diff --git a/README.md b/README.md
index a8e1426b..f89d1106 100644
--- a/README.md
+++ b/README.md
@@ -31,7 +31,7 @@ The *ISA API*  aims to provide you, the developer, with a set of tools to help y
 ----
 ### Read the Publication...
 
-Read our **open access [publication](https://doi.org/10.1093/gigascience/giab060) "SA API: An open platform for interoperable life science experimental metadata", published in GigaScience** as a `technical note`
+Read our **open access [publication](https://doi.org/10.1093/gigascience/giab060) "ISA API: An open platform for interoperable life science experimental metadata", published in GigaScience** as a `technical note`
 
 *David Johnson, Dominique Batista, Keeva Cochrane, Robert P. Davey, Anthony Etuk, Alejandra Gonzalez-Beltran, Kenneth Haug, Massimiliano Izzo, Martin Larralde, Thomas N. Lawson, Alice Minotto, Pablo Moreno, Venkata Chandrasekhar Nainala, Claire O'Donovan, Luca Pireddu, Pierrick Roger, Felix Shaw, Christoph Steinbeck, Ralf J. M. Weber, Susanna-Assunta Sansone, Philippe Rocca-Serra.
 ISA API: An open platform for interoperable life science experimental metadata. 2020.11.13.382119; doi:
diff --git a/isatools/isatab/dump/write.py b/isatools/isatab/dump/write.py
index 1fb2e9a2..d7968ead 100644
--- a/isatools/isatab/dump/write.py
+++ b/isatools/isatab/dump/write.py
@@ -62,8 +62,9 @@ def flatten(current_list):
         log.warning(s_graph.nodes())
 
         sample_in_path_count = 0
+        protocol_in_path_count = 0
         longest_path = _longest_path_and_attrs(paths, s_graph.indexes)
-
+        
         for node_index in longest_path:
             node = s_graph.indexes[node_index]
             if isinstance(node, Source):
@@ -76,8 +77,9 @@ def flatten(current_list):
                     map(lambda x: get_comment_column(
                         olabel, x), node.comments))
             elif isinstance(node, Process):
-                olabel = "Protocol REF.{}".format(node.executes_protocol.name)
+                olabel = "Protocol REF.{}".format(protocol_in_path_count)
                 columns.append(olabel)
+                protocol_in_path_count += 1
                 if node.executes_protocol.name not in protnames.keys():
                     protnames[node.executes_protocol.name] = protrefcount
                     protrefcount += 1
@@ -104,6 +106,7 @@ def flatten(current_list):
                 columns += flatten(map(lambda x: get_fv_columns(olabel, x),
                                        node.factor_values))
 
+
         omap = get_object_column_map(columns, columns)
         # load into dictionary
         df_dict = dict(map(lambda k: (k, []), flatten(omap)))
@@ -113,6 +116,7 @@ def flatten(current_list):
                 df_dict[k].extend([""])
 
             sample_in_path_count = 0
+            protocol_in_path_count = 0
             for node_index in path_:
                 node = s_graph.indexes[node_index]
                 if isinstance(node, Source):
@@ -129,8 +133,8 @@ def flatten(current_list):
                         df_dict[colabel][-1] = co.value
 
                 elif isinstance(node, Process):
-                    olabel = "Protocol REF.{}".format(
-                        node.executes_protocol.name)
+                    olabel = "Protocol REF.{}".format(protocol_in_path_count)
+                    protocol_in_path_count += 1
                     df_dict[olabel][-1] = node.executes_protocol.name
                     for pv in node.parameter_values:
                         pvlabel = "{0}.Parameter Value[{1}]".format(
@@ -263,6 +267,8 @@ def flatten(current_list):
             if _longest_path_and_attrs(paths, a_graph.indexes) is None:
                 raise IOError(
                     "Could not find any valid end-to-end paths in assay graph")
+            
+            protocol_in_path_count = 0
             for node_index in _longest_path_and_attrs(paths, a_graph.indexes):
                 node = a_graph.indexes[node_index]
                 if isinstance(node, Sample):
@@ -279,9 +285,9 @@ def flatten(current_list):
                                 node.factor_values))
 
                 elif isinstance(node, Process):
-                    olabel = "Protocol REF.{}".format(
-                        node.executes_protocol.name)
+                    olabel = "Protocol REF.{}".format(protocol_in_path_count)
                     columns.append(olabel)
+                    protocol_in_path_count += 1
                     if node.executes_protocol.name not in protnames.keys():
                         protnames[node.executes_protocol.name] = protrefcount
                         protrefcount += 1
@@ -338,12 +344,12 @@ def pbar(x):
                 for k in df_dict.keys():  # add a row per path
                     df_dict[k].extend([""])
 
+                protocol_in_path_count = 0
                 for node_index in path_:
                     node = a_graph.indexes[node_index]
                     if isinstance(node, Process):
-                        olabel = "Protocol REF.{}".format(
-                            node.executes_protocol.name
-                        )
+                        olabel = "Protocol REF.{}".format(protocol_in_path_count)
+                        protocol_in_path_count += 1
                         df_dict[olabel][-1] = node.executes_protocol.name
                         if node.executes_protocol.protocol_type:
                             oname_label = get_column_header(