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Add crosslinking proteomics SDRF annotations (batch 13/15, 50 datasets) #551

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Merged
ypriverol merged 3 commits into from
Sep 17, 2026
Merged

Add crosslinking proteomics SDRF annotations (batch 13/15, 50 datasets) #551

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689c102
Add crosslinking proteomics SDRF annotations (batch 13, 50 data…
ypriverol Sep 17, 2026
2f4ccff
Add missing characteristics[developmental stage]/[strain or breed] co…
ypriverol Sep 17, 2026
4311088
Remove invertebrates organism template layer from yeast SDRFs
ypriverol Sep 17, 2026
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84 changes: 84 additions & 0 deletions datasets/PXD051014/PXD051014.sdrf.tsv
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75 changes: 75 additions & 0 deletions datasets/PXD051047/PXD051047.sdrf.tsv
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7 changes: 7 additions & 0 deletions datasets/PXD051143/PXD051143.sdrf.tsv
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Original file line number Diff line number Diff line change
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source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[age] characteristics[sex] characteristics[biological replicate] characteristics[material type] characteristics[sample type] characteristics[enrichment process] characteristics[crosslink distance] characteristics[crosslinking reaction time] characteristics[crosslinking temperature] assay name technology type comment[data file] comment[technical replicate] comment[fraction identifier] comment[label] comment[instrument] comment[proteomics data acquisition method] comment[cleavage agent details] comment[cleavage agent details] comment[modification parameters] comment[modification parameters] comment[dissociation method] comment[collision energy] comment[precursor mass tolerance] comment[fragment mass tolerance] comment[fractionation method] comment[chemical cross-linking coupled with ms] comment[cross-linker] comment[crosslink enrichment method] comment[crosslinker concentration] comment[quenching reagent] comment[reduction reagent] comment[alkylation reagent] comment[sdrf version] comment[sdrf template] comment[sdrf template] comment[sdrf template]
PXD051143-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 4031_FC_V_Ctrl_01_EE proteomic profiling by mass spectrometry 4031_FC_V_Ctrl_01_EE.raw 1 1 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=BioID;AC=XLMOD:02250 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0
PXD051143-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 4031_FC_V_Ctrl_02_EE proteomic profiling by mass spectrometry 4031_FC_V_Ctrl_02_EE.raw 1 2 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=BioID;AC=XLMOD:02250 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0
PXD051143-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 4031_FC_V_Ctrl_03_EE proteomic profiling by mass spectrometry 4031_FC_V_Ctrl_03_EE.raw 1 3 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=BioID;AC=XLMOD:02250 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0
PXD051143-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 4031_FC_V_SOX11_01_EE proteomic profiling by mass spectrometry 4031_FC_V_SOX11_01_EE.raw 1 4 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=BioID;AC=XLMOD:02250 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0
PXD051143-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 4031_FC_V_SOX11_02_EE proteomic profiling by mass spectrometry 4031_FC_V_SOX11_02_EE.raw 1 5 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=BioID;AC=XLMOD:02250 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0
PXD051143-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 4031_FC_V_SOX11_03_EE proteomic profiling by mass spectrometry 4031_FC_V_SOX11_03_EE.raw 1 6 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=BioID;AC=XLMOD:02250 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0
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