emsl-computing / corems Goto Github PK

It would be great to have the option to export all candidate formulas for an m/z peak. This would help with gap-filling formulas across multiple samples within a dataset.

Hi Yuri,

 I hope you are doing well.  🙂
 I just wonder whether the elemental formula, one of CoreMS's outcomes, is a neutral molecular formula. Could you let me know?

Thank you,
Manhoi

Looking in the Molecular Formula Search Settings I am slightly confused about these options:

    # depending on the polarity mode it looks for [M].+ , [M].-
    # query and automatically compile add entry if it doesn't exist
    isRadical: bool = False

    # depending on the polarity mode it looks for [M + H]+ , [M - H]+
    # query and automatically compile and push options if it doesn't exist
    isProtonated: bool = True

    isAdduct: bool = False

If I understand correctly, order to search for a formula match to a deprotonated analyte (M-H)- you would set:

 isProtonated = True 
 isRadical = True 
 isAdduct = False

When isProtonated = True, coreMS reads the polarity of the raw spectra and automatically knows to search for [M-H] if the spectra was obtained in negative mode.

I initially thought the isProtonated boolean refers to [M + H] and thus I was setting this to False to search for deprotonated analytes. Only after checking my formula assignments did I realize this wasn’t giving me the expected results.

Maybe extra clarification could be provided in the comments about the isProtonated behaviour?
Specifically if True looks for [M + H]+ , [M - H]+ depending on the polarity mode

Any clarification would be great.

Running this code in corems 1.18:
from corems.transient.input.brukerSolarix import ReadBrukerSolarix
from corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFormulas
file_path= 'Ezra MS 060532_000005.d srfa iii/'
bruker_reader = ReadBrukerSolarix(file_path)
bruker_transient_obj = bruker_reader.get_transient()
mass_spectrum_obj = bruker_transient_obj.get_mass_spectrum(plot_result=False, auto_process=True)
SearchMolecularFormulas(mass_spectrum_obj, first_hit=True).run_worker_mass_spectrum()

Gives the following error:

I checked the url for the SQL database using
from corems.encapsulation.factory.parameters import MSParameters
MSParameters.molecular_search.url_database

the database is given as

'sqlite:///db/molformula.db'

this looks like a relative path to the db folder of CoreMS. However when I checked the path there is no molformula.db present. Is this a mistake or am I missing a step?

It would be good if you could declare constraints on 13C atoms during formula assignment.

For example I would like to use the following constraints:
C4–50,H4–100, O2–40, N0–2, S0–1, 13C0–1

I don’t see a way of declaring 13C limits in the MSParameters class.