.raw file waters conversion

[Kashif Bashir]

Hello Everyone!

I have query that can we convert .raw file by water to mzml format using msconvert. the file size is single methanolic extract and around 2 GB. can it be handled by GNPS.

Will be highly grateful if someone can help in this regard.

Best 

Kashif

[TonioG]

Hi Kashir,

Better avoid MSConvert with raw from Masslynx>Waters. 

1st, not essential but I will advise to first use the "Waters Compression Tool" which will remove 80% of the size of the datafile corresponding to noise. Free to download from Waters web site.

2nd, you should use the WatersDataConnect tool to create the 1st version of mzML files. Free to download from Waters web site.

3rd, you need to correct the mzML file with this tool: https://github.com/elnurgar/mzxml-precursor-corrector. This is essential to make sure high intensities MS1 are well connected to their MS2 spectra.

Antonio

[Mingxun Wang]

https://wang-bioinformatics-lab.github.io/GNPS2_Documentation/waters_conversion/

This is one thing we use. 

Ming

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