ms2rescore
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compomics
Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
Currently, the spectrum file path (and potentially the PSM `run` field) are inferred by the feature generators, if they need the file (i.e., currently only MS²PIP). Considering to make this...
Relevant output: ms2rescore.rescoring_engines.percolator // Percolator output: Exception caught: -num-threads option requires an integer between 1 and 128 ERROR ms2rescore.__main__ // Number of PSMs in original list (52729) does not match...
Currently PSMs are evaluated using psm-level FDR when using mokapot [see here](https://github.com/jonasscheid/ms2rescore/blob/fea1df1ff2bca68988136150da9809b3a32b3b06/ms2rescore/rescoring_engines/mokapot.py#L96) Peptide-level confidence estimates are also [present](https://mokapot.readthedocs.io/en/latest/api/confidence.html#mokapot.confidence.LinearConfidence) in the object mokapot returns. Would be of interest to give the...
Add more descriptive logging if not all modifications are resolvable even after mapping.
Hello @RalfG, First thanks very much for developing such wonderful tool, I really enjoyed working with it! I have a question regarding how to apply MS2rescore to bruker (.d) or...
Dear all, Thank you for creating this nice tool. I have recently tried to re-score some comet results (pin files). However, during the searches I usually set "num_output_lines" to a...
We are trying to run the maxquant example in the development version but get an error when running it without config file or with this one: https://github.com/compomics/ms2rescore/blob/main/examples/maxquant-ms2rescore.toml Is there a...
When I run DeepLCFeatureGenerator with processes=8, it takes a long time, much longer than processes=1. Python correctly starts 8 python.exe multiprocesses, but often the execution just hangs (I've waited more...
