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tsufz
transferred this issue from MassBank/MassBank-data
Dec 18, 2018
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Hi, I transfered this issue, because there was a wrong link on MassBank. |
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I totally agree with the comment. It is not very practical to normalise a peak list before submitting. The online tool should be as comfortable as possible. Usually, the people copy and paste a spectra from their MS viewer or so. We could do the normalisation in the background while handling the query? |
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Thanks for the comment, we will improve the search. |
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Fixed with 6217299 |
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The search does not handle truncations so far. It is possible to search for C8H10N4O2 and get the results for caffeine. If I truncate like C8H10N*O2, I get empty results. |
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8f87c92 implements wildcards on chemical formulas. This wildcards work only on string basis without any chemical knowledge. This means C8OP* will result in 291 results while C8PO* will have no results. Implementing chemical knowledge here would be a bigger effort. |
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Not sure what you mean by “chemical knowledge” but there are a few R functions already out there that just split the formulas into the corresponding elements and then accompanying numbers and this would be one way you could expand the wildcard functionality to be order-independent …
OR we have all formulas standardized according to the chemical rules (e.g. Hill system) in MassBank. I think this is not yet the case. I’d prefer the former for the wildcard search as it’s more universal.
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Would be some easy code: https://stackoverflow.com/questions/2974362/parsing-a-chemical-formula or could be use CDK? Needs to be Java and not R. |
dnikol1 commentedDec 17, 2018
Why is it that we cannot just search molecular formula without putting something in the Compound Name line?
Why is it that the spectrum in the format of m/z vs absolute intensity cannot be searched, but instead requires normalized intensity?