Hi! I am Master's Degree Student at University of São Paulo (Brazil)
I am using MZmine 2.9.1 for metabolomics and I am having serious doubts regarding the method of how it operates in the following steps: 1 - Complex Search; 2 - Search Adduct; 3 - Custom Database Search. 1 - Firstly, in the "Ionization Method" section (Complex Search), when we select the positive method (M + H), does MZmine add the proton mass to the peaks detected, or withdraws, or does nothing? 2 - How the "Search Adduct" tool knows who are the adduct peaks? If I inform to the sofware that the molecules are complexed with sodium (selecting M+Na), how MZmine knows that particular one peak is the sodium adduct ion or any other molecule? 3 - Finally, and most important: Since I select the ionization method (positive, eg), and the possible adducts (M + Na, eg) that form in the mass spectrometry, should we create database file with the m/z proton added to the m/z molecule and only then make the identification through the "Custom Database Search"? Should we also create a specific database file with m/z adducts? If yes, why then we should previously inform to the software that the peaks are from the positive method (1) and select the possible adducts (2)? Sincerely, Thank you very much! Felipe Antunes dos Santos------------------------------------------MSc Student - University of São Paulo - BrasilSchool of Pharmaceutical Sciences of Ribeirão Preto/ Laboratory of Pharmacognosy Web address: http://www.asterbiochem.org/ http://tematicoasteraceae2011.blogspot.com.br/
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