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MassBank / RMassBank

Playground for experiments on the official http://bioconductor.org/packages/devel/bioc/html/RMassBank.html
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Restrict reanalyse peaks to peaks < precursor #51

Open sneumann opened 10 years ago

sneumann commented 10 years ago

Issue by schymane from Friday Jan 10, 2014 at 10:31 GMT Originally opened as https://github.com/sneumann/RMassBank/issues/43

A few spectra seem to have M+H(+2) labelled via reanalyse peaks. This shouldn't happen ;) Examples: 203 (pH_120108; 209.0114 C12H3NO3+), 657 (111116_pH; 427.1889 C17H34ClN3O5S+), 2676 (111116_pH; 258.0172 C8H8Cl2N6+). All relatively low I peaks (i.e. likely noise)

Also, add a feature in the validation Suite to catch this occurrence (peaks > precursor). Has this already been done?

sneumann commented 10 years ago

Comment by schymane from Wednesday Jan 15, 2014 at 13:20 GMT

Current thought is to send all reanalysed peaks with mass > precursor to the fail peak list for manual checking, which would give the user a chance to catch those cases and review them.

sneumann commented 10 years ago

Comment by meowcat from Monday Jan 20, 2014 at 10:11 GMT

As already stated, I am not sure whether this is a good way to do it. Filtering by formula matching will always match some noise, distributed over the whole spectrum. If we only specifically remove the mismatches above precursor mass (because they're obvious to us) we might give the false appearance of a near-perfect method which it isn't. The existence of such peaks reminds the user of the fact that the annotation is automatic and always will have errors.

Anyway I can still implement it if you think this is a good solution.

meowcat commented 4 years ago

@schymane Do you still experience this issue?

schymane commented 4 years ago

Seems a catch has been added validator side ... ?