Featured workflows


Quantitative Data Independent Proteomics (DIAproteomics)

DIAproteomics: Automated quantitative analysis of DIA proteomics mass spectrometry measurements DIAproteomics is a bioinformatics analysis pipeline used for quantitative processing of data independent (DIA) proteomics data. The workflow is based on the OpenSwathWorkflow for SWATH-MS proteomic data. DIA RAW files (mzML) serve as inputs and library search is performed based on a given input spectral [...]

Data-Independent Acquisition Metabolomics Analyzer (DIAMetAlyzer)

DIAMetAlyzer is a KNIME workflow which integrates DDA and targeted DIA analysis for metabolomics, which allows for false-discovery rate estimation based a target-decoy approach (see figure 1). It performs DDA based candidate identification and constructs a target/decoy assay library, which is used for DIA target extraction and statistical validation (FDR estimation).   Fig. 1: [...]

Quantification and identification of MHC peptides (MHCquant)

MHCquant: Identify and quantify peptides from mass spectrometry raw data   MHCquant is an¬†analysis pipeline used for quantitative processing of data dependent (DDA) peptidomics data. It was specifically designed to analyze immunopeptidomics data, which deals with the analysis of affinity-purified, unspecifically cleaved peptides that have recently been discussed intensively in the context of cancer vaccines. [...]