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selenocysteine and pyrrolysine not supported in calculateFragments #21

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guideflandre opened this issue Feb 27, 2025 · 2 comments
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@guideflandre
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The 21st and 22nd amino acids selenocysteine (U) and pyrrolysine (O) are not supported in PSMatch. NA's are thus introduced in generated theoretical fragments.

This is a small issue that rarely occurs, but it happened to me and I thought it might be interesting to add their masses/characteristics into calculateFragments / getAminoAcids.

@lgatto
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lgatto commented Feb 28, 2025

I don't think that adding two rows to the getAminoAcids() data.frame would have a detrimental impact on anything, so even if the gain of adding U and O is minimal, there's no real disadvantage.

@sgibb - what do you think? If you are OK, I suggest that @guideflandre sends a PR with the two extra lines/aa.

@sgibb
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sgibb commented Feb 28, 2025

Should be fine. Let's add them.

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