1 Topic by djawed

  • djawed
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Topic: how to detect a molecule

Hello,
First of all i am so thankfull for this amazing software. i'm currently doing my internship in a lab that works on fungal extracts and  the aim of this project is to identify the molécules that are more expressed in certain conditions so i am using this software to compare my expermiental Spectrum with the database. when i try to match, it gives me lot of molécules that have the same mass but in order to be sure that it's the right molecule i need to compare also their fragmentation (MS2)and see wheather if it matches or not  so i was just wondering if this software takes this in account or at least if it contains the fragmentation of every molecule?
i also wanted to add that i used the ESI-negative mode and wanted to know if it's ok when i try to match my spoectrum with the database?

Sincerly yours.

2 Reply by Martin

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Re: how to detect a molecule

Hi,
mMass doesn't contain any library of spectra. It is only capable to simulate fragments of peptides, in the meaning of possible masses, not intensities..

3 Reply by djawed

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Re: how to detect a molecule

thank you for your answer,

But what about the libraries that we can download from this website like norine, lipid maps. cause i'm using the same approach that  was described in an article where they used mmass software and compared their Spectrum with the databses that they downloaded from this website (norine, lipid maps and fungal métabolites)in order to compare every mass detected in their Spectrum with the mass of molécules in those libraries?

Sincerly yours.

4 Reply by Martin

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Re: how to detect a molecule

Now got the point… :-) These libraries are in fact just libraries of elemental compositions, from which the exact mass is calculated. So no real spectra, and no fragmentation. In case of peptides, however, you could define corresponding sequence in the sequence editor, simulate fragments and compare with your MS2 scans.

5 Reply by djawed

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Re: how to detect a molecule

thank you so much for your answer !!!

everyday i'm Learning how to use it :)