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In the current Tide output format, terminal PTMs cannot be distinguished from side chain PTMs. I think we should represent them using a hyphen, so a modification of XXX on the first amino acid of PEP…
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IDFileConverter fails reading mzid if the location attribute isn't present for Modification elements. I think the key lines are:
https://github.com/OpenMS/OpenMS/blob/develop/src/openms/source/FORMAT…
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In addition to reporting how the PSM score would change by localizing a mass-difference to each amino acid position, it would be nice to report something like:
PEPT[+80]IDE
in other words, give …
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[Pantaleo G, Demarest JF, Soudeyns H, Graziosi C, Denis F, Adelsberger JW, Borrow P, Saag MS, Shaw GM, Sekaly RP, et al. Major expansion of CD8+ T cells with a predominant V beta usage during the prim…
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Hi,
I am currently trying to test spectralis for de novo peptide sequencing of DDA datasets, and I currently have a problem.
While it is possible to get it running on a standard PC with open web con…
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Is it necessary to filter out the results based on the peptide matching score after performing the estimation of FDRs?
For example, would you avoid reporting a PPI based on a small matching score v…
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For the results of Stats objects -- Allow both G-test and ANOVA run across selected group comparisons, then remove the results that are not valid instead of restricting the G-test/ANOVA options for th…
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Quantitative Behavior of Mass Spectrometers
To apply the theory we learnt in the last chapters of this unit to quantitative analyses with mass spectrometers, we need to think about the limitations th…
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Dear peptide-shaker team,
I receive this error when loading MSFragger result files :
> Sat Mar 09 23:03:26 CST 2024 Importing sequences from human_uniprot-proteome_UP000005640-2021.06.20.fa…
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If an empty JSON is returned from the server as result of a fetch, the model should be reseted. For now, nothing is changed and no event is fired neither.