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Sign upIdeas for Validator #158
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I stumbled over this spectrum and noticed the fragment m/z's compared to the parent-ion-mz (423.5989 and 782.2591 vs 147.0441). If the validator could reveal fragments which are too heavy, than we would at least be aware of that. |
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That spectrum looks like it is only noise (those are the only two peaks).
Note that spectra processed with RMassBank can sometimes contain heavier peaks if they have certain adducts (up to +N2O allowed), so this should be considered in any validation. There are, however, many spectra with bogus heavy peaks that are clearly just noise (where it is clear from mass defect etc, like in this case) and maybe the (sub)formula assignment routine in RMB could be integrated into the validator to help separate the possible goodies from the baddies?
What is going to be the procedure for spectra that the validator identifies as (likely) pure noise, like the example you just raised?
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I have no idea for the proper procedure, especially in this case, because its experimental data, not meta data. I wouldn't touch it. One could flag it or raise an issue with the original contributor, but sometimes this will be complicated. |
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Check CH$NAME for
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In light of issues found/raised by Herbert Oberacher recently, I see a couple of new ideas we should consider implementing in the validator:
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schymane
changed the title
Ideas vor Validator
Ideas for Validator
Mar 25, 2019
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Please check whether all fragment-m/z in the |
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Good idea, I suggest to build in a slight tolerance to avoid decimal place issues. I wouldn't check on the reverse, i.e. there may be fewer PK$ANNOTATION entries than PK$PEAK but there should not be more PK$ANNOTATION entries than PK$PEAK (unless anyone puts out multiple annotations for a given PK$PEAK, I am not aware of this case ... RMassBank only puts out one formula per peak and tags if more were possible ... |
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meowcat
commented
Apr 11, 2019
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Agree with @meowcat - in principle no problem with having multiple annotations for one peak |
meier-rene commentedFeb 27, 2019
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edited
I want collect Ideas for automatic Validation in this Issue:
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check for duplicate entries in CH$NAMEimplemented and applied, 242 records fixed-
check for InChIKey-style pattern in CH$NAMEimplemented and applied, 131 records fixed-perhaps flag for super-short names that contain letters and numbers (as these are e.g. database codes, like CID1233 or something, a lot of ZINC and CHEBI sneak through