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Hi @mwalzer
For pride resources I have updated this ontology with better cross references to unimod. If you like the idea we can work with that updated file instead of the old one.

Best regards
Yasset

New Term Request: glutaminylated residue

possible new child term (if appropriate): glutaminylated glutamate

reference: PMID:28801462 Jank T, et al. (2017) Protein glutaminylation is a yeast-specific posttranslational modification of elongation factor 1A. J. Biol. Chem. 292(39):16014-16023

from the intro: "Here we describe, for the first time, a novel type of posttranslational modification, the glutaminylation of a glutamate residue, that occurs within the helix A*–loop–helix A􏰂 region of yeast eEF1A. We show that the glutamine residue is attached via its amino group to the side chain carboxyl group of Glu45 within eEF1A."

PSI-MOD has all UniMod, however Unimod is the preferred format. Would anyone have major issues with changing all UniMod's to Unimod?

I found
thiolated residue (MOD:01886)
A protein modification that effectively replaces a hydrogen atom with an sulfanyl or substituted sulfanyl group.

but this is not specific enough.
I see there is a related child
MOD: 00234 L-cysteine glutathione disulfide
to describe glutathione conjugation, so probably

L-cysteine Prdxs disulfide (or L-cysteine thioredoxin peroxidase disulfide) would work?

See
PMID:37572670 (and references therein)
Title | A peroxiredoxin-P38 MAPK scaffold increases MAPK activity by MAP3K-independent mechanisms.

Figure 1 has a nice overview demonstrating Prdxs conjugated to fission yeast Sty1 MAP kinase and human MAPKKK

Seems like the MOD:00234 still has a contains: ... term instead of using relationship: contains ..., such as MOD:01148.
See issue fastobo/fastobo-py#100

Can I just edit the obo file and open a PR, or is there a slightly more complex dev workflow?

Hi,

I can’t seem to find a term for urmylation (GO: “Covalent attachment of the ubiquitin-like protein URM1 to another protein”) and would like to request a new term if possible (or point me in the right direction if I’m missing something?)

Some relevant references:

Furukawa K, et al. (2000) A protein conjugation system in yeast with homology to biosynthetic enzyme reaction of prokaryotes. J Biol Chem 275(11):7462-5
PMID: 10713047

Van der Veen AG, et al. (2011) Role of the ubiquitin-like protein Urm1 as a noncanonical lysine-directed protein modifier. Proc Natl Acad Sci U S A 108(5):1763-70
PMID: 21209336

Looks like the appropriate term would be “urmylation” or perhaps “urmylated lysine.”

Thanks for your help!

Best,
Sage (SGD curator)

All the acetylated side chains carry this note:
"Acetyl" RELATED PSI-MS-label

N-terminal acetylation (MOD:01458), however, lacks this note.

Is this intentional, or is it an omission?

Hello,
could you please add it as child of crosslinked L-lysine residue?

Example refs in:
https://en.wikipedia.org/wiki/ISG15#Intracellular_conjugate:_ISGylation

Sorely missing in our curation work at reactome.org!

Thanks,

There are are large number of orphan terms that only have root in the base that brought them in. UniMod (MOD:00003) and DeltaMass (MOD:00947).

In PSI-MOD 1.029.0, this amounts to

• MOD:00003 (UniMod): 28 orphans
• MOD:00947 (DeltaMass): 60 orphans

My proposal is to deprecate orphan terms that are:

• abiological (e.g. MOD:00508, a UniMod orphan term for gas-phase ions generated in the mass spectrometry process)
• unsupported by literature reference (MOD:00958, a DeltaMass orphan term for a crosslink between Arg and His sidechains with loss of "5"

And to properly fix terms that are incomplete such as:

• DeltaMass orphan MOD:00971 that describes oxohistidine from a properly referenced manuscript
• Unimod Orphan MOD:00576 that described crotonylation... here I will convert to something like "crotonylated residue" on amino acid X. The addition of child terms for each modified residue will come in the future.

Does anyone have strong reasons why I shouldn't do this? I assume that answer will be no, but always good to throw the question out into the ether.

All,

I'd like to propose generating cross-references in PSI-MOD with the the glycan naming ontology, GNO (http://obofoundry.org/ontology/gno.html). Working with Nathan Edwards of the GNO to determine which terms cross-reference.

