title: Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry.
abstract: MS-based proteomics and metabolomics are rapidly evolving research fields driven by the development of novel instruments, experimental approaches, and analysis methods. Monolithic analysis tools perform well on single tasks but lack the flexibility to cope with the constantly changing requirements and experimental setups. Workflow systems, which combine small processing tools into complex analysis pipelines, allow custom-tailored and flexible data-processing workflows that can be published or shared with collaborators. In this article, we present the integration of established tools for computational MS from the open-source software framework OpenMS into the workflow engine Konstanz Information Miner (KNIME) for the analysis of large datasets and production of high-quality visualizations. We provide example workflows to demonstrate combined data processing and visualization for three diverse tasks in computational MS: isobaric mass tag based quantitation in complex experimental setups, label-free quantitation and identification of metabolites, and quality control for proteomics experiments.
authors.affiliation: Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
authors.forename: Stephan
authors.initials: S
authors.lastname: Aiche
authors.forename: Timo
authors.initials: T
authors.lastname: Sachsenberg
authors.forename: Erhan
authors.initials: E
authors.lastname: Kenar
authors.forename: Mathias
authors.initials: M
authors.lastname: Walzer
authors.forename: Bernd
authors.initials: B
authors.lastname: Wiswedel
authors.forename: Theresa
authors.initials: T
authors.lastname: Kristl
authors.forename: Matthew
authors.initials: M
authors.lastname: Boyles
authors.forename: Albert
authors.initials: A
authors.lastname: Duschl
authors.forename: Christian G
authors.initials: CG
authors.lastname: Huber
authors.forename: Michael R
authors.initials: MR
authors.lastname: Berthold
authors.forename: Knut
authors.initials: K
authors.lastname: Reinert
authors.forename: Oliver
authors.initials: O
authors.lastname: Kohlbacher
mesh_terms: D003196:Computer Graphics; D003627:Data Interpretation, Statistical; D006801:Humans; D055432:Metabolomics; D040901:Proteomics; D012984:Software; D053719:Tandem Mass Spectrometry; D057188:Workflow
keywords: KNIME; Metabolomics; OpenMS; Proteomics; Workflows