Selenium heteroatoms?

[phlaaj]

Hi, firstly, thank you so much for this landmark contribution to open source MS science! 🙏

My research is on organic selenium compounds (organoselenium), which is an emerging environmental contaminant of concern. Wondering how I could go about adding Se isotopes to the list of heteroatoms searched?

Thank you

[skschum]

Hello, At the moment Selenium is not an option for MFAssignR, though it is an interesting idea and something I may try to include when I have time to work on something like that again. In the short term, your best bet for trying to assign selenium containing compounds is to remove the exact mass of selenium from the measured ion masses you suspect have selenium and then try to assign the remaining masses with MFAssignR as normal. If a formula is assigned then you can further evaluate whether or not that assignment (with selenium) is a logical assignment. You would need to be careful to make sure there are not any mistakes in the initial calculation, and make sure that the resulting formula makes sense chemically, but it is something that you can try. Please let me know if you have any other questions. Thanks, Simeon

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On Sat, Oct 8, 2022 at 2:48 PM phlaaj ***@***.***> wrote: Hi, firstly, thank you so much for this landmark contribution to open source MS science! 🙏 My research is on organic selenium compounds (organoselenium), which is an emerging environmental contaminant of concern. Wondering how I could go about adding Se isotopes to the list of heteroatoms searched? Thank you — Reply to this email directly, view it on GitHub <#26>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF72HFHA2ITB2OV5OC5YSEDWCHFYFANCNFSM6AAAAAARAMCTE4> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[phlaaj]

hi Simeon,

Thank you for your thoughtful reply.

I understand and respect of course that you have other priorities currently to not be able to add in Se heteroatoms to the code at this time. However, could this be something I could take on?

I.e., would it be possible for me to add Se atoms to the code in the same way you have included the other heteroatoms? Am I correct in understanding that the strategy you described in your comment above is effectively how the MFAssign() function works already (e.g., for halogens)? like could I edit the MFAssign() code to include Se in a similar fashion as you have for the other heteroatoms? or are there any major concerns you would have or could foresee with this approach?

Again, thank you for MFAssignR, and for your continued discussion with me here :)

Tim

[skschum]

Hello Tim, You are more than welcome to try and add selenium to the program. The main issue is with the way that the inclusion of heteroatoms is fed through the function, meaning that adding an option for selenium could lead to unforeseen issues with how the functions work (both the formula assignment and other functions that require a certain data structure to work properly). Mostly, there are a lot of dependencies in different areas of the code that will need to be addressed in order to add another heteroatom, some of which may not be too clear from the outset. In theory though, you can add selenium the same way that the halogens and any other non C,H,O atom is included in MFAssignR. If you can work through it and fix those problems along the way, that is fine, though I would recommend keeping a "clean" version in order to check whether everything else is still working. If you can get it working, I would be glad to see it and potentially incorporate it with what is already available in MFAssignR (with acknowledgement of your contribution of course). Or if you get it working you can keep it for yourself, preferentially with limited distribution so that I don't end up with questions about a version of MFAssignR that I didn't put together. The easiest way to do it would likely be automating the removal of the mass of selenium, along the lines of what I mentioned previously, but the addition of heteroatoms in MFAssign itself is handled in a slightly different fashion and is more tied in with other aspects of the code that may not be obvious. Anyway, let me know if you have any questions and I will be glad to provide whatever information I can. Thanks, Simeon

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On Fri, Oct 14, 2022 at 9:46 AM phlaaj ***@***.***> wrote: hi Simeon, Thank you for your thoughtful reply. I understand and respect of course that you have other priorities currently to not be able to add in Se heteroatoms to the code at this time. However, could this be something I could take on? I.e., would it be possible for me to add Se atoms to the code in the same way you have included the other heteroatoms? Am I correct in understanding that the strategy you described in your comment above is effectively how the MFAssign() function works already (e.g., for halogens)? like could I edit the MFAssign() code to include Se in a similar fashion as you have for the other heteroatoms? or are there any major concerns you would have or could foresee with this approach? Again, thank you for MFAssignR, and for your continued discussion with me here :) Tim — Reply to this email directly, view it on GitHub <#26 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF72HFFSMLIKWPVQTSNHFZDWDFW4FANCNFSM6AAAAAARAMCTE4> . You are receiving this because you commented.Message ID: ***@***.***>