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Add crosslinking proteomics SDRF annotations (batch 02/15, 50 datasets) (#540)
* Add crosslinking proteomics SDRF annotations (batch 02, 50 datasets) * Add missing characteristics[developmental stage]/[strain or breed] columns Required by the vertebrates/invertebrates/plants SDRF templates; value set to the spec-compliant reserved word 'not available' where the field was not previously populated. human-only files are unaffected (field optional in that template). * Fix instrument assignment for PXD009777 Orbitrap Fusion Lumos EThcD runs The 3 .raw files acquired with EThcD fragmentation were tagged with the AB Sciex TripleTOF 5600 used for the separate CID-fragmentation .wiff run. Per the PRIDE submission's sample processing protocol, EThcD data was acquired on an Orbitrap Fusion Lumos (Thermo); the CID .wiff file is unaffected. * Remove invertebrates organism template layer from yeast SDRFs comment[sdrf template] declared NT=invertebrates;VV=v1.1.0 (an animal-only template) for 4 Saccharomyces cerevisiae datasets. Removing the mismatched template column; ms-proteomics and crosslinking layers are unaffected. Confirmed by qodo-code-review[bot] and this report's own data check.
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‎datasets/PXD006715/PXD006715.sdrf.tsv‎

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‎datasets/PXD006928/PXD006928.sdrf.tsv‎

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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]
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PXD006928-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 1_NFS1-Fxn_Markley proteomic profiling by mass spectrometry 1_NFS1-Fxn_Markley.raw 1 1 AC=MS:1002038;NT=label free sample NT=6340 Ion Trap LC/MS;AC=MS:1000476 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 chemical cross-linking coupled with mass spectrometry proteomics NT=unknown crosslinker;AC=XLMOD:00000 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

‎datasets/PXD006938/PXD006938.sdrf.tsv‎

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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]
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PXD006938-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 2_NFS1-Fxn-IscU_Markley proteomic profiling by mass spectrometry 2_NFS1-Fxn-IscU_Markley.raw 1 1 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap;AC=MS:1000449 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 chemical cross-linking coupled with mass spectrometry proteomics NT=BS3;AC=XLMOD:02000 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

‎datasets/PXD007043/PXD007043.sdrf.tsv‎

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‎datasets/PXD007185/PXD007185.sdrf.tsv‎

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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]
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PXD007185-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available aleitner_C1703_349 proteomic profiling by mass spectrometry aleitner_C1703_349.raw 1 1 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Elite;AC=MS:1001910 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSS;AC=XLMOD:02001 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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PXD007185-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available aleitner_C1703_350 proteomic profiling by mass spectrometry aleitner_C1703_350.raw 1 2 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Elite;AC=MS:1001910 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSS;AC=XLMOD:02001 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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PXD007185-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available aleitner_C1703_351 proteomic profiling by mass spectrometry aleitner_C1703_351.raw 1 3 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Elite;AC=MS:1001910 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSS;AC=XLMOD:02001 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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PXD007185-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available aleitner_C1703_352 proteomic profiling by mass spectrometry aleitner_C1703_352.raw 1 4 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Elite;AC=MS:1001910 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSS;AC=XLMOD:02001 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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PXD007185-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available aleitner_C1703_354 proteomic profiling by mass spectrometry aleitner_C1703_354.raw 1 5 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Elite;AC=MS:1001910 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSS;AC=XLMOD:02001 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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PXD007185-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available aleitner_C1703_357 proteomic profiling by mass spectrometry aleitner_C1703_357.raw 1 6 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Elite;AC=MS:1001910 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSS;AC=XLMOD:02001 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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PXD007185-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available aleitner_C1703_358 proteomic profiling by mass spectrometry aleitner_C1703_358.raw 1 7 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Elite;AC=MS:1001910 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSS;AC=XLMOD:02001 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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PXD007185-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available aleitner_C1703_359 proteomic profiling by mass spectrometry aleitner_C1703_359.raw 1 8 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Elite;AC=MS:1001910 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSS;AC=XLMOD:02001 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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PXD007185-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available aleitner_C1703_360 proteomic profiling by mass spectrometry aleitner_C1703_360.raw 1 9 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Elite;AC=MS:1001910 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSS;AC=XLMOD:02001 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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PXD007185-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available aleitner_C1703_361 proteomic profiling by mass spectrometry aleitner_C1703_361.raw 1 10 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Elite;AC=MS:1001910 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSS;AC=XLMOD:02001 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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PXD007185-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available aleitner_C1703_363 proteomic profiling by mass spectrometry aleitner_C1703_363.raw 1 11 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Elite;AC=MS:1001910 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSS;AC=XLMOD:02001 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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PXD007185-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available aleitner_C1703_365 proteomic profiling by mass spectrometry aleitner_C1703_365.raw 1 12 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Elite;AC=MS:1001910 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSS;AC=XLMOD:02001 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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