diff --git a/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-injection/plugin.properties b/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-injection/plugin.properties
new file mode 100644
index 0000000000000000000000000000000000000000..45059c541e5261fb6207e548565b3b370af9f5c6
--- /dev/null
+++ b/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-injection/plugin.properties
@@ -0,0 +1,16 @@
+# ---------------------------------------------------------------------------
+# 'ms-injection' drop box for spectra data
+# ---------------------------------------------------------------------------
+# The directory to watch for incoming data.
+incoming-dir = ${data-dir}/incoming-ms-injection
+
+# Determines when the incoming data should be considered complete and ready to be processed.
+# Allowed values: 
+#  - auto-detection - when no write access will be detected for a specified 'quite-period'
+#  - marker-file		- when an appropriate marker file for the data exists. 
+# The default value is 'marker-file'.
+incoming-data-completeness-condition = auto-detection
+
+data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+type-extractor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.TypeExtractorForMSInjection
diff --git a/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties b/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties
new file mode 100644
index 0000000000000000000000000000000000000000..f14e258cb9283a672bf3ce6cb8ff43dc74b5d07f
--- /dev/null
+++ b/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties
@@ -0,0 +1,23 @@
+# ---------------------------------------------------------------------------
+# 'ms-search' drop box for protein data
+# ---------------------------------------------------------------------------
+incoming-dir = ${data-dir}/incoming-ms-search
+
+incoming-data-completeness-condition = auto-detection
+
+data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForProteinResults
+data-set-info-extractor.separator = +
+
+type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+type-extractor.file-format-type = XML
+type-extractor.locator-type = RELATIVE_LOCATION
+type-extractor.data-set-type = PROT_RESULT
+type-extractor.is-measured = false
+
+storage-processor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.StorageProcessorWithResultDataSetUploader
+storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+storage-processor.assuming-extended-prot-xml = false
+storage-processor.database.basic-name = ${data-source.basicDatabaseName}
+storage-processor.database.kind = ${data-source.databaseKind}
+storage-processor.database.owner = 
+storage-processor.database.password = 
\ No newline at end of file
diff --git a/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/maintenance-plugins/data-set-clean-up/plugin.properties b/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/maintenance-plugins/data-set-clean-up/plugin.properties
new file mode 100644
index 0000000000000000000000000000000000000000..39fd0f53fcc0de0102fbce580fa2eb28e063f0b3
--- /dev/null
+++ b/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/maintenance-plugins/data-set-clean-up/plugin.properties
@@ -0,0 +1,4 @@
+class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
+interval = 300
+data-source = data-source
+data-set-table-name = data_sets 
diff --git a/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/miscellaneous/data-sources/plugin.properties b/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/miscellaneous/data-sources/plugin.properties
new file mode 100644
index 0000000000000000000000000000000000000000..56226fbefb62cd575bbbc47b85de3b8a992a1fb0
--- /dev/null
+++ b/rtd_phosphonetx/dist/core-plugins/proteomics/1/dss/miscellaneous/data-sources/plugin.properties
@@ -0,0 +1,5 @@
+
+data-sources = data-source
+data-source.databaseEngineCode = postgresql
+data-source.basicDatabaseName = proteomics
+data-source.databaseKind = productive
diff --git a/rtd_phosphonetx/dist/etc/service.properties b/rtd_phosphonetx/dist/etc/service.properties
index 9a39b2b1b3e81317243834aa3954abd2a24bd9be..c09174beed1b500aadb2ef346e39a1eb05023b25 100644
--- a/rtd_phosphonetx/dist/etc/service.properties
+++ b/rtd_phosphonetx/dist/etc/service.properties
@@ -79,92 +79,4 @@ failure-interval = 10
 # Valid only when auto-detection method is used to determine if an incoming data are ready to be processed.
 quiet-period = 10
 
-# ---------------------------------------------------------------------------
-# Data sources
-# ---------------------------------------------------------------------------
-
-data-sources = data-source
-data-source.databaseEngineCode = postgresql
-data-source.basicDatabaseName = proteomics
-data-source.databaseKind = productive
-
-# Specifies what should happen if an error occurs during dataset processing. 
