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I noted something strange today after I was asked by a colleague to add a number of peptides column to her DiaNN pg matrix. I loaded the report.tsv in R, aggregated protein groups by modified sequence…
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Hi, I did a test run using the Escherichia coli Nissle 1917 complete genome (NCBI ACCESSION: CP058217). I expected the microcin cluster can be identified since MIBiG has the BGC0000589: microcin M bio…
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"task loading from C:\Users\Administrator\.PepPre\v1.3\PepPreIsolated.task
task loading from C:\Users\Administrator\.PepPre\v1.3\PepPreGlobal.task
task loading from C:\Users\Administrator\.PepPre\v1…
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Provide trainings with details about the algorithms of the main analysis to help user really understand what is happening .
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Dear FragPipe team,
I run FragPipe with the 'trypsin' setting in MSFragger, Cut 1 'KR' No Cut 1 'P', but I still saw some peptides from the resulted psm.tsv and peptide.tsv that are started with Pr…
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Add a "decoy" flag here:
https://github.com/OpenMS/OpenMS/blob/develop/src/openms/source/FORMAT/MascotGenericFile.cpp#L85
and then probably here check if it is set:
https://github.com/OpenMS/…
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Hi OpenMS team,
Congratulations for this great work!
I'm having difficulty with direct injection data processing.
My goal is to process a single .mzML file and obtain the corresponding MGF. Howev…
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Reported by Jean-Michel Camadro and Laurent Lignières. In their test run, only about a third of the identified peptides could be quantified using FeatureFinderIdentification (FFId). In addition, the s…
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When I set `PercDetectability` to 1, no peptide should be removed at this stage. Here, it seems that one peptide is removed.
Something similar happens at the FDR step (in the example pasted below). I…
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Hi, I'm looking to predict genes for my insect genome. For most genes the prediction is working out good, but egapx is missing predictions for some species specific, single exon genes (experiementally…