Feb 2021 Error Fixes and New Mods

[pmt706]

• Fixed several errors found in PSI-MOD.
• Using a list from Emanuele Alpi, I'm systematically adding in curated PTMs tied to known protein modifications in UniProtKB
• Updated the readme.md to fix a couple of typos and add in procedures for editing PSI-MOD.
• Created a valid OWL to accompany the update OBO

[edeutsch]

Awesome, many thanks!

[pabinz]

galactosylation (and in general glycosylation) of hydroxylysine is a mod that occurs post translationally to a hydroxylysine in collagene. The is_a tag should somehow remain, as the modified residue is here a hydroxylysine (similarly to is_a =-glycosilated residue). As far as I know, a residue is not exclusively limited to the 20 classical AAs in PSI-MOD (at least not formally)

[pabinz]

Please maka a precision that the obo file is the master source, and that the OWL is a derivative of it.

[ricardblum]

I agree with Pierre-Alain's comment on the galactosylation of hydroxylysine residues.

[pabinz]

This mod is not a crosslink, therefore please adapt the definition : replace by.
A protein modification that effectively modifies an L-serine residue with 5'-phosphouridine through a phosphodiester bond ...

[pabinz]

previous comment valid for both MODs

[pabinz]

Again, its a modification of and not a crosslink. Please change the def accordingly:
A protein modification that effectively modifies an L-serine residue with 5'-phosphoadenosine through a phosphodiester bond

[pabinz]

This PTM is obtained by a mod by itaconate. Might be interesting to mention this in the def:
A protein modification that effectively converts an L-cysteine residue to form S-methylbutanedioic acid-L-cysteine through by alkylation with itaconate through a thioether bond." [PubMed:29590092]

[pabinz]

Isn't the mod
DiffFormula: "C 4 H 6 N 0 O 2" (and not H7?)

Maybe PTMlist is also wrong...

[pabinz]

Remove:
is_a: MOD:00203 ! D-asparagine

You can create a mod for modified D-asparagine residue, which is related to D-asparagine (and parent of this mod and the current child crosslinked D-asparagine residue entry)

In this case one can also create all D-residues as unnatural forms (to be discussed)

[pabinz]

Can you doublecheck the following block:
xref: Formula: "C 24 H 40 N 1 O 2 S 1"
xref: MassAvg: "406.65"
xref: MassMono: "406.277976"

to me it seems that there is one O too much. Compared to MOD_00113 (S-geranylgeranyl-L-cysteine) there should be only a H to CH3 change ; the methyl ester comes from the fact that it is a methylation of a carboxyl group, therefore yieldig a methyl ester moiety.
The formula should be
xref: Formula: "C 24 H 40 N 1 O 21 S 1".
The trick is that for all peptides/protein, one should add H2O to all ftotal formulae in order to get the final product in a neutral form. Here the C-term is only replacing a H for a CH3, no O involved...

[pabinz]

sorry, revert my previous comment: When C-term is specified, the +H2O rule should not apply and is to be replaced by +H (N-term) and consider the Formula, MassAvg and MassMono as replacing the C-term default OH by NULL and consider only the Formula, MassAvg and MassMono as being the summ of the modified residue + the Cterm moiety.

However, this property and behavior should be specified in the beginning of the file.

[pabinz]

Hi Paul, I have responded for each individual modification. I hope they are readable and correctly attributed to each commit proposal. Let me know if that is not the case PAB De : Paul Thomas <[email protected]> Envoyé : mercredi 3 mars 2021 20:17 À : HUPO-PSI/psi-mod-CV <[email protected]> Cc : Subscribed <[email protected]> Objet : [HUPO-PSI/psi-mod-CV] Feb 2021 Error Fixes and New Mods (#56) · Fixed several errors found in PSI-MOD. · Using a list from Emanuele Alpi, I'm systematically adding in curated PTMs tied to known protein modifications in UniProtKB · Updated the readme.md to fix a couple of typos and add in procedures for editing PSI-MOD. · Created a valid OWL to accompany the update OBO

…

________________________________ You can view, comment on, or merge this pull request online at: #56 Commit Summary · Updates MOD:01914 · Cleanup of README and Adding in OWL Format · Adding in two new mods from UniProt (PubMed 22504181) · Adding in AMP-Serine · Adding in S-methylbutanedioic acid-L-cysteine · Adding HIB Lysine · Adding in betahydroxybutyryl lysine · Adding in Glutaryl Lysine · Updating Carbamoyl Lysine · Adding methyl-d-asparagine · Fix MOD:00241 · Updating Date/Time/Version and adding in Geranylgeranyl L cysteine methyl ester File Changes · M PSI-MOD.obo<https://github.com/HUPO-PSI/psi-mod-CV/pull/56/files#diff-c1678a487582c803bdbf4c4f0c65f24f8bd8607a9b39359ea98c84752a7b0e3c> (193) · M PSI-MOD.owl<https://github.com/HUPO-PSI/psi-mod-CV/pull/56/files#diff-f0e1f9fbaf4dc2ce4d642c22207bd8c5d9bc1292465bbcdb2e381a9e1ef28e65> (988) · M README.md<https://github.com/HUPO-PSI/psi-mod-CV/pull/56/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5> (11) Patch Links: · https://github.com/HUPO-PSI/psi-mod-CV/pull/56.patch · https://github.com/HUPO-PSI/psi-mod-CV/pull/56.diff — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#56>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AESGSRUQHKBW4YO3Y2EIULTTB2DLZANCNFSM4YR2FQVQ>.