-# By default this flag is set to false and user has to modify the 'faulty paths file' 
-# each time the faulty dataset should be processed again.
-# Set this flag to true if the processing should be repeated after some time without manual intervention.
-# Note that this can increase the server load.
-# reprocess-faulty-datasets = false
-
-# ---------------------------------------------------------------------------
-# ETL processing threads (aka 'Drop Boxes')
-# ---------------------------------------------------------------------------
-# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
-# E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
-inputs = ms-injection, ms-search
-
-# ---------------------------------------------------------------------------
-# 'ms-injection' drop box for spectra data
-# ---------------------------------------------------------------------------
-# The directory to watch for incoming data.
-ms-injection.incoming-dir = ${data-dir}/incoming-ms-injection
-
-# Determines when the incoming data should be considered complete and ready to be processed.
-# Allowed values: 
-#  - auto-detection - when no write access will be detected for a specified 'quite-period'
-#  - marker-file		- when an appropriate marker file for the data exists. 
-# The default value is 'marker-file'.
-ms-injection.incoming-data-completeness-condition = auto-detection
-
-ms-injection.data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection
-ms-injection.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-ms-injection.type-extractor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.TypeExtractorForMSInjection
-
-# ---------------------------------------------------------------------------
-# 'ms-search' drop box for protein data
-# ---------------------------------------------------------------------------
-# The directory to watch for incoming data.
-ms-search.incoming-dir = ${data-dir}/incoming-ms-search
-
-# Determines when the incoming data should be considered complete and ready to be processed.
-# Allowed values: 
-#  - auto-detection - when no write access will be detected for a specified 'quite-period'
-#  - marker-file		- when an appropriate marker file for the data exists. 
-# The default value is 'marker-file'.
-ms-search.incoming-data-completeness-condition = auto-detection
-
-ms-search.data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForProteinResults
-ms-search.data-set-info-extractor.separator = +
-
-ms-search.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
-ms-search.type-extractor.file-format-type = XML
-ms-search.type-extractor.locator-type = RELATIVE_LOCATION
-ms-search.type-extractor.data-set-type = PROT_RESULT
-ms-search.type-extractor.is-measured = false
-
-ms-search.storage-processor = ch.systemsx.cisd.openbis.etlserver.phosphonetx.StorageProcessorWithResultDataSetUploader
-ms-search.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-ms-search.storage-processor.assuming-extended-prot-xml = false
-ms-search.storage-processor.database.basic-name = ${data-source.basicDatabaseName}
-ms-search.storage-processor.database.kind = ${data-source.databaseKind}
-ms-search.storage-processor.database.owner = 
-ms-search.storage-processor.database.password = 
-
-# ---------------------------------------------------------------------------
-# maintenance plugins configuration
-# ---------------------------------------------------------------------------
-# Comma separated names of maintenance plugins.  
-# Each plugin should have configuration properties prefixed with its name.
-# Mandatory properties for each <plugin> include: 
-#   <plugin>.class - Fully qualified plugin class name
-#   <plugin>.interval - The time between plugin executions (in seconds)
-# Optional properties for each <plugin> include:
-#   <plugin>.start - Time of the first execution (HH:mm)
-#   <plugin>.execute-only-once - If true the task will be executed exactly once, 
-#                                interval will be ignored. By default set to false.
