Closed pmt706 closed 3 years ago
pmt706
commented
3 years ago 
ricardblum
commented
3 years ago I agree with Pierre-Alain's comment on the galactosylation of hydroxylysine residues.
pabinz
commented
3 years ago 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 notifications@github.com Envoyé : mercredi 3 mars 2021 20:17 À : HUPO-PSI/psi-mod-CV psi-mod-CV@noreply.github.com Cc : Subscribed subscribed@noreply.github.com 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:
https://github.com/HUPO-PSI/psi-mod-CV/pull/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.obohttps://github.com/HUPO-PSI/psi-mod-CV/pull/56/files#diff-c1678a487582c803bdbf4c4f0c65f24f8bd8607a9b39359ea98c84752a7b0e3c (193) · M PSI-MOD.owlhttps://github.com/HUPO-PSI/psi-mod-CV/pull/56/files#diff-f0e1f9fbaf4dc2ce4d642c22207bd8c5d9bc1292465bbcdb2e381a9e1ef28e65 (988) · M README.mdhttps://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
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pmt706
commented
3 years ago Thanks! I got these and will process through them as my workload lightens.
From: pabinz notifications@github.com Sent: Thursday, March 4, 2021 7:24 AM To: HUPO-PSI/psi-mod-CV psi-mod-CV@noreply.github.com Cc: Paul Martin Thomas paul-thomas@northwestern.edu; Author author@noreply.github.com 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 notifications@github.com<mailto:notifications@github.com> Envoyé : mercredi 3 mars 2021 20:17 À : HUPO-PSI/psi-mod-CV psi-mod-CV@noreply.github.com<mailto:psi-mod-CV@noreply.github.com> Cc : Subscribed subscribed@noreply.github.com<mailto:subscribed@noreply.github.com> 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:
https://github.com/HUPO-PSI/psi-mod-CV/pull/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.obohttps://github.com/HUPO-PSI/psi-mod-CV/pull/56/files#diff-c1678a487582c803bdbf4c4f0c65f24f8bd8607a9b39359ea98c84752a7b0e3c (193) · M PSI-MOD.owlhttps://github.com/HUPO-PSI/psi-mod-CV/pull/56/files#diff-f0e1f9fbaf4dc2ce4d642c22207bd8c5d9bc1292465bbcdb2e381a9e1ef28e65 (988) · M README.mdhttps://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
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pmt706
commented
3 years ago @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.