Add crosslinking proteomics SDRF annotations (batch 15/15, 50 datasets) - #553
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PR Summary by QodoAdd batch 15 crosslinking proteomics SDRF annotations
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Code Review by Qodo
1. Controls collapse into rat fractions
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![qodo-code-review[bot]](https://avatars.githubusercontent.com/in/484649?s=60&v=4){kind=small}
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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] | |||
| PXD065869-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available E240620_13_AMC_HSA_C1_DSSO_HCD_Energies_Inj1 proteomic profiling by mass spectrometry E240620_13_AMC_HSA_C1_DSSO_HCD_Energies_Inj1.raw 1 1 AC=MS:1002038;NT=label free sample NT=Orbitrap Eclipse;AC=MS:1003029 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=DSBSO;AC=XLMOD:02155;CL=yes;TA=K,S,T,Y,nterm not available not available re-addition 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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8. Runs receive the wrong reagent 🐞 Bug ≡ Correctness
PXD065869 declares DSBSO for runs whose identifiers explicitly specify DSSO, including a NoXL control marked CL=yes. The row-level metadata consequently misidentifies the reagent on DSSO runs and represents the uncross-linked control as cross-linked.
Agent Prompt
## Issue description
PXD065869 applies DSBSO and `CL=yes` globally even though the run identifiers specify DSSO and include an uncross-linked control.
## Fix Focus Areas
- datasets/PXD065869/PXD065869.sdrf.tsv[2-5]
- datasets/PXD065869/PXD065869.sdrf.tsv[16-17]
## Recommended Fix
Annotate the DSSO runs with the verified DSSO controlled term and represent the `NoXL` row as an uncross-linked control. Check the remaining coded run groups against the study metadata instead of applying one reagent to every row.
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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] | |||
| PXD066655-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available RS48_C1 proteomic profiling by mass spectrometry RS48_C1.raw 1 1 AC=MS:1002038;NT=label free sample NT=Q Exactive HF-X;AC=MS:1002877 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=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 | |||
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9. Distinct samples become fake fractions 🐞 Bug ≡ Correctness
PXD066655 gives all twelve runs one source, biological replicate 1, and sequential fraction identifiers despite identifiers encoding four distinct series and triplicate suffixes. Analyses using the SDRF design therefore treat separate conditions and replicates as fractions of one sample.
Agent Prompt
## Issue description
PXD066655 represents four triplicate experimental groups as twelve fractions of a single biological sample.
## Fix Focus Areas
- datasets/PXD066655/PXD066655.sdrf.tsv[2-13]
## Recommended Fix
Create source identities and condition annotations for the `RS48_C`, `RS48_D`, `RS48_F`, and `SPD2` groups, map suffixes 1-3 to their verified replicate dimension, and use fraction identifiers only when the corresponding files are actual fractions of the same sample.
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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] | |||
| PXD069844-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available CDC42_WT_1 proteomic profiling by mass spectrometry CDC42_WT_1.raw 1 1 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion;AC=MS:1002416 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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10. Experimental groups become fake fractions 🐞 Bug ≡ Correctness
PXD069844 assigns eleven triplicate experimental groups one source, biological replicate 1, and fraction identifiers 1–33. The resulting design collapses controls, wild types, mutants, and active-protein groups into fractions of one sample rather than preserving their conditions and replicate structure.
Agent Prompt
## Issue description
PXD069844 collapses eleven visibly distinct triplicate groups into one 33-fraction sample.
## Fix Focus Areas
- datasets/PXD069844/PXD069844.sdrf.tsv[2-34]
## Recommended Fix
Assign distinct source or factor annotations for each control, wild-type, mutant, pull-down, and active-protein group; map each `_1`/`_2`/`_3` suffix to the verified replicate dimension. Remove sequential fraction identifiers unless the study confirms that these files are physical fractions of one sample.
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…lumns 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).
All 10 rows were tagged with LTQ Orbitrap, but the .d.zip data files and the PRIDE submission's sample processing protocol confirm acquisition on a Bruker timsTOF Pro2 (NanoElute UPLC, PASEF).
