ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion
العنوان: | ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion |
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المؤلفون: | Lennart Martens, Yasset Perez-Riverol, Harald Barsnes, Timo Sachsenberg, Niels Hulstaert, Mathias Walzer, Jim Shofstahl |
المصدر: | J Proteome Res Journal of Proteome Research 537–542 |
بيانات النشر: | American Chemical Society (ACS), 2019. |
سنة النشر: | 2019 |
مصطلحات موضوعية: | Proteomics, 0301 basic medicine, Saccharomyces cerevisiae Proteins, Computer science, Interface (Java), Big data, Cloud computing, computer.software_genre, Biochemistry, Article, Workflow, 03 medical and health sciences, Cross-platform, Databases, Protein, 030102 biochemistry & molecular biology, business.industry, Computational Biology, General Chemistry, Modular design, File format, 030104 developmental biology, Scalability, Operating system, business, computer, Software |
الوصف: | 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. acceptedVersion |
وصف الملف: | application/pdf |
تدمد: | 1535-3907 1535-3893 |
URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a9180999ee90467b92541938fb720f01 https://doi.org/10.1021/acs.jproteome.9b00328 |
حقوق: | OPEN |
رقم الأكسشن: | edsair.doi.dedup.....a9180999ee90467b92541938fb720f01 |
قاعدة البيانات: | OpenAIRE |
تدمد: | 15353907 15353893 |
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