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Update metaproteomics examples to current SDRF required columns #1

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Update metaproteomics examples to current SDRF required columns #1

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9d376c6
Add required metaproteomics SDRF columns to examples (PXD003791, PXD0…
nithujohn Jul 29, 2026
3b269a1
Fix SDRF template declarations and required values in examples (PAD00…
nithujohn Jul 29, 2026
c4a1a5b
Annotate PAD000003 comment[platform] with PRIDE accession PRIDE:00006…
nithujohn Jul 29, 2026
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42 changes: 21 additions & 21 deletions examples/PAD000001/PAD000001.sdrf.tsv
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Original file line number Diff line number Diff line change
@@ -1,21 +1,21 @@
source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[age] characteristics[sex] characteristics[biological replicate] characteristics[sample type] characteristics[sample matrix] assay name technology type comment[technical replicate] comment[data file] comment[file uri] comment[platform] comment[quantification unit] comment[plate] comment[normalization method] comment[olink panel] comment[olink platform] comment[npx normalization] comment[sdrf version] comment[sdrf annotation tool]
PAD000001-XB6 Homo sapiens not available not available not available not available 1 not applicable blood plasma PAD000001-r00001-XB6 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_5 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB65 Homo sapiens not available not available not available not available 2 not applicable blood plasma PAD000001-r00002-XB65 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_5 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB68 Homo sapiens not available not available not available not available 3 not applicable blood plasma PAD000001-r00003-XB68 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_5 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB115 Homo sapiens not available not available not available not available 4 not applicable blood plasma PAD000001-r00004-XB115 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_7 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB20 Homo sapiens not available not available not available not available 5 not applicable blood plasma PAD000001-r00005-XB20 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_7 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB95 Homo sapiens not available not available not available not available 6 not applicable blood plasma PAD000001-r00006-XB95 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_7 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB54 Homo sapiens not available not available not available not available 7 not applicable blood plasma PAD000001-r00007-XB54 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_6 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB22 Homo sapiens not available not available not available not available 8 not applicable blood plasma PAD000001-r00008-XB22 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_9 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB25 Homo sapiens not available not available not available not available 9 not applicable blood plasma PAD000001-r00009-XB25 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_11 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB97 Homo sapiens not available not available not available not available 10 not applicable blood plasma PAD000001-r00010-XB97 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_10 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB79 Homo sapiens not available not available not available not available 11 not applicable blood plasma PAD000001-r00011-XB79 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_10 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB59 Homo sapiens not available not available not available not available 12 not applicable blood plasma PAD000001-r00012-XB59 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_10 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB114 Homo sapiens not available not available not available not available 13 not applicable blood plasma PAD000001-r00013-XB114 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_12 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB94 Homo sapiens not available not available not available not available 14 not applicable blood plasma PAD000001-r00014-XB94 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_13 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB14 Homo sapiens not available not available not available not available 15 not applicable blood plasma PAD000001-r00015-XB14 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_4 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB100 Homo sapiens not available not available not available not available 16 not applicable blood plasma PAD000001-r00016-XB100 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_2 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB112 Homo sapiens not available not available not available not available 17 not applicable blood plasma PAD000001-r00017-XB112 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_2 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB89 Homo sapiens not available not available not available not available 18 not applicable blood plasma PAD000001-r00018-XB89 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_8 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB107 Homo sapiens not available not available not available not available 19 not applicable blood plasma PAD000001-r00019-XB107 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_3 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB21 Homo sapiens not available not available not available not available 20 not applicable blood plasma PAD000001-r00020-XB21 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_3 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[age] characteristics[sex] characteristics[biological replicate] characteristics[sample type] characteristics[sample matrix] assay name technology type comment[technical replicate] comment[data file] comment[file uri] comment[platform] comment[quantification unit] comment[plate] comment[normalization method] comment[olink panel] comment[olink platform] comment[npx normalization] comment[sdrf template] comment[sdrf version] comment[sdrf annotation tool]
PAD000001-XB6 Homo sapiens not available not available not available not available 1 study sample blood plasma PAD000001-r00001-XB6 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_5 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB65 Homo sapiens not available not available not available not available 2 study sample blood plasma PAD000001-r00002-XB65 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_5 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB68 Homo sapiens not available not available not available not available 3 study sample blood plasma PAD000001-r00003-XB68 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_5 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB115 Homo sapiens not available not available not available not available 4 study sample blood plasma PAD000001-r00004-XB115 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_7 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB20 Homo sapiens not available not available not available not available 5 study sample blood plasma PAD000001-r00005-XB20 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_7 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB95 Homo sapiens not available not available not available not available 6 study sample blood plasma PAD000001-r00006-XB95 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_7 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB54 Homo sapiens not available not available not available not available 7 study sample blood plasma PAD000001-r00007-XB54 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_6 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB22 Homo sapiens not available not available not available not available 8 study sample blood plasma PAD000001-r00008-XB22 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_9 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB25 Homo sapiens not available not available not available not available 9 study sample blood plasma PAD000001-r00009-XB25 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_11 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB97 Homo sapiens not available not available not available not available 10 study sample blood plasma PAD000001-r00010-XB97 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_10 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB79 Homo sapiens not available not available not available not available 11 study sample blood plasma PAD000001-r00011-XB79 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_10 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB59 Homo sapiens not available not available not available not available 12 study sample blood plasma PAD000001-r00012-XB59 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_10 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB114 Homo sapiens not available not available not available not available 13 study sample blood plasma PAD000001-r00013-XB114 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_12 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB94 Homo sapiens not available not available not available not available 14 study sample blood plasma PAD000001-r00014-XB94 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_13 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB14 Homo sapiens not available not available not available not available 15 study sample blood plasma PAD000001-r00015-XB14 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_4 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB100 Homo sapiens not available not available not available not available 16 study sample blood plasma PAD000001-r00016-XB100 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_2 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB112 Homo sapiens not available not available not available not available 17 study sample blood plasma PAD000001-r00017-XB112 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_2 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB89 Homo sapiens not available not available not available not available 18 study sample blood plasma PAD000001-r00018-XB89 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_8 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB107 Homo sapiens not available not available not available not available 19 study sample blood plasma PAD000001-r00019-XB107 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_3 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB21 Homo sapiens not available not available not available not available 20 study sample blood plasma PAD000001-r00020-XB21 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_3 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized NT=affinity-proteomics;VV=v1.0.0 v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
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