diff --git a/AGENTS.md b/AGENTS.md
index 453c8ac72..ebc18f2a0 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -352,7 +352,7 @@ withName: 'OPENMS_PERCOLATORADAPTER' {
     publishDir = [
         path: { "${params.outdir}/intermediate_results/fdr_control" },
         mode: params.publish_dir_mode,
-        pattern: '*.idXML'
+        pattern: '*.idparquet'
     ]
 }
 ```
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 3a52d98a5..40d716fd1 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -75,7 +75,7 @@ sp:
     fn: "*_ms_info.parquet"
     num_lines: 0
   pmultiqc/idXML:
-    fn: "*.idXML"
+    fn: "*.idparquet"
     num_lines: 0
   pmultiqc/msstats:
     fn: "*msstats_in.csv"
diff --git a/conf/modules/id.config b/conf/modules/id.config
index 1b2a4ac4a..966700307 100644
--- a/conf/modules/id.config
+++ b/conf/modules/id.config
@@ -6,11 +6,6 @@
 
 process {
 
-    // FDRCONSENSUSID
-    withName: '.*:FDR_CONSENSUSID' {
-        ext.args    = "-PSM true -protein false"
-    }
-
     // ID_SCORE_SWITCHER for phospho scoring
     withName: '.*:ID:PHOSPHO_SCORING:ID_SCORE_SWITCHER' {
         ext.args    = [
@@ -47,13 +42,13 @@ process {
     // PSM FDR control ID_FILTER
     withName: '.*:ID:PSM_FDR_CONTROL:ID_FILTER' {
         ext.args    = "-score:psm \"$params.run_fdr_cutoff\""
-        ext.suffix  = '.idXML'
+        ext.suffix  = '.idparquet'
     }
 
     // DDA_ID PSM FDR control ID_FILTER
     withName: '.*:DDA_ID:PSM_FDR_CONTROL:ID_FILTER' {
         ext.args    = "-score:psm \"$params.run_fdr_cutoff\""
-        ext.suffix  = '.idXML'
+        ext.suffix  = '.idparquet'
     }
 
     // MS2RESCORE
diff --git a/conf/modules/shared.config b/conf/modules/shared.config
index c796635e1..1a9ee7c48 100644
--- a/conf/modules/shared.config
+++ b/conf/modules/shared.config
@@ -34,7 +34,7 @@ process {
     }
 
     // Result tables from multiple pipelines including LFQ, TMT, DDA
-    withName: '.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER' {
+    withName: '.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER|ISOBARIC_WORKFLOW' {
         publishDir = [
             path: { "${params.outdir}/quant_tables" },
             mode: 'copy',
diff --git a/modules/local/openms/comet/meta.yml b/modules/local/openms/comet/meta.yml
index 5f255f4f9..a36a020c2 100644
--- a/modules/local/openms/comet/meta.yml
+++ b/modules/local/openms/comet/meta.yml
@@ -29,7 +29,7 @@ output:
   - id_files_comet:
       type: file
       description: Output file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - log:
       type: file
       description: log file
diff --git a/modules/local/openms/consensusid/main.nf b/modules/local/openms/consensusid/main.nf
deleted file mode 100644
index 76346fb21..000000000
--- a/modules/local/openms/consensusid/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-process CONSENSUSID {
-    tag "$meta.mzml_id"
-    label 'process_single'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    tuple val(meta), path(id_file)
-
-    output:
-    tuple val(meta), path("${meta.mzml_id}_consensus.idXML"), emit: consensusids
-    path "versions.yml", emit: versions
-    path "*.log", emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.mzml_id}"
-
-    """
-    ConsensusID \\
-        -in ${id_file} \\
-        -out ${meta.mzml_id}_consensus.idXML \\
-        -per_spectrum \\
-        -threads $task.cpus \\
-        -algorithm $params.consensusid_algorithm \\
-        -filter:min_support $params.min_consensus_support \\
-        -filter:considered_hits $params.consensusid_considered_top_hits \\
-        -debug $params.consensusid_debug \\
-        $args \\
-        2>&1 | tee ${meta.mzml_id}_consensusID.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ConsensusID: \$(ConsensusID 2>&1  | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/consensusid/meta.yml b/modules/local/openms/consensusid/meta.yml
deleted file mode 100644
index c8a7df5a0..000000000
--- a/modules/local/openms/consensusid/meta.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-name: consensusid
-description: Computes a consensus from results of multiple peptide identification engines.
-keywords:
-  - consensus scoring
-  - peptide database search
-  - OpenMS
-tools:
-  - ConsensusID:
-      description: |
-        Tool to Computes a consensus from results of multiple peptide identification engines.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ConsensusID.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ConsensusID.html
-input:
-  - meta:
-      type: map
-      description: Groovy Map containing sample information
-  - id_file:
-      type: file
-      description: |
-        Putative peptide-spectrum matches in idXML format (potentially multiple per spectrum). Score needs to be comparable (e.g. probability)
-      pattern: "*.idXML"
-output:
-  - meta:
-      type: map
-      description: Groovy Map containing sample information
-  - id_files_idx_ForIDPEP_FDR:
-      type: file
-      description: |
-        Identifications with annotated FDR.
-      pattern: "*.idXML"
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@daichengxin"
diff --git a/modules/local/openms/extractfeatures/main.nf b/modules/local/openms/extractfeatures/main.nf
index 046921f83..16340ee11 100644
--- a/modules/local/openms/extractfeatures/main.nf
+++ b/modules/local/openms/extractfeatures/main.nf
@@ -36,4 +36,4 @@ process EXTRACTPSMFEATURES {
         PSMFeatureExtractor: \$(PSMFeatureExtractor 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
     END_VERSIONS
     """
-}
\ No newline at end of file
+}
diff --git a/modules/local/openms/false_discovery_rate/meta.yml b/modules/local/openms/extractfeatures/meta.yml
similarity index 51%
rename from modules/local/openms/false_discovery_rate/meta.yml
rename to modules/local/openms/extractfeatures/meta.yml
index 62fa100fc..eff674afc 100644
--- a/modules/local/openms/false_discovery_rate/meta.yml
+++ b/modules/local/openms/extractfeatures/meta.yml
@@ -1,33 +1,34 @@
-name: false_discovery_rate
-description: Estimates the false discovery rate on peptide and protein level using decoy searches.
+name: EXTRACTPSMFEATURES
+description: Extracts PSM features from multiple search engines for rescoring.
 keywords:
-  - FDR
-  - decoy
+  - PSM
+  - feature extraction
+  - rescoring
   - OpenMS
 tools:
-  - FalseDiscoveryRate:
+  - PSMFeatureExtractor:
       description: |
-        Tool to estimate the false discovery rate on peptide and protein level.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_FalseDiscoveryRate.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_FalseDiscoveryRate.html
+        Tool to extract PSM features from identification results for downstream rescoring.
+      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_PSMFeatureExtractor.html
+      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_PSMFeatureExtractor.html
 input:
   - meta:
       type: map
       description: Groovy Map containing sample information
-  - id_file:
+  - id_files:
       type: file
       description: |
-        Identifications from searching a target-decoy database.
-      pattern: "*.idXML"
+        Identification files from one or multiple search engines.
+      pattern: "*.idparquet"
 output:
   - meta:
       type: map
       description: Groovy Map containing sample information
-  - id_files_idx_ForIDPEP_FDR:
+  - id_files_feat:
       type: file
       description: |
-        Identifications with annotated FDR.
-      pattern: "*.idXML"
+        PSM features in Parquet format for rescoring.