Paul

I'm working with the OBOFoundry folks to get this updated and will close this ticket as soon as that's done.

we rely on this file and download it regularly into our proteomics tool nuget package mzlib.

https://github.com/smith-chem-wisc/mzLib

https://www.nuget.org/packages/mzLib/

959c9cc

Hey all,

I'm looking for a mapping for Unimod:989 Ammonium. Does such a thing exist in PSI-MOD? My searching led nowhere.

Thanks,
Ryan

Hi All,

A Specific Example:
MOD:00394 is "acetylated residue" with a mass difference of ~42... however, MOD:00648 is for N,O-diacetylated L-serine, which points up MOD:00394 (through MOD:00647, acetylated L-serine) ... the mass difference of MOD:00648 is ~84 (2x42)... All of the other children of MOD:00394 have a Mass difference of 42... should we address this?

More generally, is it understood/accepted that mass difference is transitive through the is_a relationship? If MOD_A is_a MOD_B MUST DiffMassA==DiffMassB? further... if MOD_B is_a MOD_C, MUST DiffMassA==DiffMassC?

@rfellers is working on a mapping project with the new ProForma standard and this question sort of came up while we were trying to hash identical proteoforms...

Thoughts?

Need to address these duplications.

right now, UniProt post-translational modification references (https://bioregistry.io/registry/uniprot.ptm) are written as PTM-XXXX.

This isn't CURIE syntax and doesn't make clear what the resource is that these come from. It would be good to switch them all to CURIE syntax using an appropriate prefix. I will send a PR to demonstrate.

This is needed from Asp-IsoAsp to a generic amino acid for crosslink MOD:00093 is close, but insufficient.

From
https://sourceforge.net/p/psidev/mod-controlled-vocab-changes/72/

Hi,

I was prompted to look for this ticket based on a ticket on the GO tracker.
geneontology/go-ontology#19927 (comment)

Although there are no comments in the original ticket, I found a couple of follow up comments in e-mail, and it seems complicated. However, it is something we would like to be able to capture if possible.

8-5-2018

Hi Valerie,
Sorry for the delay. We will look at the reference reporting the prolyl isomerization of CENP-A on a specific proline residue and will give you our feedback as soon as possible.
Best wishes.
Sylvie.

Hi Valerie,
This isomerization is not straightforward to describe as it does not only involve the proline residue. In fact here we talk about a prolyl isomerization cis-trans that is function of the relative geometry of the amide bond at the nterm of the proline residue and in particular of the carbonyl moiety of the previous residue. The proline itself does not change at all in this isomerization. We would need to model an isomerization of a pair of residues and not of a single residue.
Maybe one should add the term as child of MOD:000664 stereoisomerized residue with source being a double residue including Proline And child of MOD:000915 modified L-proline residue
Will check this

Pierre-Alain

Hello,
in order to be able to curate SARS-Cov-2 the Reactome team is in need of the following PTMs in PSI-MOD. Can you please import them?

• dHex(1)Hex(4)HexNAc(5) --- UNIMOD:1519
• dHex(2)Hex(4)HexNAc(5) --- UNIMOD:1785
• dHex(1)Hex(5)HexNAc(5) --- UNIMOD:1555
• dHex(1)Hex(5)HexNAc(3) --- UNIMOD:1484
• dHex(1)Hex(3)HexNAc(6) --- UNIMOD:1781
• dHex(1)Hex(6)HexNAc(3) --- UNIMOD:1509
• Hex(9)HexNAc(2) --- UNIMOD:1531
• Hex(7)HexNAc(2) --- UNIMOD:1480

These are all children of complex glycosylation MOD:00725

Hello,

I have a question about potentially missing mass values. For example, MOD:00661 seems to have enough "context" to warrant mass values to be populated. Instead, one must look to the first child (MOD:00724) to see mass values assigned. There are many more examples of this: MODs 658-663, 665, 673, 678. I could likely find more if needed. Is there a reason why masses are not assigned at these levels?

