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ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion

Hulstaert, Niels; Shofstahl, Jim; Sachsenberg, Timo; Walzer, Mathias; Barsnes, Harald; Martens, Lennart; Perez-Riverol, Yasset
Journal article, Peer reviewed
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https://hdl.handle.net/11250/2755440
Utgivelsesdato
2020
Metadata
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  • Department of Informatics [740]
  • Registrations from Cristin [5248]
Originalversjon
Journal of Proteome Research. 2020, 19(1), 537–542   10.1021/acs.jproteome.9b00328
Sammendrag
The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analyzed per experiment as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elastic compute resources such as Linux-based cluster environments and cloud infrastructures. Unfortunately, the vast majority of cross-platform proteomics tools are not able to operate directly on the proprietary formats generated by the diverse mass spectrometers. Here, we present ThermoRawFileParser, an open-source, cross-platform tool that converts Thermo RAW files into open file formats such as MGF and the HUPO-PSI standard file format mzML. To ensure the broadest possible availability and to increase integration capabilities with popular workflow systems such as Galaxy or Nextflow, we have also built Conda package and BioContainers container around ThermoRawFileParser. In addition, we implemented a user-friendly interface (ThermoRawFileParserGUI) for those users not familiar with command-line tools. Finally, we performed a benchmark of ThermoRawFileParser and msconvert to verify that the converted mzML files contain reliable quantitative results.
Utgiver
ACS
Tidsskrift
Journal of Proteome Research
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Copyright 2019 American Chemical Society

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