Liquid chromatography-coupled mass-spectrometry introduction

Hub · October 20, 2021, 2:49pm

Load mass spectra, process (e.g. filter) them "in-file", then convert them to tables, and visualize them.

This is a companion discussion topic for the original entry at https://kni.me/w/ycQ8UXk5R3vlAbO2

MikeK · December 16, 2021, 4:52pm

How did you get the demangler definitions? I would like to know how to get the “file to table” node to work. There appears to be no documentation on how to make a demangler.

MikeK · January 31, 2023, 2:39pm

Any answers on how to get demanglers to work for different data types in the file to table node.

ScottF · January 31, 2023, 4:27pm

Let’s tag the @openms-team directly (also @jpfeuffer) to see if they can provide an answer.

jpfeuffer · February 1, 2023, 9:56am

Hey! So, this is an extension point provided by the Generic KNIME Nodes plugin, on which the OpenMS plugin is based on.

github.com

genericworkflownodes/GenericKnimeNodes/blob/develop/com.genericworkflownodes.knime/schema/com.genericworkflownodes.knime.mime.demangler.Demangler.exsd#L58


      
          </element>
          
          
<element name="demangler">
             <complexType>
                <attribute name="class" type="string">
                   <annotation>
                      <documentation>
                         
                      </documentation>
                      <appinfo>
                         <meta.attribute kind="java" basedOn=":com.genericworkflownodes.knime.mime.demangler.IDemangler"/>
                      </appinfo>
                   </annotation>
                </attribute>
             </complexType>
          </element>
          
          
<annotation>
             <appinfo>
                <meta.section type="since"/>
             </appinfo>

Basically, you need to provide your own plugin, or contribute to the Java source code of the OpenMS plugin to add functionality for other file types. This is done by “just” writing a class that implements the IDemangler interface and specifying for which mimetypes/file extensions it works for.
See de.openms.knime/de.openms.knime.importers/src/de/openms/knime/importers/mzml at develop · genericworkflownodes/de.openms.knime · GitHub
for the mzml Demanglers of OpenMS.