+      pattern: "*_feat.idparquet"
   - log:
       type: file
       description: log file
diff --git a/modules/local/openms/false_discovery_rate/main.nf b/modules/local/openms/false_discovery_rate/main.nf
deleted file mode 100644
index 37a872dde..000000000
--- a/modules/local/openms/false_discovery_rate/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-process FALSE_DISCOVERY_RATE {
-    tag "$meta.mzml_id"
-    label 'process_low'
-    label 'process_single'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    tuple val(meta), path(id_file)
-
-    output:
-    tuple val(meta), path("${id_file.baseName}_fdr.idXML"), emit: id_files_idx_ForIDPEP_FDR
-    path "versions.yml", emit: versions
-    path "*.log", emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.mzml_id}"
-
-    """
-    FalseDiscoveryRate \\
-        -in ${id_file} \\
-        -out ${id_file.baseName}_fdr.idXML \\
-        -threads $task.cpus \\
-        -FDR:PSM ${params.run_fdr_cutoff} \\
-        -algorithm:add_decoy_peptides \\
-        -algorithm:add_decoy_proteins \\
-        -algorithm:conservative ${params.fdr_conservative} \\
-        $args \\
-        2>&1 | tee ${id_file.baseName}_fdr.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        FalseDiscoveryRate: \$(FalseDiscoveryRate 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/id_conflict_resolver/main.nf b/modules/local/openms/id_conflict_resolver/main.nf
deleted file mode 100644
index d9b135afc..000000000
--- a/modules/local/openms/id_conflict_resolver/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-process ID_CONFLICT_RESOLVER {
-    label 'process_low'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    path consus_file
-
-    output:
-    path "${consus_file.baseName}_resconf.consensusXML", emit: pro_resconf
-    path "versions.yml", emit: versions
-    path "*.log", emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-
-    """
-    IDConflictResolver \\
-        -in ${consus_file} \\
-        -threads $task.cpus \\
-        -out ${consus_file.baseName}_resconf.consensusXML \\
-        $args \\
-        2>&1 | tee ${consus_file.baseName}_resconf.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        IDConflictResolver: \$(IDConflictResolver 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/id_conflict_resolver/meta.yml b/modules/local/openms/id_conflict_resolver/meta.yml
deleted file mode 100644
index 62db48b4f..000000000
--- a/modules/local/openms/id_conflict_resolver/meta.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-name: id_conflict_resolver
-description: Resolves ambiguous annotations of features with peptide identifications.
-keywords:
-  - ambiguous
-  - OpenMS
-tools:
-  - IDConflictResolver:
-      description: |
-        Resolves ambiguous annotations of features with peptide identifications.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IDConflictResolver.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IDConflictResolver.html
-input:
-  - consus_file:
-      type: file
-      description: |
-        Input file (data annotated with identifications)
-      pattern: "*.{featureXML,consensusXML}"
-output:
-  - pro_resconf:
-      type: file
-      description: Output file (data with one peptide identification per feature)
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@daichengxin"
diff --git a/modules/local/openms/id_filter/main.nf b/modules/local/openms/id_filter/main.nf
index 0f939bf27..2bf6c8cf1 100644
--- a/modules/local/openms/id_filter/main.nf
+++ b/modules/local/openms/id_filter/main.nf
@@ -1,5 +1,5 @@
 process ID_FILTER {
-    tag {task.ext.suffix == ".idXML" ? "$meta.mzml_id" : "$id_file.baseName"}
+    tag {task.ext.suffix == ".idparquet" ? "$meta.mzml_id" : "$id_file.baseName"}
     label 'process_very_low'
     label 'process_single'
     label 'openms'
diff --git a/modules/local/openms/id_mapper/main.nf b/modules/local/openms/id_mapper/main.nf
deleted file mode 100644
index 1c88cede2..000000000
--- a/modules/local/openms/id_mapper/main.nf
+++ /dev/null
@@ -1,36 +0,0 @@
-process ID_MAPPER {
-    tag "$meta.mzml_id"
-    label 'process_medium'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    tuple val(meta), path(id_file), path(map_file)
-
-    output:
-    path "${id_file.baseName}_map.consensusXML", emit: id_map
-    path "versions.yml", emit: versions
-    path "*.log", emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.mzml_id}"
-
-    """
-    IDMapper \\
-        -id ${id_file} \\
-        -in ${map_file} \\
-        -threads $task.cpus \\
-        -out ${id_file.baseName}_map.consensusXML \\
-        $args \\
-        2>&1 | tee ${id_file.baseName}_map.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        IDMapper: \$(IDMapper 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/id_mapper/meta.yml b/modules/local/openms/id_mapper/meta.yml
deleted file mode 100644
index 67e9ed6d3..000000000
--- a/modules/local/openms/id_mapper/meta.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-name: id_mapper
-description: Assigns protein/peptide identifications to features or consensus features.
-keywords:
-  - feature
-  - identification
-  - OpenMS
-tools:
-  - IDMapper:
-      description: |
-        Assigns protein/peptide identifications to features or consensus features.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IDMapper.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IDMapper.html
-input:
-  - meta:
-      type: map
-      description: Groovy Map containing sample information
-  - id_file:
-      type: file
-      description: |
-        Identifications file
-      pattern: "*.{idXML, mzid}"
-  - map_file:
-      type: file
-      description: Feature map/consensus map file
-      pattern: "*.{featureXML, consensusXML, mzq}"
-output:
-  - id_map:
-      type: file
-      description: Output file
-      pattern: "*.{featureXML, consensusXML, mzq}"
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@daichengxin"
diff --git a/modules/local/openms/id_score_switcher/main.nf b/modules/local/openms/id_score_switcher/main.nf
index bedd9fd71..97a9cd768 100644
--- a/modules/local/openms/id_score_switcher/main.nf
+++ b/modules/local/openms/id_score_switcher/main.nf
@@ -12,7 +12,7 @@ process ID_SCORE_SWITCHER {
     tuple val(meta), path(id_file), val(new_score)
 
     output:
-    tuple val(meta), path("${id_file.baseName}_pep.idXML"), emit: id_score_switcher
+    tuple val(meta), path("${id_file.baseName}_pep.idparquet"), emit: id_score_switcher
     path "versions.yml", emit: versions
     path "*.log", emit: log
 
@@ -23,7 +23,7 @@ process ID_SCORE_SWITCHER {
     """
     IDScoreSwitcher \\
         -in ${id_file} \\
-        -out ${id_file.baseName}_pep.idXML \\
+        -out ${id_file.baseName}_pep.idparquet \\
         -threads $task.cpus \\
         -new_score ${new_score} \\
         $args \\
diff --git a/modules/local/openms/id_score_switcher/meta.yml b/modules/local/openms/id_score_switcher/meta.yml
index 246d603b7..d20a3c524 100644
--- a/modules/local/openms/id_score_switcher/meta.yml
+++ b/modules/local/openms/id_score_switcher/meta.yml
@@ -18,7 +18,7 @@ input:
       type: file
       description: |
         Identifications from searching a target-decoy database.
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
 output:
   - meta:
       type: map
diff --git a/modules/local/openms/index_peptides/main.nf b/modules/local/openms/index_peptides/main.nf
index e0628abb9..6849853e6 100644
--- a/modules/local/openms/index_peptides/main.nf
+++ b/modules/local/openms/index_peptides/main.nf
@@ -12,7 +12,7 @@ process INDEX_PEPTIDES {
 
 
     output:
-    tuple val(meta), path("${id_file.baseName}_idx.idXML"), emit: id_files_idx
+    tuple val(meta), path("${id_file.baseName}_idx.idparquet"), emit: id_files_idx
     path "versions.yml", emit: versions
     path "*.log", emit: log
 
@@ -45,7 +45,7 @@ process INDEX_PEPTIDES {
     """
     PeptideIndexer \\
         -in ${id_file} \\
-        -out ${id_file.baseName}_idx.idXML \\
+        -out ${id_file.baseName}_idx.idparquet \\
         -threads $task.cpus \\
         -fasta ${database} \\
         -enzyme:name "${enzyme}" \\
diff --git a/modules/local/openms/index_peptides/meta.yml b/modules/local/openms/index_peptides/meta.yml
index eb937b22d..2a784d7ff 100644
--- a/modules/local/openms/index_peptides/meta.yml
+++ b/modules/local/openms/index_peptides/meta.yml
@@ -18,7 +18,7 @@ input:
       type: file
       description: |
         Input idXML file containing the identifications.
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - database:
       type: file
       description: |
@@ -32,7 +32,7 @@ output:
       type: file
       description: |
         Output idXML file.