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| PXD060638-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available Bin1_PhosphoResults_InVivo.sky.zip proteomic profiling by mass spectrometry Bin1_PhosphoResults_InVivo.sky.zip 1 1 AC=MS:1002038;NT=label free sample NT=timsTOF Pro;AC=MS:1003005 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=TurboID;AC=XLMOD:02251 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=vertebrates;VV=v1.1.0 | ||
| PXD060638-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available Bin1interactome_InVivo_Single_Peptide_Hits.sky.zip proteomic profiling by mass spectrometry Bin1interactome_InVivo_Single_Peptide_Hits.sky.zip 1 2 AC=MS:1002038;NT=label free sample NT=timsTOF Pro;AC=MS:1003005 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=TurboID;AC=XLMOD:02251 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=vertebrates;VV=v1.1.0 |
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1. Skyline reports become instrument runs 📘 Rule violation ≡ Correctness
Rows 2, 3, and 30 of PXD060638 assign the .sky.zip Skyline result bundles to both assay name and comment[data file] while declaring timsTOF acquisition metadata. Consumers therefore treat processed analysis documents as fractions alongside the actual .d.zip measurements.
Agent Prompt
## Issue description
PXD060638 represents processed Skyline result bundles as mass-spectrometry acquisition assays and fractions in the canonical SDRF.
## Fix Focus Areas
- datasets/PXD060638/PXD060638.sdrf.tsv[2-3]
- datasets/PXD060638/PXD060638.sdrf.tsv[30-30]
## Recommended Fix
Remove the `.sky.zip` rows from the SDRF assay table and retain only files that represent acquired mass-spectrometry measurements. Preserve any supported relationships between the remaining runs and their samples, and renumber the remaining fraction identifiers if fractions are retained.
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| PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available combined.prot.xml proteomic profiling by mass spectrometry combined.prot.xml 1 10 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 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=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=vertebrates;VV=v1.1.0 | ||
| PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available combined_peptide.tsv proteomic profiling by mass spectrometry combined_peptide.tsv 1 11 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 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=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=vertebrates;VV=v1.1.0 | ||
| PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available combined_protein.tsv proteomic profiling by mass spectrometry combined_protein.tsv 1 12 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 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=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=vertebrates;VV=v1.1.0 | ||
| PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available fragger.params proteomic profiling by mass spectrometry fragger.params 1 13 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 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=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=vertebrates;VV=v1.1.0 |
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2. Analysis outputs become instrument runs 📘 Rule violation ≡ Correctness
Rows 11–15 assign combined.prot.xml, combined peptide and protein tables, fragger.params, and fragpipe.workflow to assay name and comment[data file] with a timsTOF HT instrument and data-dependent acquisition method. These processed outputs and settings are consequently represented as five additional acquisition fractions after the nine actual .d.zip runs.
Agent Prompt
## Issue description
PXD061317 incorrectly represents processed reports, result tables, and FragPipe configuration files as mass-spectrometry acquisitions.
## Fix Focus Areas
- datasets/PXD061317/PXD061317.sdrf.tsv[11-15]
## Recommended Fix
Delete rows 11–15 containing `combined.prot.xml`, the combined peptide and protein TSV reports, `fragger.params`, and `fragpipe.workflow`, so the SDRF retains only the acquired `.d.zip` files as assays. Ensure the retained fraction identifiers remain consistent.
