diff --git a/R/module-qc-server.R b/R/module-qc-server.R
index 428eb47..175f8f7 100644
--- a/R/module-qc-server.R
+++ b/R/module-qc-server.R
@@ -170,17 +170,19 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
                             which.Protein = protein,
                             originalPlot = original,
                             summaryPlot = input$summ,
-                            address = file, isPlotly = TRUE
+                            address="Ex_", isPlotly = TRUE
         )[[1]]
-        return(plot)
+        # return(plot)
         
       } else if (loadpage_input()$BIO == "PTM"){
         
-        dataProcessPlotsPTM(preprocess_data(),
+        plot <- dataProcessPlotsPTM(preprocess_data(),
                             type=input$type1,
                             which.PTM = protein,
+                            originalPlot = original,
                             summaryPlot = input$summ,
-                            address = file)
+                            address="Ex_", isPlotly = TRUE)[[1]]
+        # return(plot)
         
       } else{
         plot <- dataProcessPlots(data = preprocess_data(),
@@ -194,12 +196,14 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
                          originalPlot = original,
                          summaryPlot = input$summ,
                          save_condition_plot_result = FALSE,
-                         address = file,
+                         address="Ex_",
                          isPlotly = TRUE
 
         )[[1]]
-        return(plot)
+        # return(plot)
       }
+      enable("plotresults_qc")
+      return(plot)
     }
     else {
       return(NULL)
@@ -367,17 +371,25 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d
   #   }
   # })
   
+  
+  ### OUTPUT ####
+  output$plotresults_qc = downloadHandler(
+    filename = function() {
+      paste("SummaryPlot-", Sys.Date(), ".zip", sep="")
+    },
+    content = function(file) {
+      files <- list.files(getwd(), pattern = "^Ex_", full.names = TRUE)
+      file_info <- file.info(files)
+      latest_file <- files[which.max(file_info$mtime)]
+      print(latest_file)
+      file.copy(latest_file, file)
+    }
+  )
+  
   output$showplot = renderUI({
     ns<- session$ns
-    
-    # PTM plotly plots are still under development
-    if (loadpage_input()$BIO == "PTM") {
-      output$theplot = renderPlot(theplot())
-      op <- plotOutput(ns("theplot"))
-    } else {
-      output$theplot = renderPlotly(theplot())
-      op <- plotlyOutput(ns("theplot"))
-    }
+    output$theplot = renderPlotly(theplot())
+    op <- plotlyOutput(ns("theplot"))
 
     tagList(
       op,
diff --git a/R/module-qc-ui.R b/R/module-qc-ui.R
index 346eeba..550cc6d 100644
--- a/R/module-qc-ui.R
+++ b/R/module-qc-ui.R
@@ -227,7 +227,7 @@ qcUI <- function(id) {
                                                            "No feature legend"="NA"))
                                              
                             ),
-                            
+                            p("Use the camera icon on the top right of the plot to download as PNG"),
                             uiOutput(ns("Which")),
                             tags$br()
                           ),
@@ -235,8 +235,10 @@ qcUI <- function(id) {
                           #                  tags$br(),
                           #                  tags$br(),
                           #                  tags$h4("Calculation in progress...")),
-                          uiOutput(ns("showplot")),
+                          disabled(downloadButton(ns("plotresults_qc"), "Save plot results as Zip")),
+                          uiOutput(ns("showplot"))
                           # disabled(downloadButton(ns("saveplot"), "Save this plot"))
+                          
                  ),
                  tabPanel("Download Data", 
                           #verbatimTextOutput('effect'),
diff --git a/R/module-statmodel-server.R b/R/module-statmodel-server.R
index 0991fe5..6cb2e61 100644
--- a/R/module-statmodel-server.R
+++ b/R/module-statmodel-server.R
@@ -399,15 +399,31 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu
     }
 
     if (loadpage_input()$BIO=="PTM"){
-      plot1 = groupComparisonPlotsPTM(data_comparison(),
-                                      input$typeplot,
-                                      sig=input$sig,
-                                      FCcutoff=input$FC,
-                                      logBase.pvalue=as.integer(input$logp),
-                                      ProteinName = input$pname,
-                                      which.Comparison = input$whichComp,
-                                      address = FALSE)
-
+      tryCatch({
+        if(toupper(input$typeplot) == "COMPARISONPLOT") {
+          remove_modal_spinner()
+          stop( 'Comparison Plot is not offered by MSstatsPTM at the moment' )
+        }
+        plot = groupComparisonPlotsPTM(data_comparison(),
+                                        input$typeplot,
+                                        sig=input$sig,
+                                        FCcutoff=input$FC,
+                                        logBase.pvalue=as.integer(input$logp),
+                                        ProteinName = input$pname,
+                                        numProtein=input$nump,
+                                        which.Comparison = input$whichComp,
+                                        address = "Ex_",
+                                        isPlotly = TRUE)
+        if(length(plot) == 3) { # return adjusted if we have it
+          plot1 = plot[[3]]
+        } else {
+          plot1 = plot[[1]]
+        }
+        remove_modal_spinner()
+      },error = function(e){
+        remove_modal_spinner()
+        stop( '** Cannnot generate multiple plots in a screen. Please refine selection or save to a pdf. **' )}
+      )
 
     } else if(loadpage_input()$DDA_DIA=="TMT"){
       tryCatch({
@@ -717,18 +733,10 @@ statmodelServer <- function(input, output, session,parent_session, loadpage_inpu
 
   observeEvent(input$viewresults, {
     ns <- session$ns
-    # PTM plotly plots are still under development
-    if (loadpage_input()$BIO == "PTM") {
-      output$comp_plots = renderPlot({
-        group_comparison(FALSE, FALSE)
-      })
-      op <- plotOutput(ns("comp_plots"))
-    } else {
-      output$comp_plots = renderPlotly({
-        group_comparison(FALSE, FALSE)
-      })
-      op <- plotlyOutput(ns("comp_plots"), height = input$height)
-    }
+    output$comp_plots = renderPlotly({
+      group_comparison(FALSE, FALSE)
+    })
+    op <- plotlyOutput(ns("comp_plots"), height = input$height)
     insertUI(
       selector = paste0("#", ns("comparison_plots")),
       ui=tags$div(
diff --git a/R/module-statmodel-ui.R b/R/module-statmodel-ui.R
index 7769faa..2d17955 100644
--- a/R/module-statmodel-ui.R
+++ b/R/module-statmodel-ui.R
@@ -158,7 +158,10 @@ statmodelUI <- function(id) {
                           Volcano Plot comparison, you must save the results \
                           as a HTML."),
                  conditionalPanel(
-                   condition = "input['loadpage-BIO'] !== 'PTM'",
+                   condition = "input['loadpage-BIO'] == 'PTM' && input['statmodel-typeplot'] == 'ComparisonPlot'",
+                   p("Comparison Plot is not offered by MSstatsPTM at the moment")),
+                 conditionalPanel(
+                   condition = "input['loadpage-BIO'] !== 'PTM_'",
                    actionButton(ns("viewresults"), 
                                 "View plot in browser (only for one \
                                      comparison/protein)")),