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - log:
       type: file
       description: log file
diff --git a/modules/local/openms/isobaric_analyzer/main.nf b/modules/local/openms/isobaric_analyzer/main.nf
deleted file mode 100644
index 6db8e587a..000000000
--- a/modules/local/openms/isobaric_analyzer/main.nf
+++ /dev/null
@@ -1,79 +0,0 @@
-process ISOBARIC_ANALYZER {
-    tag "$meta.mzml_id"
-    label 'process_medium'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    tuple val(meta), path(mzml_file)
-
-    output:
-    tuple val(meta), path("${mzml_file.baseName}_iso.consensusXML"),  emit: id_files_consensusXML
-    path "versions.yml",   emit: versions
-    path "*.log",   emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.mzml_id}"
-
-    if (params.quant_activation_method == "HCD" || params.quant_activation_method == "HCID") diss_meth = "auto"
-    else if (params.quant_activation_method == "CID") diss_meth = "Collision-induced dissociation"
-    else if (params.quant_activation_method == "ETD") diss_meth = "Electron transfer dissociation"
-    else if (params.quant_activation_method == "ECD") diss_meth = "Electron capture dissociation"
-
-    def iso_normalization = params.iso_normalization ? "-quantification:normalization" : ""
-    def isotope_correction = params.isotope_correction ? "-quantification:isotope_correction true" : "-quantification:isotope_correction false"
-
-    // Check for isotope correction and load the correction matrix
-    if (params.isotope_correction) {
-        if (params.plex_corr_matrix_file == null) {
-            error("plex_corr_matrix_file is required when isotope_correction is enabled")
-        }
-
-        // Read the matrix file and format it into the command-line format
-        // Read the matrix file, skipping lines that start with '#' and process the matrix
-        def matrix_lines = new File(params.plex_corr_matrix_file).readLines()
-        .findAll { line -> !line.startsWith('#') && line.trim() } // Skip lines starting with '#' and empty lines
-        .drop(1) // Assuming the first non-comment line is a header
-        .collect { line ->
-            def values = line.split('/')
-            // Handle different labelling types
-            if (meta.labelling_type == 'tmt18plex' || meta.labelling_type == 'tmt16plex') {
-                return "\"${values[1]}/${values[2]}/${values[3]}/${values[4]}/${values[5]}/${values[6]}/${values[7]}/${values[8]}\""
-            } else {
-                return "\"${values[1]}/${values[2]}/${values[3]}/${values[4]}\""
-            }
-        }
-
-    // Join the matrix lines into a format for the C++ tool
-    def correction_matrix = matrix_lines.join(" ")
-
-    isotope_correction += " -${meta.labelling_type}:correction_matrix ${correction_matrix}"
-    }
-
-    """
-    IsobaricAnalyzer \\
-        -type ${meta.labelling_type} \\
-        -in ${mzml_file} \\
-        -threads ${task.cpus} \\
-        -extraction:select_activation "${diss_meth}" \\
-        -extraction:reporter_mass_shift ${params.reporter_mass_shift} \\
-        -extraction:min_reporter_intensity ${params.min_reporter_intensity} \\
-        -extraction:min_precursor_purity ${params.min_precursor_purity} \\
-        -extraction:precursor_isotope_deviation ${params.precursor_isotope_deviation} \\
-        ${iso_normalization} \\
-        -${meta.labelling_type}:reference_channel ${params.reference_channel} \\
-        ${isotope_correction} \\
-        -out ${mzml_file.baseName}_iso.consensusXML \\
-        ${args} \\
-        2>&1 | tee ${mzml_file.baseName}_isob.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        IsobaricAnalyzer: \$(IsobaricAnalyzer --version 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/isobaric_analyzer/meta.yml b/modules/local/openms/isobaric_analyzer/meta.yml
deleted file mode 100644
index faf4c4ae2..000000000
--- a/modules/local/openms/isobaric_analyzer/meta.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-name: isobaric_analyzer
-description: Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment.
-keywords:
-  - peak
-  - OpenMS
-tools:
-  - IsobaricAnalyzer:
-      description: |
-        Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html
-input:
-  - meta:
-      type: map
-      description: Groovy Map containing sample information
-  - mzml_file:
-      type: file
-      description: Input profile data file.
-      pattern: "*.mzML"
-output:
-  - meta:
-      type: map
-      description: Groovy Map containing sample information
-  - iso_consensusXML:
-      type: file
-      description: Output consensusXML file with quantitative information
-      pattern: "*.consensusXML"
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@daichengxin"
diff --git a/modules/local/openms/isobaric_workflow/main.nf b/modules/local/openms/isobaric_workflow/main.nf
new file mode 100644
index 000000000..8a2e54183
--- /dev/null
+++ b/modules/local/openms/isobaric_workflow/main.nf
@@ -0,0 +1,71 @@
+process ISOBARIC_WORKFLOW {
+    tag "${expdes.baseName}"
+    label 'process_high'
+    label 'openms'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:latest' :
+        'ghcr.io/bigbio/openms-tools-thirdparty:latest' }"
+
+    input:
+    val(labelling_type)
+    path(mzmls)
+    path(id_files)
+    path(expdes)
+
+    output:
+    path "${expdes.baseName}_openms.mzTab", emit: out_mztab
+    path "${expdes.baseName}_openms.consensusXML", emit: out_consensusXML
+    path "${expdes.baseName}_qpx", emit: out_qpx
+    path "*.log", emit: log
+    path "versions.yml", emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+
+    // Build isotope correction matrix argument if enabled
+    def isotope_correction = ""
+    if (params.isotope_correction && params.plex_corr_matrix_file != null) {
+        def matrix_lines = new File(params.plex_corr_matrix_file).readLines()
+            .findAll { !it.startsWith('#') && it.trim() }
+            .drop(1)
+            .collect { line ->
+                def values = line.split('/')
+                if (labelling_type == 'tmt18plex' || labelling_type == 'tmt16plex') {
+                    return "\"${values[1]}/${values[2]}/${values[3]}/${values[4]}/${values[5]}/${values[6]}/${values[7]}/${values[8]}\""
+                } else {
+                    return "\"${values[1]}/${values[2]}/${values[3]}/${values[4]}\""
+                }
+            }
+        def correction_matrix = matrix_lines.join(" ")
+        isotope_correction = "-quantification:isotope_correction true -${labelling_type}:correction_matrix ${correction_matrix}"
+    }
+
+    """
+    IsobaricWorkflow \\
+        -threads ${task.cpus} \\
+        -in ${mzmls.join(' ')} \\
+        -in_id ${id_files.join(' ')} \\
+        -exp_design ${expdes} \\
+        -type ${labelling_type} \\
+        -inference_method ${params.protein_inference_method} \\
+        -protein_quantification ${params.protein_quant} \\
+        -psmFDR ${params.psm_level_fdr_cutoff} \\
+        -proteinFDR ${params.protein_level_fdr_cutoff} \\
+        -picked_fdr ${params.picked_fdr} \\
+        -picked_decoy_string ${params.decoy_string} \\
+        -extraction:min_precursor_purity ${params.min_precursor_purity} \\
+        -extraction:precursor_isotope_deviation ${params.precursor_isotope_deviation} \\
+        -extraction:min_reporter_intensity ${params.min_reporter_intensity} \\
+        ${isotope_correction} \\
+        -out ${expdes.baseName}_openms.consensusXML \\
+        -out_mzTab ${expdes.baseName}_openms.mzTab \\
+        -out_qpx ${expdes.baseName}_qpx \\
+        $args \\
+        2>&1 | tee isobaricworkflow.log
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        IsobaricWorkflow: \$(IsobaricWorkflow 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/openms/isobaric_workflow/meta.yml b/modules/local/openms/isobaric_workflow/meta.yml
new file mode 100644
index 000000000..45971764b
--- /dev/null
+++ b/modules/local/openms/isobaric_workflow/meta.yml
@@ -0,0 +1,42 @@
+name: isobaric_workflow
+description: Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment.
+keywords:
+  - OpenMS
+  - quantification
+tools:
+  - IsobaricWorkflow:
+      description: |
+        Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment.
+      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/TOPP_IsobaricWorkflow.html
+      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/TOPP_IsobaricWorkflow.html
+  - mzmls:
+      type: file
+      description: Input Spectra in mzML format
+      pattern: "*.mzML"
+  - id_files:
+      type: file
+      description: Identifications in idparquet or mzIdentML format with posterior error probabilities as score type.
