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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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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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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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**What happened**:
13:12:11 === RUN TestMetricsDuGetCapacity
13:12:11 --- FAIL: TestMetricsDuGetCapacity (0.01s)
metrics_du_test.go:100: Unexpected Used for directory with file. Expected 4…
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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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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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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 all:
I just annotate three different projects from PRIDE (1000 raw files) more than 59 cell lines. Here the example https://github.com/bigbio/multiomics-configs/blob/master/datasets/NCI60/sdrf.…
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In annotation of PXD000612 project does not exist for the following samples:
pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep4_pH11.raw
pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep4_pH3.…
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From what I understand from the spec file, the way to report labels would be to use the column 'comment[label]'. But the only example there is a 'label free sample'.
- For TMT experiments the SDRF …