labelfree_with_protein_quantification

Identification with X!Tandem in the ID meta node, Protein Inference with Fido and protein quantification based on feature intensities with ProteinQuantifier.
Input mzML spectra files are specified in the Input Files node.
The target protein database is specified in the Input File node within the ID meta node.
Outputs are multiple boxplots that can be opened by right click -> View Boxplot on the blue Boxplot nodes.

Example input data:
To download the data from the archive, check the box on the folder and click on the download button (arrow) on the top left.
Download and unpack the "Labelfree" data into a directory "Example_data/Labelfree" next to this workflow inside your KNIME workspace.

External resources

• Example Data
• Home of the OpenMS plugin