Chromatography Forum

Hello,

Being new to metabolomics , can somebody suggest any software to de-isotope and de-convolute charge state of MS1 spectra? I wish to have list of peaks with the neutral masses assigned to them.

Thanks

you could try xcms (and camera). But do remember that you cannot have a list of neutral masses because if you only get one mass (plus its isotope peaks) in positive mode, you cannot tell whether it is a sodium adduct, a hydrogen adduct, or something more obscure. Similarly you've got the problem of source fragments. Ideally you could recognize them either because the mass difference is something very easily recognized, or because they have exactly the same peak shape and location - but there will always be situations where two ions have slightly wobbly peaks in almost the same place, and you're left uncertain whether one is a source fragment from the other, with a bit of random noise, or whether one is actually a different chemical, that very nearly coelutes.
In effect, you might have to accept that you'll have multiple entries in your peak table that belong to a single chemical, and entries where you're not sure what adduct it is, but that's honestly not tragic. You only need to worry about it if that chemical/those chemicals turn out to do something interesting, and then you can sort out manually whether you think they're the same/what adducts they might be.