OpenMS

This directory contains 18 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 […]

Phosphoproteomics_ID

Uses MSGFPlus and Percolator for peptide identification, Luciphor to identify phosphorylation sites on peptide sequences and then Epifany for protein […]

Proteomics_LFQ

Combines peptide identifications from X!Tandem and Comet. Uses normalized feature intensities for peptide quantification. No smart protein inference, all […]

ProteomicsLFQ_tool_and_MSstats_postprocessing

Uses the ProteomicsLFQ that contains the standard proteomics LFQ pipeline, after peptide and protein identification. Applies post-processing with […]

QC Metanodes

These QC metanodes are preconfigured to be plugged into your workflow. Remember to adapt contained input nodes where applicable. URL: Home of the OpenMS […]

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 […]