+      pattern: "*.idparquet"
+  - expdes:
+      type: file
+      description: An experimental design file
+      pattern: "*.tsv"
+output:
+  - out_mztab:
+      type: file
+      description: mzTab file with analysis results
+      pattern: "*.mzTab"
+  - out_consensusXML:
+      type: file
+      description: ConsensusXML file for visualization and further processing in OpenMS.
+      pattern: "*.consensusXML"
+  - log:
+      type: file
+      description: log file
+      pattern: "*.log"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "versions.yml"
+authors:
+  - "@MaLLLiYA"
diff --git a/modules/local/openms/msgf/meta.yml b/modules/local/openms/msgf/meta.yml
index 8c7c8690b..d8fe9bce1 100644
--- a/modules/local/openms/msgf/meta.yml
+++ b/modules/local/openms/msgf/meta.yml
@@ -29,7 +29,7 @@ output:
   - id_files_msgf:
       type: file
       description: Output file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - log:
       type: file
       description: log file
diff --git a/modules/local/openms/percolator/meta.yml b/modules/local/openms/percolator/meta.yml
index b7be826db..aad911da7 100644
--- a/modules/local/openms/percolator/meta.yml
+++ b/modules/local/openms/percolator/meta.yml
@@ -17,7 +17,7 @@ input:
       type: file
       description: |
         Input idXML file containing the identifications.
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
 output:
   - meta:
       type: map
diff --git a/modules/local/openms/protein_inference_epifany/main.nf b/modules/local/openms/protein_inference_epifany/main.nf
deleted file mode 100644
index ddafba50b..000000000
--- a/modules/local/openms/protein_inference_epifany/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-process PROTEIN_INFERENCE_EPIFANY {
-    label 'process_medium'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    tuple val(meta), path(consus_file)
-
-    output:
-    tuple val(meta), path("${consus_file.baseName}_epi.consensusXML"), emit: epi_inference
-    path "versions.yml", emit: versions
-    path "*.log", emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    gg = params.protein_quant == 'shared_peptides' ? 'remove_proteins_wo_evidence' : 'none'
-
-    """
-    Epifany \\
-        -in ${consus_file} \\
-        -protein_fdr true \\
-        -threads $task.cpus \\
-        -algorithm:keep_best_PSM_only $params.keep_best_PSM_only \\
-        -algorithm:update_PSM_probabilities $params.update_PSM_probabilities \\
-        -greedy_group_resolution $gg \\
-        -algorithm:top_PSMs $params.top_PSMs \\
-        -out ${consus_file.baseName}_epi.consensusXML \\
-        $args \\
-        2>&1 | tee ${consus_file.baseName}_inference.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        Epifany: \$(Epifany 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/protein_inference_epifany/meta.yml b/modules/local/openms/protein_inference_epifany/meta.yml
deleted file mode 100644
index 23d09813b..000000000
--- a/modules/local/openms/protein_inference_epifany/meta.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-name: protein_inference_epifany
-description: Runs a Bayesian protein inference.
-keywords:
-  - Bayesian
-  - inference
-  - OpenMS
-tools:
-  - Epifany:
-      description: |
-        It is a protein inference engine based on a Bayesian network.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_Epifany.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_Epifany.html
-input:
-  - consus_file:
-      type: file
-      description: |
-        identification results.
-      pattern: "*.{idXML,consensusXML}"
-output:
-  - epi_inference:
-      type: file
-      description: |
-        identification results with scored/grouped proteins.
-      pattern: "*.{idXML,consensusXML}"
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@daichengxin"
diff --git a/modules/local/openms/protein_inference_generic/main.nf b/modules/local/openms/protein_inference_generic/main.nf
deleted file mode 100644
index 8222fb632..000000000
--- a/modules/local/openms/protein_inference_generic/main.nf
+++ /dev/null
@@ -1,44 +0,0 @@
-process PROTEIN_INFERENCE_GENERIC {
-    label 'process_medium'
-    label 'openms'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
-        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
-
-    input:
-    tuple val(meta), path(consus_file)
-
-    output:
-    tuple val(meta), path("${consus_file.baseName}_epi.consensusXML"), emit: protein_inference
-    path "versions.yml", emit: versions
-    path "*.log", emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    gg = params.protein_quant == 'shared_peptides' ? '-Algorithm:greedy_group_resolution' : ''
-    groups = params.protein_quant == 'strictly_unique_peptides' ? 'false' : 'true'
-
-    """
-    ProteinInference \\
-        -in ${consus_file} \\
-        -threads $task.cpus \\
-        -picked_fdr $params.picked_fdr \\
-        -picked_decoy_string $params.decoy_string \\
-        -protein_fdr true \\
-        -Algorithm:use_shared_peptides $params.use_shared_peptides \\
-        -Algorithm:annotate_indistinguishable_groups $groups \\
-        -Algorithm:score_type "PEP" \\
-        $gg \\
-        -Algorithm:score_aggregation_method $params.protein_score \\
-        -Algorithm:min_peptides_per_protein $params.min_peptides_per_protein \\
-        -out ${consus_file.baseName}_epi.consensusXML \\
-        $args \\
-        2>&1 | tee ${consus_file.baseName}_inference.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ProteinInference: \$(ProteinInference 2>&1 | grep -E '^Version(.*) ' | sed 's/Version: //g' | cut -d ' ' -f 1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/openms/protein_inference_generic/meta.yml b/modules/local/openms/protein_inference_generic/meta.yml
deleted file mode 100644
index 983479342..000000000
--- a/modules/local/openms/protein_inference_generic/meta.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-name: protein_inference_generic
-description: Computes a protein identification score based on an aggregation of scores of identified peptides.
-keywords:
-  - protein
-  - inference
-  - OpenMS
-tools:
-  - ProteinInference:
-      description: |
-        Computes a protein identification score based on an aggregation of scores of identified peptides.
-      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteinInference.html
-      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteinInference.html
-input:
-  - consus_file:
-      type: file
-      description: |
-        identification results.
-      pattern: "*.{idXML,consensusXML}"
-output:
-  - protein_inference:
-      type: file
-      description: |
-        identification results with scored/grouped proteins.
-      pattern: "*.consensusXML"
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@daichengxin"
diff --git a/modules/local/openms/proteomicslfq/main.nf b/modules/local/openms/proteomicslfq/main.nf
index 176b71ae5..bb2216c0b 100644
--- a/modules/local/openms/proteomicslfq/main.nf
+++ b/modules/local/openms/proteomicslfq/main.nf
@@ -18,12 +18,12 @@ process PROTEOMICSLFQ {
     path "${expdes.baseName}_qpx", emit: out_qpx
     path "${expdes.baseName}_openms.consensusXML", emit: out_consensusXML
     path "*msstats_in.csv", emit: out_msstats, optional: true
-    path "debug_mergedIDs.idXML", emit: debug_mergedIDs, optional: true
-    path "debug_mergedIDs_inference.idXML", emit: debug_mergedIDs_inference, optional: true
-    path "debug_mergedIDsGreedyResolved.idXML", emit: debug_mergedIDsGreedyResolved, optional: true
-    path "debug_mergedIDsGreedyResolvedFDR.idXML", emit: debug_mergedIDsGreedyResolvedFDR, optional: true
-    path "debug_mergedIDsGreedyResolvedFDRFiltered.idXML", emit: debug_mergedIDsGreedyResolvedFDRFiltered, optional: true
-    path "debug_mergedIDsFDRFilteredStrictlyUniqueResolved.idXML", emit: debug_mergedIDsFDRFilteredStrictlyUniqueResolved, optional: true
+    path "debug_mergedIDs.idparquet", emit: debug_mergedIDs, optional: true
+    path "debug_mergedIDs_inference.idparquet", emit: debug_mergedIDs_inference, optional: true
+    path "debug_mergedIDsGreedyResolved.idparquet", emit: debug_mergedIDsGreedyResolved, optional: true
+    path "debug_mergedIDsGreedyResolvedFDR.idparquet", emit: debug_mergedIDsGreedyResolvedFDR, optional: true
+    path "debug_mergedIDsGreedyResolvedFDRFiltered.idparquet", emit: debug_mergedIDsGreedyResolvedFDRFiltered, optional: true
+    path "debug_mergedIDsFDRFilteredStrictlyUniqueResolved.idparquet", emit: debug_mergedIDsFDRFilteredStrictlyUniqueResolved, optional: true
     path "*.log", emit: log
     path "versions.yml", emit: versions
 
diff --git a/modules/local/openms/proteomicslfq/meta.yml b/modules/local/openms/proteomicslfq/meta.yml
index b8b327e16..7ca500076 100644
--- a/modules/local/openms/proteomicslfq/meta.yml
+++ b/modules/local/openms/proteomicslfq/meta.yml
@@ -18,7 +18,7 @@ input:
   - id_files:
       type: file
       description: Identifications in idXML or mzIdentML format with posterior error probabilities as score type.
