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topdownproteomics / sdk

Software solution for common top-down proteomics tasks
http://www.topdownproteomics.org/
MIT License
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Starts work on rule 6, need some feedback #29

Closed rfellers closed 6 years ago

rfellers commented 6 years ago

Not ready to merge, need feedback. Checkout Rule6_WithModificationNames() unit test ... is [mass]+S[Methyl]EQVE[14]NCE valid ProForma?

veitveit commented 6 years ago

Rule 6 states "If all tags in a proteoform use the same key ...". I would say that this example is not valid. "Methyl" does not use a key but is assigned to one.

2018-02-14 19:18 GMT+01:00 Ryan Fellers notifications@github.com:

Not ready to merge, need feedback. Checkout Rule6_WithModificationNames() unit test ... is [mass]+S[Methyl]EQVE[14]NCE valid ProForma?

You can view, comment on, or merge this pull request online at:

https://github.com/topdownproteomics/TestLib/pull/29 Commit Summary

  • start work on rule 6, need some feedback

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rfellers commented 6 years ago

Thanks Veit, apologies for not suggesting you as a reviewer. That makes sense; so, if a prefix tag is used, then all of the subsequent tags must be key-less and have a valid value for the given prefix tag. So this means that [mass]+SEQ[14]VEN[formula:C(2) H(6)]CE is also invalid, correct?

acesnik commented 6 years ago

Yes, this example is invalid. From the paper: "This prefixed key defines every tag in the sequence. This option can only be used when there is one key in the sequence."

rfellers commented 6 years ago

Thanks all! Basically, I should just RTFM! :) I'll update this branch and give you something that can be pulled in.