diff --git a/R/ISAtab-class.R b/R/ISAtab-class.R
index cadbb3b..aaf8d02 100644
--- a/R/ISAtab-class.R
+++ b/R/ISAtab-class.R
@@ -15,6 +15,7 @@ ISAtab <- setClass("ISAtab",
                      assay.filenames.per.study="list",
                      assay.files="list",
                      assay.files.per.study="list",
+                     assay.names="list",
                      assay.technology.types="character",
                      assay.measurement.types="character",
                      data.filenames="list",
diff --git a/R/ISAtab-methods.R b/R/ISAtab-methods.R
index 0b9abe7..c5ef9b9 100644
--- a/R/ISAtab-methods.R
+++ b/R/ISAtab-methods.R
@@ -15,6 +15,7 @@ setMethod(f="[",signature="ISAtab", definition=function(x, i,j, drop) {
   if (i=="assay.filenames") { return(x@assay.filenames) } else {}
   if (i=="assay.filenames.per.study") { return(x@assay.filenames.per.study) } else {}
   if (i=="assay.files") { return(x@assay.files) } else {}
+  if (i=="assay.names") { return(x@assay.names) } else {}
   if (i=="assay.files.per.study") { return(x@assay.files.per.study) } else {}
   if (i=="assay.technology.types") { return(x@assay.technology.types) } else {}
   if (i=="assay.measurement.types") { return(x@assay.measurement.types) } else {}
@@ -48,6 +49,7 @@ setReplaceMethod(f="[",signature="ISAtab", definition=function(x,i,j,value){
   if (i=="assay.filenames") { x@assay.filenames<-value } else {}
   if (i=="assay.filenames.per.study") { x@assay.filenames.per.study<-value } else {}
   if (i=="assay.files") { x@assay.files<-value } else {}
+  if (i=="assay.names") { x@assay.names<-value } else {}
   if (i=="assay.files.per.study") { x@assay.files.per.study<-value} else {}
   if (i=="assay.technology.types") { x@assay.technology.types<-value} else {}
   if (i=="assay.measurement.types") { x@assay.measurement.types<-value } else {}
@@ -144,7 +146,12 @@ setMethod(
                                                   function(i) read.table(file.path(path,afilenames.per.study[[j]][[i]]), sep="\t", header=TRUE, stringsAsFactors=FALSE, check.names=FALSE))))
     names(afiles.per.study) <- sidentifiers
     
-    .Object["assay.files.per.study"] < afiles.per.study
+    .Object["assay.files.per.study"] <- afiles.per.study
+    
+  
+    ###assay.names
+    assay.names <- lapply( afiles, function(i) i[ grep(isatab.syntax$assay.name, colnames(i) ) ])  
+    .Object["assay.names"] <- assay.names
         
     ## Assay technology types
     #data frame with types
diff --git a/R/Risa-ms.R b/R/Risa-ms.R
index c25ef48..dcf82bc 100644
--- a/R/Risa-ms.R
+++ b/R/Risa-ms.R
@@ -1,6 +1,5 @@
 ### Methods to deal with assays whose technology type is mass spectrometry 
 
-
 ### specific function to deal with assays whose technology type is mass spectrometry using the xcms package
 ### it returns an xcmsSet
 processAssayXcmsSet.1factor = function(isa, assay.filename, ...){
@@ -47,6 +46,12 @@ processAssayXcmsSet.1factor = function(isa, assay.filename, ...){
 ### it returns an xcmsSet
 ### TODO - change implementation to include all factors
 processAssayXcmsSet = function(isa, assay.filename, ...){
+  
+  
+  phenodata.data.frame <- as.data.frame(isa["factors"])
+  
+  
+  
   for(i in seq_len(length(isa["assay.filenames"]))){
     
     if (isa["assay.filenames"][[i]]==assay.filename){
@@ -55,7 +60,7 @@ processAssayXcmsSet = function(isa, assay.filename, ...){
       {
         #mass spectrometry files
         msfiles = isa["data.filenames"][[i]][[ isatab.syntax$raw.spectral.data.file ]]
-        
+                
         pd = try(read.AnnotatedDataFrame(file.path(isa["path"], isa["assay.filenames"][i]),
                                          row.names = NULL, blank.lines.skip = TRUE, fill = TRUE,
                                          varMetadata.char = "$", quote="\""))
diff --git a/R/Risa.R b/R/Risa.R
index b5d023f..3b1b51e 100755
--- a/R/Risa.R
+++ b/R/Risa.R
@@ -16,7 +16,8 @@ isatab.syntax <- list(
   free.induction.decay.data.file="Free Induction Decay Data File",
   array.data.file="Array Data File",
   raw.spectral.data.file="Raw Spectral Data File",
-  factor.name="Factor Name"
+  factor.name="Factor Name",
+  assay.name="Assay Name"
   )
 
 technology.types <- list(
diff --git a/man/ISAtab-class.Rd b/man/ISAtab-class.Rd
index e25fb30..5b71970 100644
--- a/man/ISAtab-class.Rd
+++ b/man/ISAtab-class.Rd
@@ -23,6 +23,7 @@ Objects can be created by calls of the form \code{new("ISAtab", ...)}.
     \item{\code{assay.filenames.per.study}:}{Object of class \code{"list"}, the names of the assay files according to the study they belong to }
     \item{\code{assay.files}:}{Object of class \code{"list"}, a list of data frames with the contents of the assay files }
     \item{\code{assay.files.per.study}:}{Object of class \code{"list"}, a list of data frames with the contents of the assay files divided per study they belong to }
+    \item{\code{assay.names}:}{Object of class \code{"list"}, which is a list of data frames, containing, per each assay file, the column of the assay file corresponding to the "Assay Name" }
     \item{\code{assay.technology.types}:}{Object of class \code{"character"}, a list with the technology types corresponding to each assay }
     \item{\code{assay.measurement.types}:}{Object of class \code{"character"}, a list with the names of the data files }
     \item{\code{data.filenames}:}{Object of class \code{"list"},    a list with the names of the samples }