diff --git a/Changelog b/Changelog
index f1e3fab2..2dedf90f 100644
--- a/Changelog
+++ b/Changelog
@@ -1,5 +1,7 @@
 ### Added
+-- Adding Zenodo DOI.
 ### Changed
 
 ### Fixed
--- Wrong assignment for the subFDR filtering
\ No newline at end of file
+-- Wrong assignment for the subFDR filtering.
+-- PTMPRophet was having issue in replacing the PeptideProphet file.
\ No newline at end of file
diff --git a/go.mod b/go.mod
index bd94d814..83a734f5 100644
--- a/go.mod
+++ b/go.mod
@@ -12,6 +12,7 @@ require (
 	github.com/konsorten/go-windows-terminal-sequences v1.0.2 // indirect
 	github.com/kr/text v0.2.0 // indirect
 	github.com/mattn/go-colorable v0.1.6
+	github.com/mitchellh/gox v1.0.1 // indirect
 	github.com/niemeyer/pretty v0.0.0-20200227124842-a10e7caefd8e // indirect
 	github.com/nlopes/slack v0.6.0
 	github.com/pierrre/archivefile v0.0.0-20170218184037-e2d100bc74f5
diff --git a/lib/pip/pip.go b/lib/pip/pip.go
index 21756a81..60d9b3b4 100644
--- a/lib/pip/pip.go
+++ b/lib/pip/pip.go
@@ -384,6 +384,7 @@ func PTMProphet(meta met.Data, p Directives, dir string, data []string) met.Data
 			var files []string
 			files = append(files, "interact.pep.xml")
 			meta.PTMProphet.InputFiles = files
+			meta.PTMProphet.KeepOld = true
 			ptmprophet.Run(meta, files)
 			meta.Serialize()
 		}
@@ -545,9 +546,9 @@ func FilterQuantifyReport(meta met.Data, p Directives, dir string, data []string
 
 			if len(p.Filter.Pex) == 0 {
 				meta.Filter.Pex = "interact.pep.xml"
-				// if p.Commands.PTMProphet == "yes" {
-				// 	meta.Filter.Pex = "interact.mod.pep.xml"
-				// }
+				if p.Commands.PTMProphet == "yes" {
+					meta.Filter.Pex = "interact.mod.pep.xml"
+				}
 			} else {
 				meta.Filter.Pex = p.Filter.Pex
 			}