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Tutorial Workflows OpenMS 3.0

This directory contains 19 workflows.

Iconbasic_​peptide_​identification 

This workflow performs a basic peptide identification search. The mzML files are searched with X!Tandem against a protein database. The results are […]

Iconbasic_​peptide_​identification_​with_​inference 

This workflow performs a basic peptide identification search, infers proteins and computes abundances using spectral counting. The mzML files are searched […]

IconDIAMetAlyzer_​2.0 

Uses Decoy generation from DDA data, targeted DIA analysis using OpenSWATH and pyprophet for statistical validation. Example input data: To download the […]

IconIdentification_​quantification_​with_​inference_​isobaric_​epifany_​MSstatsTMT 

## Description OpenMS exam workflow for the analysis of isobaric data (e.g. TMT). A) Quantification via the IsobaricAnalzyer B) Score estimation and […]

Iconlabelfree_​with_​protein_​quantification 

Identification with X!Tandem in the ID meta node, Protein Inference with Fido and protein quantification based on feature intensities with […]

IconMetabolite_​Adduct_​Grouping 

Uses accurate mass based on multiple adduct grouping steps (adducts, neutral losses). Example input data: To download the data from the archive linked […]

IconMetabolite_​DeNovoID 

Uses adduct grouping and de-novo identification with SIRIUS/CSI:FingerID. Example input data: To download the data from the archive linked below, check […]

IconMetabolite_​ID 

Quantification and identification via accurate mass search with downstream processing and visualisation. Example input data: To download the data from […]

IconMetabolite_​SpectralID 

Identification of small molecules via spectral library search using MetaboliteSpectralMatcher. Example input data: To download the data from the archive […]

IconMSstats_​statPostProcessing_​iPRG2015 

Uses MSstatsConverter to make tables that are processed in short R code scripts in various nodes. A consensusXML file from an LFQ workflow is required as […]