Thanks for your detailed response. it is much more clear now!
1,2. Yes, I used the isotope+adduct option. so correct me if I got it wrong - it means that the isotopes data adds constraints to the compound search and match, but if no isotopes were detected, a (less accurate) match can be found? (many hits on non-isotopic compounds in my list, but less for isotopes [M]). 3. I just mean that I should do the same as the XCMS when I conduct the manual searches on Metlin, and not include m/z of isotopes on my batch search. 4. I was thinking maybe creating 4 different fields (dppm; name; id...), and in each of them have the values separated by |, of course in the same order. so if parsed field by field, each in loop, it would still match according to the order (when inserted to file/db record). For me it will just be easier because I'm interested in the id only ; ) I would totally understand if it doesn't make sense to others.
I just started playing with some urine samples and try to create an easier workflow between XCMS-online/Metlin/MassTrix.
Some Qs I've collected: 1. Does the metlin compound search in XCMS-online take in account the spectra and any detected isotopes? 2. If 1 is false, then it means that when I search Metlin (I do a 500 compound batch) based on the m/z from diffreport and under the same parameters I'm supposed to find exactly the same hits? 3. Following 2, Wouldn't it be logical to omit any C13 isotopes from my metlin batch search (hence include only [M] and non-isotopic m/z)? 4. I'm importing the results tsv file to excel, and find it time-consuming to manually parse the metlin hits column, which includes 4 fields for each hit (dppm::name::adduct::id ). for example: 2::2-Acetolactic acid::M-H:: 293|2::3-hydroxy-3-methyl-2-oxo-Butyric acid::M-H:: 3253|2::Glutaric acid::M-H:: 3254|... Is there any way around it apart from learning R so altogether I could handle the files with more flexibility?
Many thanks for anyone who finds the time to respond.
