How to convert raw spectra data into centroid mode?

MetaboAnalyst
1

Using Proteowizard is highly recommended.

  1. If you are using GUI of Proteowizard, please set the parameters according to the screenshot below.

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    Note: the “peak Picking” parameter has to be set as the first filtering condition to ensure the centroiding works properly.

  2. If you are using docker version of Proteowizard, please use the following command to run the conversion:

docker run -it --rm -e WINEDEBUG=-all -v /YOUR/ABSOLUTE/DATA/DIR/:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert *.raw --mzML --filter "peakPicking true 1-" --filter "zeroSamples removeExtra" --filter "msLevel 1" --64 --zlib

Note: Please modify “*.raw” based the extension of your vendor MS files.

1 Like
2

Hi, I am a beginner to bioinformatics and would like to explore on its metabolomics application. I have a zip of mzml files containing lc-ms spectra and tried to analyse the data into MetaboAnalyst website. However, when uploading it stated that my files are not centroided and can’t be converted using the MetaboAnalyst website. I have tried to download the ProteoWizard msconvert however still can’t resolve the problem. Can anybody encounter the similar problem, would really appreciate for the help.

Thank you so much!

3

Sounds like you should ask the ProteoWizard team, and make sure to provide more specific details - simply “not working” does not give any clue

4

Thanks for the reply.

is it possible to check for the centroid mode through code with either python or R? If yes, do you know where to find the source?