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A biologist wrote to me:

... C- or N-terminus,... For example, a C-terminal tryptic peptide like AGWRGSDSHSR, would be...

I don't have any idea what that is. When I google the term ("C-terminal tryptic peptide"), nothing obvious came up. What's that? Why AGWEGSDSHSR is a "C-terminal tryptic peptide"?

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    $\begingroup$ Did a biologist really write this to you? Seems strange as it's clearly not your field. But really how do you expect a decent answer unless you give us the full text and context of what appears to me as a quite bizarre communication. $\endgroup$
    – David
    Apr 12, 2018 at 18:52

2 Answers 2

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Its quite simple if you look at the basics! Lets have a look at the sequence you give:

AGWRGSDSHSR

Write that in 3-letter terms1:

Ala-Gly-Trp-Arg-Gly-Ser-Asp-Ser-His-Ser-Arg

Pay attention to the C-terminus. The last amino acid residue in the sequence is Arginine. Now, its well established that Trypsin cleaves a polypeptide after (i.e. towards the C-terminal side of) Lysine and Arginine2.

Thus, C-terminal tryptic peptide is the peptide that remains after a polypeptide has been treated with Trypsin.

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  • $\begingroup$ Its just about getting the clues @smallchess $\endgroup$ Apr 12, 2018 at 11:08
  • $\begingroup$ Ah, so it refers to where the peptide was cleaved, not where the peptide was located on the original protein. Unintuitive for me :) $\endgroup$
    – Armatus
    Apr 12, 2018 at 11:10
  • $\begingroup$ @armatus haha I've been working on peptide sequencing for a while now, so I got the point there ;) $\endgroup$ Apr 12, 2018 at 11:12
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    $\begingroup$ Trypsin does not cleave at the "carboxy-terminus" of any amino acid, as that term is used to designate one end of a protein (that with a free alpha-COOH). I also do not believe "C-terminal lysis by trypsin" means anything, or if it did it would mean the removal of the C-terminal amino acid, which is here not the case. Your answer does not represent usage and is clearly wrong. $\endgroup$
    – David
    Apr 12, 2018 at 18:47
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    $\begingroup$ Downvotes are free that is why instead of giving input to improve the answer people go around anon downvoting. $\endgroup$
    – Roni Saiba
    Apr 13, 2018 at 6:32
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Unless your corespondent is off their rocker (or I am), this is rather unambiguously referring to the peptide released from the C-terminal end of a polypeptide by tryptic digestion.

This means that the final arginine in your sequence would have been the C-terminus of the original polypeptide, not the trypsin cleavage site. It also means that your sequence was preceded by R or K.

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  • $\begingroup$ Quite, which is why it looks like some sort of homework question, with the R in the sequence as red herring. $\endgroup$
    – David
    Apr 13, 2018 at 5:34

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