Why does this matter to me you might ask? Because Uniprot entry O43676 (and likely others) defined methyl histidine using the ID 'Methylhistidine' which is mapped to MOD:00661 in Uniprot's ptmlist. This means our searching logic cannot assign a proper mass to the PTM without additional logic.

Thoughts? Thanks!

Would everyone be ok if I were to run through the psi-mod CV and put in appropriate links to the amino acids modified? For instance, right now, MOD:01356 is_a MOD:00916 (modified serine), when I would categorize it instead as MOD:01356 is_a MOD:00002 (O-glycosyl serine, which itself is_a MOD:00916). There are many such circumstances in the MOD:01157 (protein modification characterized by amino acid modified) side of the CV that need addressing.

D-amino acids are handled less than optimally. We need to address this better.

Should there be a term under MOD:00850, unnatural residue that houses all D-amino acid residues?

Having D amino acid residues related through is_a to their modified L amino acid counterparts doesn't seem quite right.

New term request received via the old SourceForge site:
https://sourceforge.net/p/psidev/mod-controlled-vocab-changes/73/

Hello,

I would like to annotate the protein modification reported here:
PMID:28801462
"Protein glutaminylation is a yeast-specific posttranslational modification of elongation factor 1A."

but I can't locate anything relevent searching on "glutamin...."

Does it exist as another name, or does it need to be added

Not sure how to define, but it seems to be the attachment of a specific glutamine residue in a glutamate in ef1A

Thanks,

Val

PSI-MOD.obo.xml update after #4 missing

Throughout PSI-MOD, when a heavy labelled atom is added in place of a "regular" atom, it's listed as

(12)C -X (13)C X , where X is the number of atoms being replaced.

Technically this is wrong, it should be

C -X (13)C X , where X is the number of atoms being replaced.

The issue is that the atom being replaced isn't "pure carbon 12" (100% 12C), but rather "natural carbon" (98.9%12C, 1.1%13C) This won't have any effect on the DiffMono's, but will on the DiffAvg's and thus should be done... thoughts?

Hi, we have a few term requests that are not exactly protein modifications, but we use them in our data in a similar way that we use PSI-MOD terms, so we are hoping that you can help us with them. If the are not appropriate for PSI-MOD, we hope you can suggest a different home for them. They are:
D-aminoacid
Stereoisomer
I/L uncertainty (when eluted peptide are sequenced, this is a common issue)
Unidentified amino acid (when eluted peptide are sequenced, this is a common issue)
artificial modification/molecular tag - is this already a concept in PSI-MOD? Iodo-4-azidosalicylic acid (IASA) is an example that we have.
Please let me know which, if any are within your scope and I can work towards definitions, etc.
thanks, Randi

PSI-MOD indicates that this modification is 'hypothetical'. However, many of the cited references--including RESID:AA0307--indicate that this is a natural residue. Can you verify and, potentially, update?

Having systematic names in PSI-MOD would be nice, where available. Right now, the systematic names are "EXACT RESID-systematic" but with no new RESID names, there's no way to add new ones... should these be categorized as "EXACT PSI-MOD-systematic"?

Hi!

There's no term for N-methylated valine residues currently; this would be useful to describe some peptides such as omphalotin A, which contains MeVal residues:

(from Thern B, Rudolph J, Jung G. Total synthesis of the nematicidal cyclododecapeptide omphalotin A by using racemization-free triphosgene-mediated couplings in the solid phase. Angew Chem Int Ed Engl. 2002 Jul 2;41(13):2307-9. doi: 10.1002/1521-3773(20020703)41:13<2307::AID-ANIE2307>3.0.CO;2-Y. PMID: 12203574.)

Add a mod that represents the average of all 4 Itraq4PLEX reporter+balance mods; it is a representing average iTRAQ4plex reporter+balance for all iTRAQ at a resolution of below 0.1Da

