Dataset Information

Automated workflow composition in mass spectrometry-based proteomics.

ABSTRACT:

Motivation

Numerous software utilities operating on mass spectrometry (MS) data are described in the literature and provide specific operations as building blocks for the assembly of on-purpose workflows. Working out which tools and combinations are applicable or optimal in practice is often hard. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design.

Results

We provide a toolkit to support researchers in identifying, comparing and benchmarking multiple workflows from individual bioinformatics tools. Automated workflow composition is enabled by the tools' semantic annotation in terms of the EDAM ontology. To demonstrate the practical use of our framework, we created and evaluated a number of logically and semantically equivalent workflows for four use cases representing frequent tasks in MS-based proteomics. Indeed we found that the results computed by the workflows could vary considerably, emphasizing the benefits of a framework that facilitates their systematic exploration.

Availability and implementation

The project files and workflows are available from https://github.com/bio-tools/biotoolsCompose/tree/master/Automatic-Workflow-Composition.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Palmblad M

PROVIDER: S-EPMC6378944 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Publications

Automated workflow composition in mass spectrometry-based proteomics.

Palmblad Magnus M Lamprecht Anna-Lena AL Ison Jon J Schwämmle Veit V

Bioinformatics (Oxford, England) 20190201 4

<h4>Motivation</h4>Numerous software utilities operating on mass spectrometry (MS) data are described in the literature and provide specific operations as building blocks for the assembly of on-purpose workflows. Working out which tools and combinations are applicable or optimal in practice is often hard. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design.<h4>Results</h4>We provide a toolkit to support researchers in ...[more]

PMID: 30060113

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Dataset Information

Automated workflow composition in mass spectrometry-based proteomics.

Motivation

Results

Availability and implementation

Supplementary information

Publications

Automated workflow composition in mass spectrometry-based proteomics.

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