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Hi there,
I'm working with a DIA dataset that was analyzed with DIA-NN and the IQ package. As someone who is not very familiar with this package yet and has little programming experience I am wonde…
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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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Hi, I'm processing a peptidomics data set and was wondering if, when I select 'normalise data', does it normalise only the protein intensities or the peptide intensities too? Does it do it for each bi…
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I would like to make group fdr control different from Fragpipe to PSM level 1% and 5%. I can't find a way to proceed with FDR control at a different rate, so I would appreciate it if you could tell …
JWJW1 updated
3 hours ago
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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,
There is something fishy with the cpu cores allocation, we have noticed that if we process with absolutely the same parameters a number of 6 sciex wiff swath files, it allocates 64 cores.…
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Primary: milestone biorxiv
- enable loading peptide data
- implement peptide coverage and overlap analysis
- analyze intra-protein scatter of peptide profiles
Secondary:
- analyze intra-protein…
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I would like to compare kmers from two nucleotide sequence fasta files but at the amino acid level, whereby DNA sequence --> peptide sequence --> kmer comparison at aa level --> extract non-unique kme…
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Hello,
I am using the latest version (3.07.01) of Percolator and trying to run the RESET algorithm using the following command:
percolator -Y --reset-algorithm --num-threads 32 --subset-max-train …
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Hi,
The FDP calculation at the precursor level for from a proteogenomic search consisting >400,000 peptide precursor is resulting with only zero values. I am not able to figure out the issue here. …