Term]
id: MOD:nnnnnnnn
name: iTRAQ4plex reporter+balance reagent acylated residue, average mass modification
def: "A protein modification that effectively replaces a hydrogen atom of a residue with one of the Applied Biosystems iTRAQ4plex reagent reporter+balance groups." [Unimod:214]
comment: The reagent consists of a reporter group, a balance group and a protein reactive N-oxysuccinimide group. The reporter group, an isotopically labeled 1,4-dimethylpiperazine, is connected to a carbonyl balance group that is isotopically labeled to produce a nominally isobaric combined modification. Four versions of chemically identical iTRAQ4plex moyeties, but with different isotope distribution. This modification is calculated as the average of the four species. It has no isotopic distribution reality, the exact mass does not correspond to any real isotopic distribution.
subset: PSI-MOD-slim
synonym: "(4-methylpiperazin-1-yl)acetyl" EXACT PSI-MOD-alternate []
synonym: "iTRAQ" RELATED Unimod-interim []
xref: DiffAvg: "144.10"
xref: DiffFormula: "none"
xref: DiffMono: "144.102411"
xref: Formula: "none"
xref: MassAvg: "none"
xref: MassMono: "none"
xref: Origin: "X"
xref: Source: "artifact"
xref: TermSpec: "none"
is_a: MOD:01426 ! isotope tagged reagent derivatized residue
is_a: MOD:01705 ! isotope tagged reagent acylated residue
is_a: MOD:01709 ! iTRAQ4plex reporter+balance reagent N-acylated residue
is_a: MOD:01513 ! modifications with monoisotopic mass differences that are nominally equal at a resolution below 0.1 Da

MOD:01080,
xref: Source: "artifact

missing " at end of line

Hi,

It is very minor suggestion, but would it make sense to append the postfix -CV to the repo to be consistent with other ontologies (e.g psi-ms-CV and psi-mi-CV) if it is going to host psi-mod.obo? On the other hand I can see it is fork and I don't know if it is possible.

Regards,

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

The definitions:

MOD:00647 "monoacetylated L-serine" - A protein modification that effectively converts an L-serine residue to either N-acetyl-L-serine, O-acetyl-L-serine, or N,O-diacetyl-L-serine.
MOD:02080 "diacetylated-L-serine" -   A protein modification that effectively converts an L-serine residue to either N-acetyl-L-serine, O-acetyl-L-serine, or N,O-diacetyl-L-serine.

The definitions are identical, and written as if intended to be a more general 'acetylated L-serine' term (which itself would be useful).

N-phosphorylated residue MOD:01456 and O-phosphorylated residue MOD:01455 have both been given the Short label curated by PSI-MOD
OPhosRes

Please could that of MOD:01456 be changed to NPhosRes with some urgency as the wrong term is being used by IMEx as a result.

synonym: ubiquitinated cysteine

this paper notes ubiquitination on a cysteine residue in yeast Pso2p: https://onlinelibrary.wiley.com/doi/epdf/10.1111/mmi.15145

quick browse of the web shows that ubiquitination of cysteine residues has become recognized and known to occur since late 2010's.

In the midst of working with one of our collaborators, we ran into the need to annotate an “S-CysGly” modification (monoisotopic +176.026). My search of RESID, PSI-MOD, and Unimod turned up nothing. Paul Thomas then informed us that it is a breakdown product of S-glutathione (AA0229) and you can see evidence of its existence in manuscript form here: http://www.sciencedirect.com/science/article/pii/S1046202311002520 (Table 1). Would you be willing to add this mod?

Hi!

I suppose this is caused by OBO-edit, but the current way of declaring the properties for modified residues using Xrefs is not giving a very useful translation in OWL2, because the resulting property value ends as an rdf:label.

The proper way to add annotations would be to use property-value clauses, also allowing for the datatype to be specified:

[Term]
id: MOD:00007
name: selenium substitution for sulfur
property_value: DiffAvg "46.91" xsd:float

which will have ROBOT translate the result in a correct OWL2 annotation, considering DiffAvg as an annotation property (it would be even better to use OWL2 data properties instead but there is no way to do that from an OBO document... yet).

It would be helpful to review old tickets here:
https://sourceforge.net/p/psidev/mod-controlled-vocab-changes/

and take care of if still relevant or close if not.

Glycosylation of collagens is a common PTM. Right now, many of the glyco modifications of hydroxylated amino acids have the naked amino acid as the origin, when this should be the hydroxylated amino acid.

Is this correct? My question is: For a MOD:01914 is it changing from lysine to galactosyl-hydroxy-lysine in a single step OR is the modification hydroxy-lysine being galactosylated to galactosyl-hydroxy-lysine?