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - expdes:
       type: file
       description: An experimental design file
diff --git a/modules/local/openms/sage/meta.yml b/modules/local/openms/sage/meta.yml
index 11eed615a..49690e826 100644
--- a/modules/local/openms/sage/meta.yml
+++ b/modules/local/openms/sage/meta.yml
@@ -29,7 +29,7 @@ output:
   - id_files_sage:
       type: file
       description: Output file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - log:
       type: file
       description: log file
diff --git a/modules/local/utils/msrescore_features/main.nf b/modules/local/utils/msrescore_features/main.nf
index 79b4244a2..449f2fd61 100644
--- a/modules/local/utils/msrescore_features/main.nf
+++ b/modules/local/utils/msrescore_features/main.nf
@@ -3,8 +3,8 @@ process MSRESCORE_FEATURES {
     label 'process_medium'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.16' :
-        'ghcr.io/bigbio/quantms-rescoring:0.0.17' }"
+        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.18' :
+        'ghcr.io/bigbio/quantms-rescoring:0.0.18' }"
 
     input:
     tuple val(meta), path(id_files), path(mzml), path(model_weight)
diff --git a/modules/local/utils/msrescore_features/meta.yml b/modules/local/utils/msrescore_features/meta.yml
index 208da0e7f..fe8162c1d 100644
--- a/modules/local/utils/msrescore_features/meta.yml
+++ b/modules/local/utils/msrescore_features/meta.yml
@@ -13,7 +13,7 @@ input:
   - idxml_file:
       type: file
       description: idXML identification file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - mzml:
       type: file
       description: spectrum data file
@@ -25,7 +25,7 @@ output:
   - idxml:
       type: file
       description: idXML identification file after MS2 rescoring
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - version:
       type: file
       description: File containing software version
diff --git a/modules/local/utils/msrescore_fine_tuning/main.nf b/modules/local/utils/msrescore_fine_tuning/main.nf
index aa7ae59b3..23636619f 100644
--- a/modules/local/utils/msrescore_fine_tuning/main.nf
+++ b/modules/local/utils/msrescore_fine_tuning/main.nf
@@ -3,23 +3,23 @@ process MSRESCORE_FINE_TUNING {
     label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.16' :
-        'ghcr.io/bigbio/quantms-rescoring:0.0.16' }"
+        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.18' :
+        'ghcr.io/bigbio/quantms-rescoring:0.0.18' }"
 
     input:
-    tuple val(meta), path(idxml), path(mzml), val(groupkey), path(ms2_model_dir)
+    tuple val(meta), path(idparquet), path(mzml), path(ms2_model_dir)
 
     output:
-    tuple val(groupkey), path("retained_ms2.pth") , emit: model_weight
-    path "versions.yml"                           , emit: versions
-    path "*.log"                                  , emit: log
+    path("retained_ms2.pth") , emit: model_weight
+    path "versions.yml"      , emit: versions
+    path "*.log"             , emit: log
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${groupkey}_fine_tuning"
+    def prefix = task.ext.prefix ?: "fine_tuning"
 
     // Initialize tolerance variables
     def ms2_tolerance = null
@@ -49,8 +49,8 @@ process MSRESCORE_FINE_TUNING {
 
     """
     rescoring transfer_learning \\
-        --idxml ./ \\
-        --mzml ./ \\
+        --idparquet ${idparquet.join(' --idparquet ')} \\
+        --mzml ${mzml.join(' --mzml ')} \\
         --save_model_dir ./ \\
         --ms2_tolerance $ms2_tolerance \\
         --ms2_tolerance_unit $ms2_tolerance_unit \\
@@ -62,7 +62,7 @@ process MSRESCORE_FINE_TUNING {
         ${force_transfer_learning} \\
         ${consider_modloss} \\
         $args \\
-        2>&1 | tee ${groupkey}_fine_tuning.log
+        2>&1 | tee fine_tuning.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/utils/msrescore_fine_tuning/meta.yml b/modules/local/utils/msrescore_fine_tuning/meta.yml
index dd98ac3fa..72fb9a60e 100644
--- a/modules/local/utils/msrescore_fine_tuning/meta.yml
+++ b/modules/local/utils/msrescore_fine_tuning/meta.yml
@@ -18,7 +18,7 @@ input:
   - idxml_file:
       type: file
       description: idXML identification file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - mzml:
       type: file
       description: spectrum data file
@@ -30,7 +30,7 @@ output:
   - idxml:
       type: file
       description: idXML identification file after MS2 rescoring
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - version:
       type: file
       description: File containing software version
diff --git a/modules/local/utils/psm_clean/main.nf b/modules/local/utils/psm_clean/main.nf
index aa8fc3b43..650ffc907 100644
--- a/modules/local/utils/psm_clean/main.nf
+++ b/modules/local/utils/psm_clean/main.nf
@@ -3,8 +3,8 @@ process PSM_CLEAN {
     label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.16' :
-        'ghcr.io/bigbio/quantms-rescoring:0.0.16' }"
+        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.18' :
+        'ghcr.io/bigbio/quantms-rescoring:0.0.18' }"
 
     input:
     tuple val(meta), path(idparquet), path(mzml)
@@ -23,11 +23,11 @@ process PSM_CLEAN {
 
     """
     rescoring psm_feature_clean \\
-        --idparquet $idparquet \\
+        --idparquet ${idparquet.join(' --idparquet ')} \\
         --mzml $mzml \\
-        --output ${idxml.baseName}_clean.idparquet \\
+        --output ${mzml.baseName}_clean.idparquet \\
         $args \\
-        2>&1 | tee ${idxml.baseName}_clean.log
+        2>&1 | tee ${mzml.baseName}_clean.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/utils/psm_clean/meta.yml b/modules/local/utils/psm_clean/meta.yml
index 84b1505b0..32fb1c400 100644
--- a/modules/local/utils/psm_clean/meta.yml
+++ b/modules/local/utils/psm_clean/meta.yml
@@ -13,7 +13,7 @@ input:
   - idxml_file:
       type: file
       description: idXML identification file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - mzml:
       type: file
       description: spectrum data file
@@ -25,7 +25,7 @@ output:
   - idxml:
       type: file
       description: idXML identification file after postprocessing
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - version:
       type: file
       description: File containing software version
diff --git a/modules/local/utils/psm_conversion/meta.yml b/modules/local/utils/psm_conversion/meta.yml
index b3b3317f8..86b6171d9 100644
--- a/modules/local/utils/psm_conversion/meta.yml
+++ b/modules/local/utils/psm_conversion/meta.yml
@@ -13,7 +13,7 @@ input:
   - idxml_file:
       type: file
       description: idXML identification file
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - spectrum_df:
       type: file
       description: spectrum data file
diff --git a/modules/local/utils/spectrum_features/main.nf b/modules/local/utils/spectrum_features/main.nf
index baaa989b5..101b8f7c2 100644
--- a/modules/local/utils/spectrum_features/main.nf
+++ b/modules/local/utils/spectrum_features/main.nf
@@ -3,14 +3,14 @@ process SPECTRUM_FEATURES {
     label 'process_low'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.16' :
-        'ghcr.io/bigbio/quantms-rescoring:0.0.16' }"
+        'oras://ghcr.io/bigbio/quantms-rescoring-sif:0.0.17' :
+        'ghcr.io/bigbio/quantms-rescoring:0.0.17' }"
 
     input:
-    tuple val(meta), path(id_file), val(search_engine), path(ms_file)
+    tuple val(meta), path(id_file), path(ms_file)
 
     output:
-    tuple val(meta), path("${id_file.baseName}_snr.idXML"), val(search_engine), emit: id_files_snr
+    tuple val(meta), path("${id_file.baseName}_snr.idparquet"), emit: id_files_snr
     path "versions.yml", emit: versions
     path "*.log", emit: log
 
@@ -21,8 +21,8 @@ process SPECTRUM_FEATURES {
     """
     rescoring spectrum2feature \\
         --mzml "${ms_file}" \\
-        --idxml "${id_file}" \\
-        --output "${id_file.baseName}_snr.idXML" \\
+        --idparquet "${id_file}" \\
+        --output "${id_file.baseName}_snr.idparquet" \\
         $args \\
         2>&1 | tee "${id_file.baseName}_snr_feature.log"
 
diff --git a/modules/local/utils/spectrum_features/meta.yml b/modules/local/utils/spectrum_features/meta.yml
index 1c53ddf9a..4cfb9b9da 100644
--- a/modules/local/utils/spectrum_features/meta.yml
+++ b/modules/local/utils/spectrum_features/meta.yml
@@ -22,7 +22,7 @@ input:
       type: file
       description: |
         Input idXML file containing the identifications.
