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- [x] Write simple input that takes tsv or csv file with: peptidoform, spectrum_id, precursor_mz and write to Peptidoforms
- [ ] Write a function that takes a peptidoform removes modifications and ge…
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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 sta…
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![image](https://user-images.githubusercontent.com/16883585/119867399-db411680-beeb-11eb-925c-da19c179fbf2.png)
I made a file that contained 8 PrSMs at each of the proteoform ambiguity classificati…
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Re-do hierarchy, and find example where a canonical has glycoproteoforms AND proteoforms not involving glycans.
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Files containing sequences that are annotated according to the nomenclature:
_Suggestions_:
Extension: .ptm.fasta or just .proteoforms
Format name: Proteoform format, PTM format
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wondering about reading/writing multiple proteoforms. Does a proteoform have to be completely on a single line? if not, is there a line length (like fasta). Does each proteoform have to start with a s…
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These may come from kelleher's database of already identified proteoforms. We could search against these in ET and/or use them to support other identifications.
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PR should *only* be used in col2 in the GAF
```
curl -L -s "http://current.geneontology.org/annotations/mgi.gaf.gz" | gzip -dc | grep ^PR | wc
2139 51464 494819
```
Examples:
```
P…
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In MS proteomics sometimes iodoacetamide is used to break the disulfide bonds. This yield to iodoacetylated cysteine residues ([Unimod:4](http://www.unimod.org/modifications_view.php?editid1=4)).
C…
sgibb updated
6 years ago