Hi Felipe, Please find the answers to your questions below.
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? In electrospray ionization (ESI), you can often see that when one ion [M1+H]+ coelutes with another ion [M2+H]+, you will also observe the peak of a complex ion [M1+M2+H]+. This is what MZmine is searching for. Therefore, if you select M+H as ionization type, it will substract proton mass from all peaks, then add the mass of 2 individual peaks together, and add the proton mass to this complex, and look for a peak of that mass. This process is fairly basic and not at all comperehensive - for example, it does not take into account situations where the two ions have different type of ionization (e.g. M+H and M+NH4). 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? The adduct search finds pairs of peaks that have very similar retention time and specified mass difference (relative to each other). Of course MZmine cannot know for sure that the peaks are truly M+Na adducts, but as long as your mass accuracy is high enough (e.g. +-0.001 m/z) and retention time is almost same, you can have very good confidence in the results. 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)? The "Custom database search" is one of the methods to assign identity to some peaks. The "Adduct search" and "Complex search" are other methods for the same purpose. You can find your adducts using the "Adduct search", or you can add them to your custom database and find them using the "Custom database search" - either way is fine. Best regards, Tomas =============================================== Tomas Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan WWW: https://groups.oist.jp/g0 TEL: +81-98-966-8684 Fax: +81-98-966-2890
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