KNIME

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Targeted feature detection for label-free quantification

[bibshow file=2017_2.bib] [bibcite key=weisser2017targeted] References: [/bibshow]

Parallel execution of OpenMS tools in KNIME

This workflow shows both the use of standard ZipLoop nodes for iterative OpenMS tool execution, as well as how to execute OpenMS tools in parallel in a high-throughput manner (e.g., to use all computing power for a large number of files)!

DNA heteroconjugate detection (Flett et al.)

Differential Enzymatic 16O/18O Labelling for the Detection of Cross-Linked Nucleic Acid-Protein Heteroconjugates  

Non-targeted LC-MS-based lipidomics

This is a lipidomics demonstration workflow as presented during the Metabolomics 2016 conference. It shows how OpenMS can be used in KNIME to cover various steps in MS lipidomics analyses. Used OpenMS algorithms include: detection of lipid features (i.e., m/z, intensity and retention time centroids with their convex peak hulls for a specific lipid ion) [...]

Basic Peptide Identification

This KNIME workflow shows the very basics of peptide identification using OpenMS. What it does: It shows how to use a peptide search engine adapter (here: OMSSA) on multiple input files using the same database multiple times. This workflow is part of the OpenMS tutorial and described in detail in the tutorial. Preset parameter assumptions: [...]

Consensus Peptide Identification

The workflow exemplifies how to increase peptide identification rates in shotgun proteomics experiments by parallel usage of different search engines. The ConsensusID algorithm used is based on the calculation of posterior error probabilities (PEP) and a combination of the normalized scores by considering missing peptide sequences. What it does: It shows how to apply the [...]

Peptide Identification and Label-free Quantification

The workflow exemplifies the analysis capabilities of OpenMS in combination with KNIME. Identification and quantification results are combined and subjected to a simple analysis controlling for the concentration of background peptides being constant and visualize the fold change of investigated peptides across several runs. What it does: Quantification will be done with the aid of the [...]

Protein Inference

This workflow uses a label-free quantification on top of which protein inference and protein quantification are executed. What it does: Protein inference is performed using FIDO and performs a statistical validation of the protein inference results using advanced KNIME nodes. Protein quantification is done by summarizing all quantified peptides of observed charge states for the [...]

SWATH Analysis

Example workflow for SWATH analysis using OpenSWATH. This workflow is part of the OpenMS tutorial and described in detail in the tutorial.

Small Molecule Identification and Quantification

Example workflow for small molecule identification and quantification. Features: accurate mass search detection of differential small molecules This workflow is part of the OpenMS tutorial and described in detail in the tutorial.