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basic_​peptide_​identification

This workflow performs a basic peptide identification search.
The mzML files are searched with X!Tandem against a protein database.
The results are written out in idXML format into a specified directory.

Example input data:
To download the data from the archive linked below, check the box on the folder and click on the download button (arrow) on the top left.
Download and unpack the "Example_Data" data into a directory "Example_data" right inside your KNIME workspace.

URL: Home of the OpenMS plugin https://www.openms.de/
URL: Download Example Data https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/

Basic Peptide IdentificationThis workflow performs a basic peptide identification search.The mzML files are searched with X!Tandem against a protein database.The results are written out in idXML format into a specified directory. Define input data here.If the example data is used, itshould be in Example_Datanext to this workflow. Define the outputdirectory here.One idXML outputfile for each mzMLinput file will bewritten out in thisdirectory. Node 2Node 4Node 78Spectrum Files (.mzML)OutputProtein Database (.fasta)ZipLoopStart ZipLoopEnd XTandemAdapter File Importer File Exporter File Importer Basic Peptide IdentificationThis workflow performs a basic peptide identification search.The mzML files are searched with X!Tandem against a protein database.The results are written out in idXML format into a specified directory. Define input data here.If the example data is used, itshould be in Example_Datanext to this workflow. Define the outputdirectory here.One idXML outputfile for each mzMLinput file will bewritten out in thisdirectory. Node 2Node 4Node 78Spectrum Files (.mzML)OutputProtein Database (.fasta)ZipLoopStart ZipLoopEnd XTandemAdapter File Importer File Exporter File Importer

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: walzer
Created at: 2014-08-25
On NodePit since: 2018-06-16
Last update: 2024-11-16
Created with KNIME version: v5.2.1
Tags: OpenMSMass spectrometryPeptide identificationDatabase search

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