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MetAdata fRom Mass SpectromETry - command line tool
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MARMoSET_C
README.md

README.md

MARMoSET_C

MARMoSET is a commandline tool written in C#. Due to the design of the Thermo Fischer RawFileReader it is running as 64 bit code on Windows only. Compiled in Visual Studio Community 2017 (Version 15.8.7, .net 4.7.03056) on Windows 10 (64 bit), it was tested for the following Instruments:

  • Thermo EASY-nLC
  • RSLCnano
  • Q Exactive Plus - Orbitrap MS
  • Q Exactive HF - Orbitrap MS
  • Q Exactive - Orbitrap MS
  • LTQ Orbitrap Velos MS
  • Orbitrap Fusion

How to use

MARMoSET.exe [input path] [output jsonfile]

The command line tool has implemented one mandatory parameter on the command line. It requires a raw file, or a path to a directory containing raw files as input information. While by default the output is written to standard output, commiting filename as a second parameter forces it to write an output file instead. With -r <path+filename> a full output path can be used.

The output can be easily accessed by using any text editor.

Implementation

The parser runs the following way. It collects all input raw file names before opening each of the files in a parallelised foreach loop. By using methods of the RawFileReader it collects the meta data of each file separately. The instrument and partly the tune data is transformed to json strings, these strings are used to create a hashcode assigned to the file. By adding the files to a dictionary using the hashcode as key, the files get grouped by simmilar data. Therefore the output of the MARMoSET is a json file containing the meta data of the entered raw files, grouped by similar instrument data. These groups are one-based numbered and each group includes “Instruments”, “Names” and “Files”. Instruments again comprises the components of the device, for example the nLC-pump and the Q-Exactive . Each of these stores method data and instrument information like name or softwareversion. The collocation of the data in “Method” varies and depends on the type of instrument. For some mass spectrometer type there is also shared tune data. While “Names” is a list of the filenames sorted to this group, “Files” contains additional information seperately for each file. This information is split into “FileInformation” and “SampleInformation”, further, depending on the type of mass spectrometer “AdditionalTuneData”.

R Package

https://github.molgen.mpg.de/loosolab/MARMoSET

How to cite:

Kiweler M, Looso M and Graumann J. MARMoSET – Extracting Publication-Ready Mass Spectrometry Metadata from RAW Files. Molecular & Cellular Proteomics (2019), DOI: 10.1074/mcp.TIR119.001505

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