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Hi
We ran DIA_spec_diaPASEF workflow and DIA NN output protein group files does not have protein name. However, if i run DIA NN without using FragP
[PG_output.xlsx](https://github.com/user-attachme…
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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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Dear TIES developers,
I would like to setup some FEP simulations for a protein-peptide system where I mutate a residue of the peptide. This seems similar to TIES-PM (https://doi.org/10.1021/acs.jct…
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Where is the instructions to make these datasets?
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At PSI 2013 some preliminary work was done on supporting crosslinking in
mzIdentML. A sketch of one possible solution is as follows:
RVDKSGLHCPLLPDDR
NGVTL…
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In the X!Tandem adapter (2.3) I chose the modification 'Acetyl (N-term)' as a fixed modification to identify peptides with acetylated N-termini (introduced as a chemical modification). The adapter g…
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Dear Vadim,
I am currently looking into how to work with the report.parquet file generated by DIANN, specifically at this point I want to aggregate (or rather filter) the output to the protein leve…
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From one of our astute users...
> I believe I understand why MetaMorpheus incorrectly assigned 50% of the HydroxyLeu and HydroxyIle spectra (about 100 each in the HeLa proteome).
>
> If you reme…
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Since #6 needs an update to the specification from my side I would like some things to be specified a bit clearer in text in the specification. For these there does not have to be any changes in the f…
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Hello, have the designed peptides been synthesized and subsequently verified through wet lab experiments? What were the results?