Tutorial Workflows OpenMS 3.0
This directory contains 19 workflows.
MSstatsTMT
Post processing workflow for MSstatsTMT. Requires output from MSstatsConverter output. As an example input, an intermediate result from the […]
openmsLFQ_iPRG2015
Simple workflow for peptide identification and quantification. No smart protein inference is done and all possible proteins are reported for each […]
OpenSwath
Directly uses the OpenSWATHWorkflow node with inputs and outputs. Requires an existing Assay Library as input. Example input data: To download the data […]
Phosphoproteomics_ID
Uses MSGFPlus and Percolator for peptide identification, Luciphor to identify phosphorylation sites on peptide sequences and then Epifany for protein […]
Protein label-free quantification
This workflow performs a quantification of proteins from (label-free) mass-spectrometry data. The final results are relative comparisons of protein levels […]
Proteomics_LFQ
Combines peptide identifications from X!Tandem and Comet. Uses normalized feature intensities for peptide quantification. No smart protein inference, all […]
QC Metanodes
These QC metanodes are preconfigured to be plugged into your workflow. Remember to adapt contained input nodes where applicable.
QC_with_OpenMS
Uses X!Tandem to identify peptides and then uses various Meta Nodes for QC metrics. Requires mzML spectrum files as input, and a protein database has to be […]
QC_with_OpenMS_noggplot
Uses X!Tandem to identify peptides and then uses various Meta Nodes for QC metrics. Requires mzML spectrum files as input, and a protein database has to be […]