Waters MSe data conversion with MSconvert

[Zhenlong Wu]

Hi,

Recently I used the MSconvert to convert the waters MSe data, after that I submit the mzML file to build the molecular networking, but it came out several errors indicating file problems. Is this the matter with the MSe data (including the MS level 0 and 1 spectra)? I have tried to filter the MS lever 0 spectra MSconvert, it doesn't work either.

I appreciate for kind suggestions to figure this out.

Below is the linkage of the submitted job.

https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=d349ee0b91ab4847b9e7d3ec3444c355

Best,

Zhenlong

[Mingxun Wang]

Hi,

Please refer to our documentation on how to handle MSe data from waters:

https://ccms-ucsd.github.io/GNPSDocumentation/fileconversion/

Thanks!

Ming

[Aloooooog]

Many thanks, Ming. I wonder if there is an alternative method for the conversion because the MSconvert doesn't work for the MSe file, and I am unable to use the recommonded waters Symphony software right now.

Thanks again, Best regards.

Zhenlong

在 2019年8月13日星期二 UTC-5下午6:00:25，Mingxun Wang写道：

[Mingxun Wang]

Zhenlong you're not making it easy!

Another alternative is using Progenesis to perform feature detection as it will also do the de-convolution. Then you can use the output to work with Feature Based Molecular Networking. We've already got support for Progenesis support but the documentation is still in development. 

Hope this helps. 

Ming