parse compound names and MS2 from waters

[sardnar]

Hello,

Thank you very much for this work! it's the cleanest way to parse waters data. In waters .raw there is a file called _FUNC001.CMP that contains the compound names. I think it should be easy to parse this as an attribute and save also as csv while looping. Also there must be a file in .raw that contains MS2 reads. The reads it self may not be important, but the mapping between which parent mass and child mass is of interest.

Thanks again!

[sardnar]

I am uploading small example here. example.raw.zip

If there is a way to add _FUNC001.CMP names to the metadata, it would be so useful.

[ekwan]

Thanks! We'll look into this.

[OmarAshkar]

I tried to work this out before, I shared my code in the pull request.

There is a file called "_FUNC001.CMP" that has compound names and transitions that are easy to parse. However, the MS2 transitions are not clear where they are. They are there for sure somewhere though as other software are able to see them only from these files.

[ekwan]

Thanks! I see the pull request now and we'll take a look at it. Can you help us out by illustrating what these names look like in other software? Maybe some screenshots with highlighted sections?

[OmarAshkar]

You can just use SeeMS from ProteoWizard.

This is the example from @sardnar So it gives both MS2 and MS2 for each read

[sardnar]

Thanks a lot!