[pmt706]

Thanks! I got these and will process through them as my workload lightens. From: pabinz <[email protected]> Sent: Thursday, March 4, 2021 7:24 AM To: HUPO-PSI/psi-mod-CV <[email protected]> Cc: Paul Martin Thomas <[email protected]>; Author <[email protected]> Subject: Re: [HUPO-PSI/psi-mod-CV] Feb 2021 Error Fixes and New Mods (#56) Hi Paul, I have responded for each individual modification. I hope they are readable and correctly attributed to each commit proposal. Let me know if that is not the case PAB De : Paul Thomas <[email protected]<mailto:[email protected]>> Envoyé : mercredi 3 mars 2021 20:17 À : HUPO-PSI/psi-mod-CV <[email protected]<mailto:[email protected]>> Cc : Subscribed <[email protected]<mailto:[email protected]>> Objet : [HUPO-PSI/psi-mod-CV] Feb 2021 Error Fixes and New Mods (#56) · Fixed several errors found in PSI-MOD. · Using a list from Emanuele Alpi, I'm systematically adding in curated PTMs tied to known protein modifications in UniProtKB · Updated the readme.md to fix a couple of typos and add in procedures for editing PSI-MOD. · Created a valid OWL to accompany the update OBO

…

________________________________ You can view, comment on, or merge this pull request online at: #56 Commit Summary · Updates MOD:01914 · Cleanup of README and Adding in OWL Format · Adding in two new mods from UniProt (PubMed 22504181) · Adding in AMP-Serine · Adding in S-methylbutanedioic acid-L-cysteine · Adding HIB Lysine · Adding in betahydroxybutyryl lysine · Adding in Glutaryl Lysine · Updating Carbamoyl Lysine · Adding methyl-d-asparagine · Fix MOD:00241 · Updating Date/Time/Version and adding in Geranylgeranyl L cysteine methyl ester File Changes · M PSI-MOD.obo<https://github.com/HUPO-PSI/psi-mod-CV/pull/56/files#diff-c1678a487582c803bdbf4c4f0c65f24f8bd8607a9b39359ea98c84752a7b0e3c> (193) · M PSI-MOD.owl<https://github.com/HUPO-PSI/psi-mod-CV/pull/56/files#diff-f0e1f9fbaf4dc2ce4d642c22207bd8c5d9bc1292465bbcdb2e381a9e1ef28e65> (988) · M README.md<https://github.com/HUPO-PSI/psi-mod-CV/pull/56/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5> (11) Patch Links: · https://github.com/HUPO-PSI/psi-mod-CV/pull/56.patch · https://github.com/HUPO-PSI/psi-mod-CV/pull/56.diff — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#56>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AESGSRUQHKBW4YO3Y2EIULTTB2DLZANCNFSM4YR2FQVQ>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/HUPO-PSI/psi-mod-CV/pull/56*issuecomment-790615067__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!Fi_xaCOpdsY89ssP40Vww-i6nz3-vLm2qqP0qEyhJT9zHy-J8hKVEnrErtk71A7QFJKkU19Stg$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/ABMODCQPXGHCWOCQTAOQCBTTB6CXPANCNFSM4YR2FQVQ__;!!Dq0X2DkFhyF93HkjWTBQKhk!Fi_xaCOpdsY89ssP40Vww-i6nz3-vLm2qqP0qEyhJT9zHy-J8hKVEnrErtk71A7QFJJDw_DD1A$>.

per his request in the next comment!

[pmt706]

@pabinz, @ricardblum For MOD:01914, the issue that removed the is_a for monogalactosylated residue is the difference in mass between this mod, MOD:01914 at ~178 Da and MOD:00476 at 162 Da (differing by the oxygen that makes it hydroxylysine). This isn't allowed. If modA has a diffmass of "X" AND if modA is_a: modB, then it follows that modB's diffmass MUST also be "X".

Since it's known that the modification is to hydroxylysine and not to lysine, I'm going to change the origin on MOD:01914 from K to MOD:00037 (5-hydroxy-L-lysine). This will change the diffMass to 162 and fulfill the obligation above.

[pabinz]

OK, thx

[pabinz]

ok, thx

[pabinz]

ok thx