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
 output:
   - meta:
       type: map
@@ -31,7 +31,7 @@ output:
       type: file
       description: |
         Output file in idXML format
-      pattern: "*.idXML"
+      pattern: "*.idparquet"
   - log:
       type: file
       description: log file
diff --git a/subworkflows/local/dda_id/main.nf b/subworkflows/local/dda_id/main.nf
index 29daeebab..a145297c4 100644
--- a/subworkflows/local/dda_id/main.nf
+++ b/subworkflows/local/dda_id/main.nf
@@ -1,9 +1,7 @@
 //
 // MODULE: Local to the pipeline
 //
-include { MSRESCORE_FEATURES   } from '../../../modules/local/utils/msrescore_features/main'
 include { PERCOLATOR           } from '../../../modules/local/openms/percolator/main'
-include { EXTRACTPSMFEATURES           } from '../../../modules/local/openms/extractfeatures/main'
 include { PSM_CONVERSION       } from '../../../modules/local/utils/psm_conversion/main'
 include { PHOSPHO_SCORING      } from '../phospho_scoring/main'
 
@@ -41,62 +39,11 @@ workflow DDA_ID {
     //
     // SUBWORKFLOW: Rescoring
     //
-    if (params.search_engines.tokenize(",").unique().size() > 1) {
-        if (params.ms2features_enable == true) {
-        // Only add ms2_model_dir if it's actually set and not empty
-            // Handle cases where parameter might be empty string, null, boolean true, or whitespace
-            // When --ms2features_model_dir is passed with no value, Nextflow may set it to boolean true
-            if (params.ms2features_model_dir && params.ms2features_model_dir != true) {
-                ms2_model_dir = channel.from(file(params.ms2features_model_dir, checkIfExists: true))
-            } else {
-                // create a fake channel when don't specify model dir
-                ms2_model_dir = channel.from(file("pretrained_models"))
-            }
 
-            ch_id_files_feats.groupTuple(size: params.search_engines.tokenize(",").unique().size())
-                .combine(ch_mzmls_search, by: 0)
-                .combine(ms2_model_dir).set{ ch_id_rescoring }
+    PERCOLATOR(ch_id_files_feats)
+    ch_rescoring_results = PERCOLATOR.out.id_files_perc
+    ch_software_versions = ch_software_versions.mix(PERCOLATOR.out.versions)
 
-            MSRESCORE_FEATURES(ch_id_rescoring)
-            ch_software_versions = ch_software_versions.mix(MSRESCORE_FEATURES.out.versions)
-            ch_id_files_feats = MSRESCORE_FEATURES.out.idxml
-            ch_id_files_feats.map { v -> [v[0], v[1]] }.set {ch_perc_input}
-
-        } else{
-            EXTRACTPSMFEATURES(ch_id_files_feats.groupTuple(size: params.search_engines.tokenize(",").unique().size()))
-            ch_consensus_input = EXTRACTPSMFEATURES.out.id_files_feat
-            ch_perc_input = ch_consensus_input
-        }
-        PERCOLATOR(ch_perc_input)
-        ch_rescoring_results = PERCOLATOR.out.id_files_perc
-        ch_software_versions = ch_software_versions.mix(PERCOLATOR.out.versions)
-    } else {
-        if (params.ms2features_enable == true) {
-            // Only add ms2_model_dir if it's actually set and not empty
-            // Handle cases where parameter might be empty string, null, boolean true, or whitespace
-            // When --ms2features_model_dir is passed with no value, Nextflow may set it to boolean true
-            if (params.ms2features_model_dir && params.ms2features_model_dir != true) {
-                ms2_model_dir = channel.from(file(params.ms2features_model_dir, checkIfExists: true))
-            } else {
-                // create a fake channel when don't specify model dir
-                ms2_model_dir = channel.from(file("pretrained_models"))
-            }
-
-            ch_id_files_feats.groupTuple(size: params.search_engines.tokenize(",").unique().size())
-                .combine(ch_mzmls_search, by: 0)
-                .combine(ms2_model_dir).set{ ch_id_rescoring }
-
-            MSRESCORE_FEATURES(ch_id_rescoring)
-            ch_software_versions = ch_software_versions.mix(MSRESCORE_FEATURES.out.versions)
-            ch_id_files_feats = MSRESCORE_FEATURES.out.idxml
-            ch_id_files_feats.map { v -> [v[0], v[1]] }.set {ch_perc_input}
-        } else {
-            ch_perc_input = ch_id_files_feats
-        }
-        PERCOLATOR(ch_perc_input)
-        ch_software_versions = ch_software_versions.mix(PERCOLATOR.out.versions)
-        ch_rescoring_results = PERCOLATOR.out.id_files_perc
-    }
 
     PSM_FDR_CONTROL(ch_rescoring_results)
     ch_software_versions = ch_software_versions.mix(PSM_FDR_CONTROL.out.versions)
diff --git a/subworkflows/local/feature_mapper/main.nf b/subworkflows/local/feature_mapper/main.nf
deleted file mode 100644
index 308293da7..000000000
--- a/subworkflows/local/feature_mapper/main.nf
+++ /dev/null
@@ -1,26 +0,0 @@
-//
-// Assigns protein/peptide identifications to features or consensus features.
