Molecular networking with data data acquired simultaneously in postive and negative modes

[Vinícius Galvão Wakui]

Hi everyone,

I´m working with a data acquired simultaneously in postive and negative modes, and I notice that GNPS has annotated only precursor ions in positive ion mode. I didn´t found any annotation for data in negative ion mode. My doubt is: is possible to do a molecular networking with a data acquired simultaneously in negative and positive ion mode? Actually it´s the first time I received a data in this conditions, I used to work with data acquired in negative and positive ion mode separately, I mean different files for which analysis.

[Mingxun Wang]

Yes, reach out to my lab, we have tools for this if you'd like to work together can connect you with my phd student putting this out. 

[Ahmed Tawfike]

Hi Ming,

I have more or less similar problem. Collected data in both modes and generated MGF and quant table using MZmine but the job failed due to error. Would mind investigating this and let me know what is done wrong? Job ID=474e5d11108349edbc6d670e8985a2f2

Thanks

Ahmed

[Vinícius Galvão Wakui]

Hi Ahmed,

I had a similar problem that I manage to solve using the MSConvert software to separate positive and negative ion mode data. Using the scan polarity filter it´s possible to separate the data and analyse them separately as usual. 

Vinícius

[Ahmed Tawfike]

Thanks Vinicius, I used to separate polarities and convert RAW to MzML using MSconvert before I process the data on MZmine. But since MZmine accepts dual polarity RAW files, I skipped MSconvert bit. But it seems that GNPS still works only on separate polarities.

BR

Ahmed