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Hi,
I'm using FragPipe v22.0 to perform Open Search on a dataset, and I have seen that there is an option in the “Validation” module, specifically in “PSM Validation”, called “single combined pepxm…
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Add a search to retreive all signal peptides. None urgent
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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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Hello everyone,
I am using DIA-NN to analyze ultralow sample data acquired with diaPASEF and VistaScan modes from timsTOF Ultra 2.
Multiple peptides of interest fall outside of the fragmentation win…
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DeepPeptide predicts cleavage peptides from amino acid sequences. It reports both peptides and propeptides. For propeptides, it uses the [uniprot definition](https://www.uniprot.org/help/propep): "a p…
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Imagine a case where one peptide should have multiple small distal motifs. Need to intersect which peptides contain all of the queries.
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Systematic ID | Gene name | Product description
-- | -- | --
SPBC56F2.09c | arg5 | arginine specific carbamoyl-phosphate synthase subunit Arg5
SPAC25G10.02 | cce1 | cruciform-cutting endonuclease…
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Make `assign_peptide_type()` recognise if the initial methionine of a protein is missing in all peptides and assign "fully-tryptic" instead of "semi-tryptic".
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**- Upload your log file**
(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the…
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Hi, I want to build a protein-ligand system where the ligand has more than 150 atoms.
Here is my script:
```
def read protein(protein_file):
protein = pdbfile.PDBFile(protein_file)
retu…