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My pipeline fails when using Lys-C as a digestion enzyme, ```NT=Lys-C;AC=MS:1001309 ``` or ```NT=Lys-C/P;AC=MS_1001310```. It works with trypsin ```NT=Trypsin;AC=MS_1001251```. My command is:
```
n…
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Hey,
so just to be sure and document it here. Veit mentioned this project to us for potential use in ProteoBench. We aim to parse parameter files into a common format (or at least parts of it).
…
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```
#!python
[INFO, L:57] -process experiment E-GEOD-26688-
[INFO, L:138] get experiment info from http://www.ebi.ac.uk/arrayexpress/json/v2/experiments/arrays.txt
[INFO, L:152] get experiment file i…
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It would be better to not manually work with path strings but use the modern `pathlib` instead.
https://github.com/bigbio/sdrf-pipelines/blob/837af51f360e81d5b9b6b10a21698fc4c7a3c582/sdrf_pipelines…
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We could also overwrite the experimental design generated from the SDRF but I don't know if that gets even more confusing.
Maybe in the long run we even deprecated the "--expdesign" parameter and req…
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```
#!python
[INFO, L:74] -process experiment E-GEOD-38516-
[INFO, L:155] get experiment info from http://www.ebi.ac.uk/arrayexpress/json/v2/experiments/arrays.txt
[INFO, L:169] get experiment file i…
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@ypriverol Do you have a set of SDRF files for experiments of all different kinds of expected flavors?
If not we should systematically generate SDRF example files with all the different labelling t…
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Hi everyone,
Our group is recently working with TMT datasets from published data. When we search for the dataset, we found that very few research provide the imputrity correction factors for the TM…
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I always use the same SDRF temple. 2024-4-4 it worked, no error, but today it said 'Value is not match with ontology'. I can't tell what is wrong here. I am using px-submission 2.7.3
Here is the file…
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```
#!python
[INFO, L:74] -process experiment E-GEOD-49355-
[INFO, L:155] get experiment info from http://www.ebi.ac.uk/arrayexpress/json/v2/experiments/arrays.txt
[INFO, L:169] get experiment file i…