-//
-
-include { ISOBARIC_ANALYZER } from '../../../modules/local/openms/isobaric_analyzer/main'
-include { ID_MAPPER         } from '../../../modules/local/openms/id_mapper/main'
-
-workflow FEATURE_MAPPER {
-    take:
-    ch_mzml_files
-    ch_id_files
-
-    main:
-    ch_version = channel.empty()
-
-    ISOBARIC_ANALYZER(ch_mzml_files)
-    ch_version = ch_version.mix(ISOBARIC_ANALYZER.out.versions)
-
-    ID_MAPPER(ch_id_files.combine(ISOBARIC_ANALYZER.out.id_files_consensusXML, by: 0))
-    ch_version = ch_version.mix(ID_MAPPER.out.versions)
-
-    emit:
-    id_map  = ID_MAPPER.out.id_map
-
-    versions = ch_version
-}
diff --git a/subworkflows/local/feature_mapper/meta.yml b/subworkflows/local/feature_mapper/meta.yml
deleted file mode 100644
index e2c40d976..000000000
--- a/subworkflows/local/feature_mapper/meta.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "feature_mapper"
-description: Subworkflow for mapping features across different runs and conditions
-keywords:
-  - feature
-  - mapping
-  - alignment
-  - proteomics
-components:
-  - isobaric/analyzer
-  - id/mapper
-input:
-  - ch_input:
-      type: file
-      description: |
-        Channel containing input files for feature mapping
-output:
-  - ch_mapped_features:
-      type: file
-      description: |
-        Channel containing mapped features
-  - versions:
-      type: file
-      description: |
-        Software versions used in this subworkflow
-authors:
-  - "@bigbio"
-maintainers:
-  - "@bigbio"
diff --git a/subworkflows/local/peptide_database_search/main.nf b/subworkflows/local/peptide_database_search/main.nf
index e22ac32dc..96c8aec31 100644
--- a/subworkflows/local/peptide_database_search/main.nf
+++ b/subworkflows/local/peptide_database_search/main.nf
@@ -91,57 +91,40 @@ workflow PEPTIDE_DATABASE_SEARCH {
                 } else {
 
                     // Preparing train datasets and fine tuning MS2 model
-                    sage_train_datasets = ch_id_sage
+                    // Randomly select one search engine for fine-tuning sampling
+                    engine_opts = []
+                    if (params.search_engines.contains("sage"))  engine_opts.add("sage")
+                    if (params.search_engines.contains("msgf"))  engine_opts.add("msgf")
+                    if (params.search_engines.contains("comet")) engine_opts.add("comet")
+                    selected_engine = engine_opts[new Random(2025).nextInt(engine_opts.size())]
+
+                    ch_selected_engine = (selected_engine == "sage") ? ch_id_sage :
+                                        (selected_engine == "msgf") ? ch_id_msgf :
+                                        ch_id_comet
+
+                    train_datasets = ch_selected_engine
                         .combine(ch_mzmls_search, by: 0)
                         .toSortedList()
                         .flatMap()
                         .randomSample(params.fine_tuning_sample_run, 2025)
-                        .combine(channel.value("sage"))
                         .groupTuple(by: 3)
 
-                    msgf_train_datasets = ch_id_msgf
-                        .combine(ch_mzmls_search, by: 0)
-                        .toSortedList()
-                        .flatMap()
-                        .randomSample(params.fine_tuning_sample_run, 2025)
-                        .combine(channel.value("msgf"))
-                        .groupTuple(by: 3)
-
-                    comet_train_datasets = ch_id_comet
-                        .combine(ch_mzmls_search, by: 0)
-                        .toSortedList()
-                        .flatMap()
-                        .randomSample(params.fine_tuning_sample_run, 2025)
-                        .combine(channel.value("comet"))
-                        .groupTuple(by: 3)
-
-                    sage_train_datasets.mix(msgf_train_datasets)
-                        .mix(comet_train_datasets)
-                        .combine(ms2_model_dir)
-                        .set { train_datasets }
-                    MSRESCORE_FINE_TUNING(train_datasets)
+                    MSRESCORE_FINE_TUNING(train_datasets.combine(ms2_model_dir))
                     ch_versions = ch_versions.mix(MSRESCORE_FINE_TUNING.out.versions)
 
-                    channel.value("msgf").combine(ch_id_msgf.combine(ch_mzmls_search, by: 0))
-                        .combine(MSRESCORE_FINE_TUNING.out.model_weight, by:0)
-                        .map { v -> [v[1], v[2], v[3], v[4], v[0] ] }
-                        .set { msgf_features_input }
-
-                    channel.value("sage").combine(ch_id_sage.combine(ch_mzmls_search, by: 0))
-                        .combine(MSRESCORE_FINE_TUNING.out.model_weight, by:0)
-                        .map { v -> [v[1], v[2], v[3], v[4], v[0] ] }
-                        .set { sage_features_input }
-
-                    channel.value("comet").combine(ch_id_comet.combine(ch_mzmls_search, by: 0))
-                        .combine(MSRESCORE_FINE_TUNING.out.model_weight, by:0)
-                        .map { v -> [v[1], v[2], v[3], v[4], v[0] ] }
-                        .set { comet_features_input }
+                    if (params.search_engines.tokenize(",").unique().size() > 1) {
+                        ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage).groupTuple(size: params.search_engines.tokenize(",").unique().size())
+                        .combine(ch_mzmls_search, by: 0)
+                        .combine(MSRESCORE_FINE_TUNING.out.model_weight).set{ ch_id_rescoring }
+                    } else {
+                        ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage).combine(ch_mzmls_search, by: 0)
+                            .combine(MSRESCORE_FINE_TUNING.out.model_weight).set{ ch_id_rescoring }
+                    }
 
-                    MSRESCORE_FEATURES(msgf_features_input.mix(sage_features_input).mix(comet_features_input))
+                    MSRESCORE_FEATURES(ch_id_rescoring)
                     ch_versions = ch_versions.mix(MSRESCORE_FEATURES.out.versions)
                     ch_id_files_feats = MSRESCORE_FEATURES.out.idparquet
 
-
                 }
             } else{
                 if (params.search_engines.tokenize(",").unique().size() > 1) {
@@ -167,16 +150,16 @@ workflow PEPTIDE_DATABASE_SEARCH {
             }
 
         } else if (params.search_engines.tokenize(",").unique().size() > 1) {
-            EXTRACTPSMFEATURES(ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage).groupTuple(size: params.search_engines.tokenize(",").unique().size()))
-            ch_id_files_out = EXTRACTPSMFEATURES.out.id_files_feat
+            PSM_CLEAN(ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage).groupTuple(size: params.search_engines.tokenize(",").unique().size()).combine(ch_mzmls_search, by: 0))
+            ch_id_files_out = PSM_CLEAN.out.idparquet
         } else {
             ch_id_files_out = ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage)
         }
-        
+
     } else if (params.psm_clean == true) {
         ch_id_files = ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage)
         PSM_CLEAN(ch_id_files.combine(ch_mzmls_search, by: 0))
-        ch_id_files_out = PSM_CLEAN.out.idxml
+        ch_id_files_out = PSM_CLEAN.out.idparquet
         ch_versions = ch_versions.mix(PSM_CLEAN.out.versions)
     } else {
         ch_id_files_out = ch_id_msgf.mix(ch_id_comet).mix(ch_id_sage)
@@ -185,4 +168,4 @@ workflow PEPTIDE_DATABASE_SEARCH {
     emit:
     ch_id_files_idx = ch_id_files_out
     versions        = ch_versions
-}
\ No newline at end of file
+}
diff --git a/subworkflows/local/phospho_scoring/main.nf b/subworkflows/local/phospho_scoring/main.nf
index 13d5a80c3..a233c33c2 100644
--- a/subworkflows/local/phospho_scoring/main.nf
+++ b/subworkflows/local/phospho_scoring/main.nf
@@ -12,16 +12,9 @@ workflow PHOSPHO_SCORING {
 
     main:
     ch_version = channel.empty()
-    if (params.search_engines.split(",").size() != 1){
-        ID_SCORE_SWITCHER(ch_id_files.combine(channel.value("\"Posterior Error Probability_score\"")))
-        ch_version = ch_version.mix(ID_SCORE_SWITCHER.out.versions)
