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eugenemel / maven

Maven GUI: Metabolomics Analysis and Visualization Engine
https://github.com/eugenemel/maven/releases
GNU General Public License v3.0
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Maven Isotope Reporting Incorrect for some Analytes #130

Closed cmsand closed 4 years ago

cmsand commented 4 years ago

Maven reporting zero values for C12 parent isomer of L-Valine. Spectra view looks OK, though. Manual integration did not fix problem.

Raw data to reproduce bug in Metabolomics Core -> GitHub Issues

PMSeitzer commented 4 years ago

This is likely linked to how the correlation is being computed in mzSample->correlation().

Everything might be techinically correct, potentially slightly confusing UI.

Note related issue #102 (also has to do with correlation computation)

cmsand commented 4 years ago

I can resolve the issue for Valine by decreasing the isotope-parent correlation to -0.1, but that seems to introduce lots of noise into other amino acids. It's an OK work-around for now, but would be good to fix the issue directly.

PMSeitzer commented 4 years ago

New approach implemented as of 5a011b4e3fc8289036d74b85fcc4ea6d65b56f6f

PMSeitzer commented 4 years ago

Consider the molarity of the adduct when considering formulas - eg [2M+H]+ should enumerate 2*molecular_formula worth of atoms

PMSeitzer commented 4 years ago

Implemented molarity of adduct consideration in maven_core

e1f3b27c82f29754ee8c8ef2e637615aa318b25d
PMSeitzer commented 4 years ago

Implemented with bug fixes as of d1e4d095d307e423008ba4a541bda11d7d4753a5