Nomenclature for proteoforms #30
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Great stuff. I will definitively use this if applicable but currently I am not sure where/when. Maybe it is worth to consider this in the planned unimod package. |
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I saw your unimod package. What is it exactly about?
The nomenclature is strongly related on unimod being a rather complete and
up-to-date resource (compared to RESID and PSI-MOD). Actually, all 3
databases can be interlinked to provide the full picture (RESID is amino
acid based). I wrote some R code to map the entries onto one table, maybe
that interests you.
2017-07-28 22:21 GMT+02:00 Sebastian Gibb <[email protected]>:
… Great stuff. I will definitively use this if applicable but currently I am
not sure where/when. Maybe it is worth to consider this in the planned
unimod <https://github.com/ComputationalProteomicsUnit/unimod> package.
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We recognize that we have to do fragment calculation in a few packages, namely MSnbase, Pbase, and now topdown. While fragment calculation is relatively easy it becomes complicated if you want to respect modifications (which is the most requested feature in The idea for the unimod package was to provide a general interface to the database unimod.org and an unified interface to describe modifications for proteomics packages in R. Currently it is in a very early state. The import of the unimod data is working but there is no real user interface yet. Mostly because I am not sure how to describe:
I believe the proteoform nomenclatur could be an easy solution to provide a sequence with modification information that could be used in a general Currently the package is called unimod but we could integrate RESID and PSI-MOD as well.
Of course, I am really interested. If you like to discuss/share ideas and contribute code you are very welcome! |
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In the long run we could use the proteoforms nomenclature as input instead of fasta files and an additional |
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Points 1.-3. should be covered. Point 4 is quite interesting and I created
an issue (
topdownproteomics/ProteoformNomenclatureStandard#18
).
Does that mean that you want to include sequence, PTMS, ... to describe the
fragments (SEQUE[PTM]N), instead of by series and ion number?
I'll check my code and the unimod package to see whether and how it could
be added.
2017-07-29 12:28 GMT+02:00 Sebastian Gibb <[email protected]>:
… We recognize that we have to do fragment calculation in a few packages,
namely MSnbase, Pbase, and now topdown. While fragment calculation is
relatively easy it becomes complicated if you want to respect modifications
(which is the most requested feature in MSnbase::calculateFragments).
The idea for the unimod package was to provide a general interface to the
database unimod.org and an unified interface to describe modifications
for proteomics packages in R. Currently it is in a very early state. The
import of the unimod data is working but there is no real user interface
yet. Mostly because I am not sure how to describe:
1. global modifications, like: Carbamidomethyl, which replaces all C
with C + 57.02146
2. local modifications, like: Phosphorylation on the second Serin in
the sequence
3. modification on the n/c-term
4. neutral loss
I believe the proteoform nomenclatur could be an easy solution to provide
a sequence with modification information that could be used in a general
calculateMass/Fragments method.
Currently the package is called unimod but we could integrate RESID and
PSI-MOD as well.
I wrote some R code to map the entries onto one table, maybe that
interests you.
Of course, I am really interested.
If you like to discuss/share ideas and contribute code you are very
welcome!
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How is point 1 covered? I created an issue myself 😉 topdownproteomics/ProteoformNomenclatureStandard#21
Would be great. Because now nobody knows whether a |
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Ups. sorry. I was probably a bit too optimistic :-)
You are right, point 1 in not (yet) covered.
We will discuss the issues in a conference call to come and I hope that
there will be answers soon.
2017-07-31 13:34 GMT+02:00 Sebastian Gibb <[email protected]>:
… How point 1 is covered? I created an issue myself 😉
topdownproteomics/ProteoformNomenclatureStandard#21
<topdownproteomics/ProteoformNomenclatureStandard#21>
Does that mean that you want to include sequence, PTMS, ... to describe
the fragments (SEQUE[PTM]N), instead of by series and ion number?
Would be great. Because now nobody knows whether a c3 with sequence ACE
is [Acetyl]AC[Carbamidomethyl]E-[NH(4)] or just ACE.
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The top down consortium recently presented a new nomenclature to describe the (modified) sequences:
https://github.com/topdownproteomics/proteoform-nomenclature-standard
We hope it will become a standard as there is none to date.
It might be worth supporting it in this project
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