diff --git a/psi-ms.owl b/psi-ms.owl
index 051d34a..bc3aa87 100644
--- a/psi-ms.owl
+++ b/psi-ms.owl
@@ -10,14 +10,13 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ms.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ms/4.1.184/ms.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ms/4.1.185/ms.owl"/>
         <oboInOwl:NamespaceIdRule>* MS:$sequence(7,0,9999999)$</oboInOwl:NamespaceIdRule>
         <oboInOwl:NamespaceIdRule>* PEFF:$sequence(7,0,9999999)$</oboInOwl:NamespaceIdRule>
-        <oboInOwl:auto-generated-by>OBO-Edit 2.3.1</oboInOwl:auto-generated-by>
-        <oboInOwl:date>01:11:2024 10:15</oboInOwl:date>
+        <oboInOwl:date>31:10:2024 10:20</oboInOwl:date>
         <oboInOwl:default-namespace>MS</oboInOwl:default-namespace>
         <oboInOwl:hasOBOFormatVersion>1.2</oboInOwl:hasOBOFormatVersion>
-        <oboInOwl:saved-by>Yasset Perez-Riverol</oboInOwl:saved-by>
+        <oboInOwl:saved-by>Nithu Sara John</oboInOwl:saved-by>
         <rdfs:comment>For any queries contact psidev-ms-vocab@lists.sourceforge.net</rdfs:comment>
         <rdfs:comment>This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.</rdfs:comment>
         <rdfs:comment>To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.</rdfs:comment>
@@ -36,6 +35,7 @@
         <rdfs:comment>creator: Mathias Walzer &lt;walzer &lt;-at-&gt; ebi.ac.uk&gt;</rdfs:comment>
         <rdfs:comment>creator: Matt Chambers &lt;matt.chambers &lt;-at-&gt; vanderbilt.edu&gt;</rdfs:comment>
         <rdfs:comment>creator: Nils Hoffmann &lt; nils.hoffmann &lt;-at-&gt; cebitec.uni-bielefeld.de&gt;</rdfs:comment>
+        <rdfs:comment>creator: Nithu Sara John &lt;nithu &lt;-at-&gt; ebi.ac.uk&gt;</rdfs:comment>
         <rdfs:comment>creator: Pierre-Alain Binz &lt;pierre-alain.binz &lt;-at-&gt; chuv.ch&gt;</rdfs:comment>
         <rdfs:comment>creator: Wout Bittremieux &lt;wout.bittremieux &lt;-at-&gt; uantwerpen.be&gt;</rdfs:comment>
         <rdfs:comment>creator: Yasset Perez-Riverol &lt;yperez &lt;-at-&gt; ebi.ac.uk&gt;</rdfs:comment>
@@ -135,12 +135,6 @@
     
 
 
-    <!-- http://www.geneontology.org/formats/oboInOwl#auto-generated-by -->
-
-    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#auto-generated-by"/>
-    
-
-
     <!-- http://www.geneontology.org/formats/oboInOwl#created_by -->
 
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by">
@@ -71568,6 +71562,140 @@
     
 
 
+    <!-- http://purl.obolibrary.org/obo/MS_1003426 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/MS_1003426">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001139"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001456"/>
+        <obo:IAO_0000115>A software to identify cross-linked peptides from LC-MS/MS spectra.</obo:IAO_0000115>
+        <oboInOwl:hasOBONamespace>MS</oboInOwl:hasOBONamespace>
+        <oboInOwl:id>MS:1003426</oboInOwl:id>
+        <rdfs:label>xQuest/xProphet</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MS_1003426"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>A software to identify cross-linked peptides from LC-MS/MS spectra.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>PMID:18327264</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/MS_1003427 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/MS_1003427">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001139"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001456"/>
+        <obo:IAO_0000115>A software for spectral analysis and data interrogation in qualitative review of LC-MS and MS/MS data.</obo:IAO_0000115>
+        <oboInOwl:hasOBONamespace>MS</oboInOwl:hasOBONamespace>
+        <oboInOwl:id>MS:1003427</oboInOwl:id>
+        <rdfs:label>PeakView</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MS_1003427"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>A software for spectral analysis and data interrogation in qualitative review of LC-MS and MS/MS data.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>PMID:32275110</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/MS_1003428 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/MS_1003428">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001139"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001456"/>
+        <obo:IAO_0000115>A software for interpreting protein quantification, interaction and post-translational modification data.</obo:IAO_0000115>
+        <oboInOwl:hasOBONamespace>MS</oboInOwl:hasOBONamespace>
+        <oboInOwl:id>MS:1003428</oboInOwl:id>
+        <rdfs:label>Perseus</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MS_1003428"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>A software for interpreting protein quantification, interaction and post-translational modification data.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>PMID:27348712</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/MS_1003429 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/MS_1003429">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001139"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001456"/>
+        <obo:IAO_0000115>A computational platform for analyzing mass spectrometry-based proteomics data.</obo:IAO_0000115>
+        <oboInOwl:hasOBONamespace>MS</oboInOwl:hasOBONamespace>
+        <oboInOwl:id>MS:1003429</oboInOwl:id>
+        <rdfs:label>FragPipe</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MS_1003429"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>A computational platform for analyzing mass spectrometry-based proteomics data.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>PMID:37878603</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/MS_1003430 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/MS_1003430">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001139"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001456"/>
+        <obo:IAO_0000115>A software for LC-MS data management and analysis.</obo:IAO_0000115>
+        <oboInOwl:hasOBONamespace>MS</oboInOwl:hasOBONamespace>
+        <oboInOwl:id>MS:1003430</oboInOwl:id>
+        <rdfs:label>OpenMS</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MS_1003430"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>A software for LC-MS data management and analysis.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>PMID:38366242</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/MS_1003431 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/MS_1003431">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001139"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001456"/>
+        <obo:IAO_0000115>A tool for the analysis of chemically cross-linked proteins using mass spectrometry.</obo:IAO_0000115>
+        <oboInOwl:hasOBONamespace>MS</oboInOwl:hasOBONamespace>
+        <oboInOwl:id>MS:1003431</oboInOwl:id>
+        <rdfs:label>pLink</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MS_1003431"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>A tool for the analysis of chemically cross-linked proteins using mass spectrometry.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>PMID:22772728</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    
+
+
+    <!-- http://purl.obolibrary.org/obo/MS_1003432 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/MS_1003432">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001139"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1001456"/>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MS_1003431"/>
+        <obo:IAO_0000115>Upgraded version of pLink tool, provides a graphical user interface and faster with newly designed index structure.</obo:IAO_0000115>
+        <oboInOwl:hasOBONamespace>MS</oboInOwl:hasOBONamespace>
+        <oboInOwl:id>MS:1003432</oboInOwl:id>
+        <rdfs:label>pLink2</rdfs:label>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MS_1003432"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Upgraded version of pLink tool, provides a graphical user interface and faster with newly designed index structure.</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>PMID:31363125</oboInOwl:hasDbXref>
+    </owl:Axiom>
+    
+
+
     <!-- http://purl.obolibrary.org/obo/MS_4000000 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/MS_4000000">