetamorpheusFiles}.}
+}
+\value{
+data.table
+}
+\description{
+Clean raw Metamorpheus files
+}
+\keyword{internal}