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Annotating PXD009203 I nearly caused an accidental de-anonymization:
In the paper the individuals are mostly statistically aggregated. In supplemental table 1 nevertheless the study cohort is charac…
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In the PMID: 25043054 experiment, three softwares were used to identify the peptides, and the parameter settings for each were different, as follows:
> Pepitome and MyriMatch used precursor toleran…
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@julianus @timosachsenberg :
When running the id part only, I guess the proteomicslfq node should only report the protein inference and not the quant part. Currently, I have an error like for this…
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I tried going through the annotated datasets with [sdrf-pipelines](https://github.com/bigbio/sdrf-pipelines) validator. On some of them, it breaks with a traceback, and on others it shows error messag…
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Hi all:
We have discussed before in other topics this issue #267, #218 but never as the central point of the discussion. I have presented today the format to HUPO-PSI, and one suggestion is to mak…
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In this file:
https://github.com/bigbio/proteomics-metadata-standard/blob/master/annotated-projects/PXD018117/sdrf.tsv
I am surprised that oxidation is a fixed mod. I think the submitters used a v…
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https://github.com/bigbio/proteomics-metadata-standard/blob/master/annotated-projects/PXD000561/sdrf.tsv
@ypriverol should the sample id be the same for all of its fractions
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Hi,
it would be great to add more clarity and/or more examples about the relationship between:
source name, individual and replicates
I understand individual as individual (human) being. In m…
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How should a mixed sample be reflected in the annotation? For example, there is a separate analysis of different individuals and all pooled together or just a commercial plasma sample from lots of dif…
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I see `Material Type` in many annotations but it is not specified anywhere in the standard description. Is it allowed, and if yes, why is it needed?
Material type sounds like a sample characteristi…