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@andrewrobertjones @timosachsenberg @jgriss :
We have an ongoing project to map the Genome coordinates into ESENBML, we have been doing this for a while. Internally, PRIDE has moved into mztab lon…
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Hi,
I'm having trouble at the first step of reading in data and generating a IBSpectra object. I am using the readIBSpectra() function. From the documentation the id.file parameter can be mzIdentml o…
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```
While looking at the recent CV release candidate I found problems with the
existing mzIdentML examples and with the validation and/or schema.
Here are the SearchDatabase values from the MPC exam…
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Bibliospec (proteowizard) gives the following error.
ERROR: ../dataSearchResults/SearchGUI/GRAY_MS/tpp_psm_export.pep.xml(line 7): Missing required attribute 'base_name'.
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For a while, we have been avoiding `Protein Group` modelling in the psm and feature in the format. @jpfeuffer triggered this issue a long time ago. Our main tools DIA-NN, OpenMS TMT, and OpenMS LFQ pi…
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The current `Modification` object is a simple class that contains mainly the unimod ID, the composition and the avg/mono mass of the modification as integer/double vectors of length 1. Additionally it…
sgibb updated
6 years ago
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```
While looking at the recent CV release candidate I found problems with the
existing mzIdentML examples and with the validation and/or schema.
Here are the SearchDatabase values from the MPC exam…
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```
Copied to the issues list, so we don't lose track - see detail below.
I agree this is not ideal, although I don't know if using a zero code is more
useful than just leaving the attribute out. I …
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My CV term validator finds these issues with this file:
ERROR: cvParam distinct peptide-level q-value should have units, but it does not!
WARNING: MS:1001062 should be 'Mascot MGF format' instead of '…
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Hdf files can be written and read a lot faster (e.g. msgfplus unify results):
```
start = datetime.datetime.now()
df.to_csv(kwargs["output_filenames"][0], index=False)
print((datetime.datetime.n…