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License: BSD 2-Clause "Simplified" License
CoreMS is a comprehensive mass spectrometry software framework
License: BSD 2-Clause "Simplified" License
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. π
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 wasnβt 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()
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:
C4β50,H4β100, O2β40, N0β2, S0β1, 13C0β1
I donβt see a way of declaring 13C limits in the MSParameters class.
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