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I observe the following error when running SearchGUI from Galaxy (using the latest version available for Galaxy, i.e. 4.0.12)
```
Fri Mar 12 15:12:56 CET 2021 Importing spectrum files.
10% 20% 30…
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I see messages like `Unknown (or deprecated) Parameter 'in' given in outdated parameter file! Ignoring parameter.` when running
```
OpenPepXL -test -decoy_string "decoy" -in OpenPepXL_input.mzML …
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I'm trying to load a .mzid file into PS and running into trouble. Could be that the file doesn't contain all the values you folks are looking for or that it is in the wrong format. I don't see any doc…
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I am trying to perform PSM with SearchCLI. The input are peak-picked MGF datasets, and I am trying to use Myri-match, X!Tandem and MS-GF+. Both Myri-match and MS-GF+ fail, with X!Tandem managing to fi…
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Writing plain CVs in UserParams to XML e.g. "MS:0001234" might be extended by placing the CV name in the same line by the XML writer (if it is a known CV term).
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Hi all,
I believe to have seen somewhere that SearchGUI/PeptideShaker can be used with ProgenesisQI for quantification. Which data-format do I need to export from Progenesis for this?
I tried with '…
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When specifying -maxMissedCleavages 1, the value is not being output in the mzIdentML:
Actual:
` `
Expected:
` `
From a glance at the data, it se…
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Hi all,
can we please add xlmod to OBOFoundry? I attached the xlmod.md and XLMOD.obo files.
Requested prefix: xlmod
Ontology Title: HUPO-PSI cross-linking and derivatization reagents controlled…
germa updated
4 years ago
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Hi,
I've recently been using a series of tools from compomics and when exporting a cpsx file to a mzid file using PeptideShaker version 1.16.45, the export never succeeds if I use the CLI command l…