-        ONSITE(ch_mzml_files.join(ID_SCORE_SWITCHER.out.id_score_switcher))
-        ch_version = ch_version.mix(ONSITE.out.versions)
-    } else{
-        ONSITE(ch_mzml_files.join(ch_id_files))
-        ch_version = ch_version.mix(ONSITE.out.versions)
-    }
 
+    ONSITE(ch_mzml_files.join(ch_id_files))
+    ch_version = ch_version.mix(ONSITE.out.versions)
 
 
     emit:
diff --git a/subworkflows/local/protein_inference/main.nf b/subworkflows/local/protein_inference/main.nf
deleted file mode 100644
index 96381089a..000000000
--- a/subworkflows/local/protein_inference/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-//
-// ProteinInference
-//
-
-include { PROTEIN_INFERENCE_EPIFANY } from '../../../modules/local/openms/protein_inference_epifany/main'
-include { PROTEIN_INFERENCE_GENERIC } from '../../../modules/local/openms/protein_inference_generic/main'
-include { ID_FILTER                 } from '../../../modules/local/openms/id_filter/main'
-
-workflow PROTEIN_INFERENCE {
-    take:
-    ch_consus_file
-
-    main:
-    ch_version = channel.empty()
-
-    if (params.protein_inference_method == "bayesian") {
-        PROTEIN_INFERENCE_EPIFANY(ch_consus_file)
-        ch_version = ch_version.mix(PROTEIN_INFERENCE_EPIFANY.out.versions)
-        ch_inference = PROTEIN_INFERENCE_EPIFANY.out.epi_inference
-    } else {
-        PROTEIN_INFERENCE_GENERIC(ch_consus_file)
-        ch_version = ch_version.mix(PROTEIN_INFERENCE_GENERIC.out.versions)
-        ch_inference = PROTEIN_INFERENCE_GENERIC.out.protein_inference
-    }
-
-    ID_FILTER(ch_inference.combine(channel.value("-score:type_protein q-value")))
-    ch_version = ch_version.mix(ID_FILTER.out.versions)
-    ID_FILTER.out.id_filtered
-        .multiMap{ it ->
-            meta: it[0]
-            results: it[1]
-            }
-        .set{ ch_epi_results }
-
-    emit:
-    epi_idfilter    = ch_epi_results.results
-
-    versions         = ch_version
-
-}
diff --git a/subworkflows/local/protein_inference/meta.yml b/subworkflows/local/protein_inference/meta.yml
deleted file mode 100644
index 7bab69e8d..000000000
--- a/subworkflows/local/protein_inference/meta.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "protein_inference"
-description: Subworkflow for protein inference from peptide identifications
-keywords:
-  - protein
-  - inference
-  - proteomics
-  - peptides
-components:
-  - protein/inference/epifany
-  - protein/inference/generic
-  - id/filter
-input:
-  - ch_input:
-      type: file
-      description: |
-        Channel containing input files for protein inference
-output:
-  - ch_protein_results:
-      type: file
-      description: |
-        Channel containing protein inference results
-  - versions:
-      type: file
-      description: |
-        Software versions used in this subworkflow
-authors:
-  - "@bigbio"
-maintainers:
-  - "@bigbio"
diff --git a/subworkflows/local/protein_quant/main.nf b/subworkflows/local/protein_quant/main.nf
deleted file mode 100644
index 6c9f295bf..000000000
--- a/subworkflows/local/protein_quant/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-//
-// ProteinQuant
-//
-
-include { ID_CONFLICT_RESOLVER as ID_CONFLICT_RESOLVER } from '../../../modules/local/openms/id_conflict_resolver/main'
-include { PROTEIN_QUANTIFIER as PROTEIN_QUANTIFIER  } from '../../../modules/local/openms/protein_quantifier/main'
-include { MSSTATS_CONVERTER as MSSTATS_CONVERTER   } from '../../../modules/local/openms/msstats_converter/main'
-
-workflow PROTEIN_QUANT {
-    take:
-    ch_conflict_file
-    ch_expdesign_file
-
-    main:
-    ch_version = channel.empty()
-
-    ID_CONFLICT_RESOLVER(ch_conflict_file)
-    ch_version = ch_version.mix(ID_CONFLICT_RESOLVER.out.versions)
-
-    PROTEIN_QUANTIFIER(ID_CONFLICT_RESOLVER.out.pro_resconf, ch_expdesign_file)
-    ch_version = ch_version.mix(PROTEIN_QUANTIFIER.out.versions)
-
-    MSSTATS_CONVERTER(ID_CONFLICT_RESOLVER.out.pro_resconf, ch_expdesign_file, "ISO")
-    ch_version = ch_version.mix(MSSTATS_CONVERTER.out.versions)
-
-    emit:
-    msstats_csv = MSSTATS_CONVERTER.out.out_msstats
-    out_mztab   = PROTEIN_QUANTIFIER.out.out_mztab
-    versions = ch_version
-}
diff --git a/subworkflows/local/protein_quant/meta.yml b/subworkflows/local/protein_quant/meta.yml
deleted file mode 100644
index 71ae589f2..000000000
--- a/subworkflows/local/protein_quant/meta.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "protein_quant"
-description: Subworkflow for protein quantification from MS data
-keywords:
-  - protein
-  - quantification
-  - proteomics
-  - ms
-components:
-  - id/conflict/resolver
-  - protein/quantifier
-  - msstats/converter
-input:
-  - ch_input:
-      type: file
-      description: |
-        Channel containing input files for protein quantification
-output:
-  - ch_quant_results:
-      type: file
-      description: |
-        Channel containing protein quantification results
-  - versions:
-      type: file
-      description: |
-        Software versions used in this subworkflow
-authors:
-  - "@bigbio"
-maintainers:
-  - "@bigbio"
diff --git a/workflows/tmt.nf b/workflows/tmt.nf
index 6a882cefb..a8b9f0d66 100644
--- a/workflows/tmt.nf
+++ b/workflows/tmt.nf
@@ -7,14 +7,12 @@
 //
 // MODULES: Local to the pipeline
 //
-include { FILE_MERGE  } from '../modules/local/openms/file_merge/main'
+include { ISOBARIC_WORKFLOW } from '../modules/local/openms/isobaric_workflow/main'
+include { MSSTATS_CONVERTER } from '../modules/local/openms/msstats_converter/main'
 
 //
 // SUBWORKFLOWS: Consisting of a mix of local and nf-core/modules
 //
-include { FEATURE_MAPPER    } from '../subworkflows/local/feature_mapper/main'
-include { PROTEIN_INFERENCE } from '../subworkflows/local/protein_inference/main'
-include { PROTEIN_QUANT     } from '../subworkflows/local/protein_quant/main'
 include { ID                } from '../subworkflows/local/id/main'
 
 /*
@@ -40,28 +38,28 @@ workflow TMT {
     ch_software_versions = ch_software_versions.mix(ID.out.versions)
 
     //
-    // SUBWORKFLOW: FEATUREMAPPER
+    // SUBWORKFLOW: ISOBARIC_WORKFLOW
     //
-    FEATURE_MAPPER(ch_file_preparation_results, ID.out.id_results)
-    ch_software_versions = ch_software_versions.mix(FEATURE_MAPPER.out.versions)
+    // Extract labelling_type from meta (auto-detected from SDRF)
+    ch_file_preparation_results.join(ID.out.id_results)
+        .multiMap { it ->
+            labelling_type: it[0].labelling_type
+            mzmls: it[1]
+            ids: it[2]
+        }
+        .set{ ch_iso_workflow }
+    ISOBARIC_WORKFLOW(ch_iso_workflow.labelling_type.first(),
+                ch_iso_workflow.mzmls.collect(),
+                ch_iso_workflow.ids.collect(),
+                ch_expdesign
+            )
+    ch_software_versions = ch_software_versions.mix(ISOBARIC_WORKFLOW.out.versions)
 
     //
-    // MODULE: FILEMERGE
+    // SUBWORKFLOW: MSSTATS_CONVERTER
     //
-    FILE_MERGE(FEATURE_MAPPER.out.id_map.collect())
-    ch_software_versions = ch_software_versions.mix(FILE_MERGE.out.versions)
-
-    //
-    // SUBWORKFLOW: PROTEININFERENCE
-    //
-    PROTEIN_INFERENCE(FILE_MERGE.out.id_merge)
-    ch_software_versions = ch_software_versions.mix(PROTEIN_INFERENCE.out.versions)
-
-    //
-    // SUBWORKFLOW: PROTEINQUANT
-    //
-    PROTEIN_QUANT(PROTEIN_INFERENCE.out.epi_idfilter, ch_expdesign)
-    ch_software_versions = ch_software_versions.mix(PROTEIN_QUANT.out.versions)
+    MSSTATS_CONVERTER(ISOBARIC_WORKFLOW.out.out_consensusXML, ch_expdesign, "ISO")
+    ch_software_versions = ch_software_versions.mix(MSSTATS_CONVERTER.out.versions)
 
     ID.out.psmrescoring_results
         .map { it -> it[1] }
@@ -74,7 +72,7 @@ workflow TMT {
     emit:
     ch_pmultiqc_ids         = ch_pmultiqc_ids
     ch_pmultiqc_consensus   = ch_pmultiqc_consensus
-    final_result            = PROTEIN_QUANT.out.out_mztab
-    msstats_in              = PROTEIN_QUANT.out.msstats_csv
+    final_result            = ISOBARIC_WORKFLOW.out.out_mztab
+    msstats_in              = MSSTATS_CONVERTER.out.out_msstats
     versions                = ch_software_versions
 }