diff --git a/bin/diann_convert.py b/bin/diann_convert.py
index fb2bdd22..f385b607 100755
--- a/bin/diann_convert.py
+++ b/bin/diann_convert.py
@@ -292,7 +292,7 @@ def diann_version(self) -> str:
         return diann_version_id
 
     def validate_diann_version(self) -> None:
-        supported_diann_versions = ["1.8.1"]
+        supported_diann_versions = ["1.8.1", "1.9.beta.1"]
         if self.diann_version not in supported_diann_versions:
             raise ValueError(f"Unsupported DIANN version {self.diann_version}")
 
diff --git a/modules/local/assemble_empirical_library/main.nf b/modules/local/assemble_empirical_library/main.nf
index 14eb19e2..853925c2 100644
--- a/modules/local/assemble_empirical_library/main.nf
+++ b/modules/local/assemble_empirical_library/main.nf
@@ -3,8 +3,8 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
     label 'process_low'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
-        'docker.io/biocontainers/diann:v1.8.1_cv1' }"
+        'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' :
+        'ghcr.io/bigbio/diann:1.9.1dev' }"
 
     input:
     // In this step the real files are passed, and not the names
@@ -58,7 +58,7 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
+        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?")
     END_VERSIONS
     """
 }
diff --git a/modules/local/diann_preliminary_analysis/main.nf b/modules/local/diann_preliminary_analysis/main.nf
index fe995ece..e5401c2c 100644
--- a/modules/local/diann_preliminary_analysis/main.nf
+++ b/modules/local/diann_preliminary_analysis/main.nf
@@ -3,8 +3,8 @@ process DIANN_PRELIMINARY_ANALYSIS {
     label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
-        'docker.io/biocontainers/diann:v1.8.1_cv1' }"
+        'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' :
+        'ghcr.io/bigbio/diann:1.9.1dev' }"
 
     input:
     tuple val(meta), path(ms_file), path(predict_library)
@@ -61,7 +61,7 @@ process DIANN_PRELIMINARY_ANALYSIS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
+        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?")
     END_VERSIONS
     """
 }
diff --git a/modules/local/diannsummary/main.nf b/modules/local/diannsummary/main.nf
index 4677b3e3..70b707c1 100644
--- a/modules/local/diannsummary/main.nf
+++ b/modules/local/diannsummary/main.nf
@@ -3,8 +3,8 @@ process DIANNSUMMARY {
     label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
-        'docker.io/biocontainers/diann:v1.8.1_cv1' }"
+        'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' :
+        'ghcr.io/bigbio/diann:1.9.1dev' }"
 
     input:
     // Note that the files are passed as names and not paths, this prevents them from being staged
@@ -24,7 +24,8 @@ process DIANNSUMMARY {
     path "diann_report.gg_matrix.tsv", emit: gg_matrix
     path "diann_report.unique_genes_matrix.tsv", emit: unique_gene_matrix
     path "diannsummary.log", emit: log
-    path "empirical_library.tsv.speclib", emit: final_speclib
+    path "empirical_library.tsv", emit: final_speclib
+    path "empirical_library.tsv.skyline.speclib", emit: skyline_speclib
     path "versions.yml", emit: version
 
     when:
@@ -69,7 +70,7 @@ process DIANNSUMMARY {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
+        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?")
     END_VERSIONS
     """
 }
diff --git a/modules/local/individual_final_analysis/main.nf b/modules/local/individual_final_analysis/main.nf
index f80b047a..21c0d375 100644
--- a/modules/local/individual_final_analysis/main.nf
+++ b/modules/local/individual_final_analysis/main.nf
@@ -3,8 +3,8 @@ process INDIVIDUAL_FINAL_ANALYSIS {
     label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
-        'docker.io/biocontainers/diann:v1.8.1_cv1' }"
+        'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' :
+        'ghcr.io/bigbio/diann:1.9.1dev' }"
 
     input:
     tuple val(meta), path(ms_file), path(fasta), path(diann_log), path(library)
@@ -53,7 +53,7 @@ process INDIVIDUAL_FINAL_ANALYSIS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
+        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?")
     END_VERSIONS
     """
 }
diff --git a/modules/local/silicolibrarygeneration/main.nf b/modules/local/silicolibrarygeneration/main.nf
index e5f6e2f3..55169a7b 100644
--- a/modules/local/silicolibrarygeneration/main.nf
+++ b/modules/local/silicolibrarygeneration/main.nf
@@ -3,8 +3,8 @@ process SILICOLIBRARYGENERATION {
     label 'process_medium'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
-        'docker.io/biocontainers/diann:v1.8.1_cv1' }"
+        'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif' :
+        'ghcr.io/bigbio/diann:1.9.1dev' }"
 
     input:
     file(fasta)
@@ -49,7 +49,7 @@ process SILICOLIBRARYGENERATION {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
+        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "\\d+\\.\\d+(\\.\\w+)*(\\.[\\d]+)?")
     END_VERSIONS
     """
 }