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Mol Cell Proteomics. 2019 Aug;18(8):1700-1702. doi: 10.1074/mcp.TIR119.001505. Epub 2019 May 16.

MARMoSET - Extracting Publication-ready Mass Spectrometry Metadata from RAW Files.

Author information

1
‡Bioinformatics Core Unit, Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff Institute, Ludwigstr. 43, Bad Nauheim, Germany.
2
‡Bioinformatics Core Unit, Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff Institute, Ludwigstr. 43, Bad Nauheim, Germany mario.looso@mpi-bn.mpg.de.
3
¶The German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main.
4
§Scientific Service Group Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff Institute, Ludwigstr. 43, Bad Nauheim, Germany johannes.graumann@mpi-bn.mpg.de.

Abstract

In the context of publishing data sets acquired by mass spectrometry or works based on such molecular screens, metadata documenting the instrument settings are of central importance to the evaluation and reproduction of results. A single experiment may be linked to hundreds of data acquisitions, which are frequently stored in proprietary file formats. Together with community-, repository-, as well as publisher-specific reporting standards, this state of affairs frequently leads to manual -and thus error prone-metadata extraction and formatting. Data extracted from a single file also often stand in for an entire file set, implying a risk for unreported parameter divergence. To support quality control and data reporting, the C# application MARMoSET extracts and reduces publication relevant metadata from Thermo Fischer Scientific RAW files. It is integrated with an R package for easy reporting. The tool is expected to be particularly useful to high throughput environments such as service facilities with large project numbers and/or sizes.

KEYWORDS:

Bioinformatics; Bioinformatics software; Data standards; Mass Spectrometry; Quality control and metrics

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