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Hi,
I'm using pyPept to build simple peptide macrocycles. I'm finding the BILN notation extremely useful for this and the pyPept interface is very straightforward to use.
Unfortunately, there se…
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Dear Vadim,
I analysed thermo raw files with DIA-NN 1.8.1 and 1.9. I matched the generated pg_matrix and pr_matrix to find the number of proteotypic peptides for each reported protein in the pg_matri…
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How to predict the structure of cyclic peptides (amide bonds forming a ring)
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Dear philosopher team,
After i ran a LFQ-MBR workflow using fragpipe, and inspected the result: i found a wierd row in the protein.tsv:sp|P27870|VAV_MOUSE P27870 VAV_MOUSE Vav1 845 …
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Hi Vadim.
I analyzed the DIA data acquired by Q-Exactive using DIA-NN, but the output report did not assign any proteins or peptides.
What could be the cause of this?
The measured samples were BS…
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Hello, I found a weird interaction between the scater package and scp.
When using both packages in a script I got the following error:
```
Error in .FUN(object[[from]], ...) : '.FUN' is defunct…
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Hi,
How would one process DIA data in DIA-NN from a digested lysate spiked with Heavy Lys and Arg 13C and 15N labeled protein standards?
Thanks,
Stoyan
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Hi, I did phospho analysis in Fragpipe-DIA-NN.
I see one strange thing in output file. I see that for …
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I was wondering whether it would be possible to use this tool to predict toxicity of peptides that contain unnatural amino acids.
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