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Hello,
we have generated an HLA-peptides library using PeptDeep-HLA for the prediction of peptides and alphapeptdeep for library generation and conversion to .tsv for compatibility with DIANN. Then…
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(If a log
[log_2024-06-28_09-55-41.txt](https://github.com/user-attachments/files/16030806/log_2024-06-28_09-55-41.txt)
file hasn't been generated, go to the 'Run' tab i…
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In recent data, we encountered a problem with peptides, that are so stable they do not undergo exchange in both states. For our own use, we call them "płaszczaki". The issue is that the maximal exchan…
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Hello, I'm having a lot of difficulty understanding how to map pepquery output to TMT tag of GTEx so that I can correctly map peptide to sample_ID.
I know this issue was opened before, but I do not…
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Hi,
We are performing glycopeptide identification and quantification across many samples. The data in the "assigned modifications" column of the "combined_modified_peptide.tsv" file gives only the …
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Hey Michael,
For a current project we are working on, we are trying to use Sage with HLA peptides, specifically from the [thunderPASEF method](https://www.nature.com/articles/s41467-024-46380-y). W…
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Hi Vadim
Thanks for your work in DiaNN. I find that in the main out, the largest number of fragments used in quantification is 12. I mean the number of values showed in 'Fragment.Quant.Raw' colum…
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Hi,
I have discovered a bug with Philosopher.
Console Information:
INFO[21:32:23] Executing Filter v5.1.0
INFO[21:32:23] Processing peptide identification files
INFO[2…
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Hi
Thanks for your work in DiaNN. I'm currently using the latest version of DIANN to process phosphoproteomics data, and I have obtained wonderful results. Which include tables of phosphorylation sit…
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- [x] Number of Peptides identified: Total number of peptide Sequences identified.
- [x] Number of PeptidoForms: Number of Peptides + modifications + position of the modification.
- [x] Number of …