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SequenceWindow, Ile over-representation on the n-term side #500
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It just uses the sequence of the assigned protein in the fasta file. Best, Fengchao |
Since it was very strange, I checked the sequences manually, this is what I see <style> </style>
The first one is correct, the others are not. |
The second one is also correct because there is a peptide Best, Fengchao |
Indeed, `ALKLQLDNQY` would be right, but FragPipe reports `AIKIQLDNQY`. To
me it seems that all `L` are converted to `I` in the fasta file used to
create the SequenceWindow.
Case closed :)
…On Thu, Jul 18, 2024, 21:59 Fengchao ***@***.***> wrote:
The second one is also correct because there is a peptide ALKLQLDNQY in
the protein. We don't distinguish I and L when mapping peptides to
proteins because they have the identical mass.
Best,
Fengchao
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Yes, this is a known bug: #430 |
Hi,
I was inspecting the files generated in the tmt-report folder. I noticed a suspicious over-representation of Ile in the SequenceWindow on the n-term side, i.e. before the detected peptide sequence.
Can you comment on how that is
calculated
?It might be real, but I was expecting a Leu to be over-represented...
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