Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Added some more advanced examples #5

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Added some more advanced examples #5

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 9 additions & 2 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,9 @@ This format specification represents the consensus for the standard representati
## Use cases supported (with examples)
The ProForma notation is a string of characters that represent linearly one or more peptidoform/proteoform primary structures with possibilities to link peptidic chains together. It is not meant to represent secondary or tertiary structures.

##### Canonical [IUPAC amino acids](http://publications.iupac.org/pac/1984/pdf/5605x0595.pdf)
##### Canonical [IUPAC amino acids](http://publications.iupac.org/pac/1984/pdf/5605x0595.pdf) and [ambiguous/unusual amino acids](https://www.insdc.org/submitting-standards/feature-table/#7.4.3)
* `EMEVEESPEK`
* `VAEJNPSNGGTT` (J indicates either I or L)
##### PTMs using common ontologies or controlled vocabularies (e.g. [Unimod](http://www.unimod.org/), [PSI-MOD](https://www.ebi.ac.uk/ols/ontologies/mod), and [RESID](https://proteininformationresource.org/resid/))
* `EM[Oxidation]EVEES[UNIMOD:21]PEK`
* `EM[L-methionine sulfoxide]EVEES[MOD:00046]PEK`
Expand Down Expand Up @@ -38,4 +39,10 @@ The ProForma notation is a string of characters that represent linearly one or m
* `<[S-carboxamidomethyl-L-cysteine]@C>ATPEILTCNSIGCLK`
##### Additional user-supplied information and multi-valued tags
* `ELV[info:AnyString]IS`
* `ELV[+11.9784|info:suspected frobinylation]IS`
* `ELV[+11.9784|info:suspected frobinylation]IS`
##### Defined charges, or charge cariers (ProForma extension see section 7.1)
* `VAEINPSNGGTT/2`
* `VAEINPSNGGTT/2[1Na+,1H+]`
##### Chimeric spectra (ProForma extension see section 7.2)
* `VAEINPSNGGTT+FNEKFKGGKATJ`
* `[iTRAQ4plex]-EMEVNESPEK-[Methyl]+[Phospho]?EMEVTSESPEK`