Icon

Peptide-spectrum matching

Peptide identification from mass-spectrometry data

This workflow performs a simple peptide identification from mass-spectrometry experiments (in mzML format). It matches fragment spectra against theoretical spectra from a protein database and visualizes the results interactively in a table together with a spectrum viewer.
Potential input data can be found under Links. Save the files as mzML and fasta and configure the Input File nodes to read them from your disk.


This workflow performs a simple peptide identification from mass-spectrometry experiments (in mzML format). It matches fragment spectra against theoretical spectra from a proteindatabase and visualizes the results interactively in a table together with a spectrum viewer. For more information see the workflow metadata. Find it here: View -> Description CAUTION: Can create alarge table for large datasets If using own data, you can configure the nodeand set the path. Example data is stored in theworkflow data path and referenced already. Rightclick -> Interactive Viewto explore matched spectra To collections.SpectraProtein DatabaseIdentify/matchTo TablefileTo KNIME tablePick first of collectionsOnly fragment spectraNode 51 FileToTable Input File View matchedspectra Input File SimpleSearchEngine MzTabExporter MzTabReader Map mods to masses String Manipulation Row Filter Joiner This workflow performs a simple peptide identification from mass-spectrometry experiments (in mzML format). It matches fragment spectra against theoretical spectra from a proteindatabase and visualizes the results interactively in a table together with a spectrum viewer. For more information see the workflow metadata. Find it here: View -> Description CAUTION: Can create alarge table for large datasets If using own data, you can configure the nodeand set the path. Example data is stored in theworkflow data path and referenced already. Rightclick -> Interactive Viewto explore matched spectra To collections.SpectraProtein DatabaseIdentify/matchTo TablefileTo KNIME tablePick first of collectionsOnly fragment spectraNode 51FileToTable Input File View matchedspectra Input File SimpleSearchEngine MzTabExporter MzTabReader Map mods to masses String Manipulation Row Filter Joiner

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: pfeuffer
Created at: 2019-08-12
On NodePit since: 2021-10-20
Last update: 2026-01-20
Created with KNIME version: v4.4.1
Tags: mass-spectrometryOpenMSpeptide identificationdatabase search

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!