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I've tried importing the mzIdentML file exported by PEAKS Studio 8 for use by Scaffold (both v 1.0 and 1.1 - see attached screenshot) but PeptideShaker fails to find PSM in the file. The PeptideShaker…
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Hello,
When using msgf2pin converter to prepare MSGFPlus output for Percolator, there will be an error if there is C-terminal modification. The mzIdentML standard says
> Modification to the C-terminu…
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Hello,
First of all, I'm a new a newbie using PIA and KNIME. Perhaps the problem I have is in fact entirely due to my bad understanding of either PIA or KNIME.
So, I would like to use the Protein In…
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Hi @jotsetung
I am referring to this code chunk in `.applyFun2SpectraOfFileSlow` and the equivalent one in `applyFun2SpectraOfFile` and `.applyFun2SpectraOfFileMulti`
``` r
res
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MzTab, mzQuantML and mzIdentML need to store the original file name(s) of the experiment (usually the mzML). This information should be also preserved in idXML, featureXML, consensusXML.
This issue i…
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Validating for XSD conformation in file mzidLib_Rosetta2a_Ecoli_spectra_msgfplus_fdr_threshold_groups.mzid
Error at file /net/db/projects/PSI/mzIdentML/1.2/genDoc/mzidLib_Rosetta2a_Ecoli_spectra_msgf…
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And this file doesn't pass my XML validator with these errors:
Error at file /net/db/projects/PSI/mzIdentML/1.2/genDoc/mzidLib_peaklist2a_plus_ecoli_versus_unimod_full_xtandem_fdr_threshold_groups.mz…
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What should the approved schemaLocation be? The various example files have many different ones:
mzidLib_peaklist2a_plus_ecoli_versus_unimod_full_xtandem_fdr_threshold_groups.mzid - `xsi:schemaLocati…
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current version: v2016.06.29, released June 29, 2016
available at: https://omics.pnl.gov/software/ms-gf
source code available at: https://github.com/sangtaekim/msgfplus
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Error at file /net/db/projects/PSI/mzIdentML/1.2/genDoc/OpenxQuest_example_added_annotations.mzid, line 7, char 37
Message: Schema in mzIdentML1.2.0.xsd has a different target namespace from the one…