-
-maintenance-plugins = data-set-clean-up
-
-data-set-clean-up.class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
-data-set-clean-up.interval = 300
-data-set-clean-up.data-source = data-source
-data-set-clean-up.data-set-table-name = data_sets 
+core-plugins-folder = ../core-plugins
\ No newline at end of file
diff --git a/rtd_phosphonetx/dist/tarball/installer/dss-service.properties b/rtd_phosphonetx/dist/tarball/installer/dss-service.properties
index d84255f9f6a2749e4cc7290026ed27aff41feac4..bec215c03123a2ec4738edff0d628e0313183973 100644
--- a/rtd_phosphonetx/dist/tarball/installer/dss-service.properties
+++ b/rtd_phosphonetx/dist/tarball/installer/dss-service.properties
@@ -9,86 +9,4 @@ host-address = https://$HOSTNAME
 quiet-period = 10
 check-interval = 5
 
-# ---------------------------------------------------------------------------
-# Data sources
-
-data-sources = data-source
-data-source.databaseEngineCode = postgresql
-data-source.basicDatabaseName = proteomics
-data-source.databaseKind = productive
-
-# ---------------------------------------------------------------------------
-# ETL processing threads (aka 'Drop Boxes')
-# ---------------------------------------------------------------------------
-
-inputs = ms-injection, ms-search
-
-# ---------------------------------------------------------------------------
-# 'ms-injection' drop box for spectra data
-# ---------------------------------------------------------------------------
-# The directory to watch for incoming data.
-ms-injection.incoming-dir = ${root-dir}/incoming-ms-injection
-
-# Determines when the incoming data should be considered complete and ready to be processed.
-# Allowed values: 
-#  - auto-detection - when no write access will be detected for a specified 'quite-period'
-#  - marker-file		- when an appropriate marker file for the data exists. 
-# The default value is 'marker-file'.
-ms-injection.incoming-data-completeness-condition = auto-detection
-
-ms-injection.data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection
-ms-injection.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-ms-injection.type-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.TypeExtractorForMSInjection
-
-# ---------------------------------------------------------------------------
-# 'ms-search' drop box for spectra data
-# ---------------------------------------------------------------------------
-# The directory to watch for incoming data.
-ms-search.incoming-dir = ${root-dir}/incoming-ms-search
-
-# Determines when the incoming data should be considered complete and ready to be processed.
-# Allowed values: 
-#  - auto-detection - when no write access will be detected for a specified 'quite-period'
-#  - marker-file		- when an appropriate marker file for the data exists. 
-# The default value is 'marker-file'.
-ms-search.incoming-data-completeness-condition = auto-detection
-
-ms-search.data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForProteinResults
-ms-search.data-set-info-extractor.separator = +
-
-ms-search.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
-ms-search.type-extractor.file-format-type = XML
-ms-search.type-extractor.locator-type = RELATIVE_LOCATION
-ms-search.type-extractor.data-set-type = PROT_RESULT
-ms-search.type-extractor.is-measured = false
-
-ms-search.storage-processor = ch.systemsx.cisd.openbis.etlserver.proteomics.StorageProcessorWithResultDataSetUploader
-ms-search.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-ms-search.storage-processor.assuming-extended-prot-xml = false
-ms-search.storage-processor.database.basic-name = ${data-source.basicDatabaseName}
-ms-search.storage-processor.database.kind = ${data-source.databaseKind}
-ms-search.storage-processor.database.owner = 
-ms-search.storage-processor.database.password = 
-
-# ---------------------------------------------------------------------------
-# maintenance plugins configuration
-# ---------------------------------------------------------------------------
-# Comma separated names of maintenance plugins.  
-# Each plugin should have configuration properties prefixed with its name.
-# Mandatory properties for each <plugin> include: 
-#   <plugin>.class - Fully qualified plugin class name
-#   <plugin>.interval - The time between plugin executions (in seconds)
-# Optional properties for each <plugin> include:
-#   <plugin>.start - Time of the first execution (HH:mm)
-#   <plugin>.execute-only-once - If true the task will be executed exactly once, 
-#                                interval will be ignored. By default set to false.
-
-maintenance-plugins = data-set-clean-up
-
-data-set-clean-up.class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
-data-set-clean-up.interval = 300
-data-set-clean-up.data-source = data-source
-data-set-clean-up.data-set-table-name = data_sets 
-
-
-
+core-plugins-folder = ../core-plugins
\ No newline at end of file