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Hi & thanks for your reply,
I am trying to use pyopenms 3.1.0 to store spectrum (read from .mzml file) and its corresponding peptide identification (identified by other software or manually validatio…
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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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Dear developers,
I am encountering an issue with peptide-shaker, which I paste here:
# ------------------------------------------------------------------
# PeptideShaker 2.2.25 Report File
#
…
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### PXD001819 Analysis
Currently, we have a workflow that can perform peptide identification using: `-> ms2rescore -> SNR + spectrum properties -> percolator`
Here the results can be found (http…
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I am encountering an issue with software v.1.0.2. It reports that 25 identified peptides were assigned to a protein, 4 of which are unique. I expected to see which peptides are shared and which are un…
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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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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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Expanding the metaproteomics workflow
There are two limitations of the current metaproteomics workflow that limit its utility for the community,
(i) peptide sequence identification currently requires …
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Hi,
First of all, thank you for such wonderful tool. I'm working with proteins translated from new ORFs and I predicted that the new protein interact with another protein, say for e.g. protein X. N…
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Hi, thanks for creating this tool. But recently when I use pepquery2 in web application and stand alone version, there was error about the mgf file in s3 bucket is not exist. I attached the screenshot…