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| PXD062293-sample synechocystis sp. pcc 6803 not applicable not applicable not applicable 1 synthetic reference not available not available not available not available Fl09ZZW_TB_1_1_F6_1_2424.d.zip proteomic profiling by mass spectrometry Fl09ZZW_TB_1_1_F6_1_2424.d.zip 1 7 AC=MS:1002038;NT=label free sample NT=timsTOF Pro 2;AC=MS:1003230 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=TurboID;AC=XLMOD:02251 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 | ||
| PXD062293-sample synechocystis sp. pcc 6803 not applicable not applicable not applicable 1 synthetic reference not available not available not available not available Fl09ZZW_TB_2_2_A7_1_2425.d.zip proteomic profiling by mass spectrometry Fl09ZZW_TB_2_2_A7_1_2425.d.zip 1 8 AC=MS:1002038;NT=label free sample NT=timsTOF Pro 2;AC=MS:1003230 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=TurboID;AC=XLMOD:02251 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 | ||
| PXD062293-sample synechocystis sp. pcc 6803 not applicable not applicable not applicable 1 synthetic reference not available not available not available not available Fl09ZZW_TB_3_3_B7_1_2426.d.zip proteomic profiling by mass spectrometry Fl09ZZW_TB_3_3_B7_1_2426.d.zip 1 9 AC=MS:1002038;NT=label free sample NT=timsTOF Pro 2;AC=MS:1003230 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=TurboID;AC=XLMOD:02251 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 | ||
| PXD062293-sample synechocystis sp. pcc 6803 not applicable not applicable not applicable 1 synthetic reference not available not available not available not available maxquant_result.zip proteomic profiling by mass spectrometry maxquant_result.zip 1 10 AC=MS:1002038;NT=label free sample NT=timsTOF Pro 2;AC=MS:1003230 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=TurboID;AC=XLMOD:02251 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 |
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3. A result archive becomes a raw run 📘 Rule violation ≡ Correctness
Row 11 assigns maxquant_result.zip to both assay name and comment[data file], with timsTOF Pro 2/DDA metadata and a tenth fraction identifier. Because this archive is a downstream MaxQuant result rather than an acquisition, it is mapped as a tenth instrument assay alongside the nine preceding .d.zip vendor runs.
Agent Prompt
## Issue description
PXD062293 represents a processed MaxQuant result archive as an acquired timsTOF mass-spectrometry run.
## Fix Focus Areas
- datasets/PXD062293/PXD062293.sdrf.tsv[11-11]
## Recommended Fix
Remove the `maxquant_result.zip` row and retain only the nine `.d.zip` vendor files as the accession's instrument assays.
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| PXD062557-sample caenorhabditis elegans not applicable not applicable not applicable not available not available 1 synthetic reference not available not available not available not available 20220512_E3_RSLC1_Jelenic_Saha_IMBA_ID722_onbead_dig_5per_control_1A_N2_A proteomic profiling by mass spectrometry 20220512_E3_RSLC1_Jelenic_Saha_IMBA_ID722_onbead_dig_5per_control_1A_N2_A.raw 1 1 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion;AC=MS:1002416 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=TurboID;AC=XLMOD:02251 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=invertebrates;VV=v1.1.0 | ||
| PXD062557-sample caenorhabditis elegans not applicable not applicable not applicable not available not available 1 synthetic reference not available not available not available not available 20220512_E3_RSLC1_Jelenic_Saha_IMBA_ID722_onbead_dig_5per_control_1B_N2_B proteomic profiling by mass spectrometry 20220512_E3_RSLC1_Jelenic_Saha_IMBA_ID722_onbead_dig_5per_control_1B_N2_B.raw 1 2 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion;AC=MS:1002416 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=TurboID;AC=XLMOD:02251 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=invertebrates;VV=v1.1.0 | ||
| PXD062557-sample caenorhabditis elegans not applicable not applicable not applicable not available not available 1 synthetic reference not available not available not available not available 20220512_E3_RSLC1_Jelenic_Saha_IMBA_ID722_onbead_dig_5per_control_1C_N2_C proteomic profiling by mass spectrometry 20220512_E3_RSLC1_Jelenic_Saha_IMBA_ID722_onbead_dig_5per_control_1C_N2_C.raw 1 3 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion;AC=MS:1002416 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=TurboID;AC=XLMOD:02251 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=invertebrates;VV=v1.1.0 | ||
| PXD062557-sample caenorhabditis elegans not applicable not applicable not applicable not available not available 1 synthetic reference not available not available not available not available 20220512_E3_RSLC1_Jelenic_Saha_IMBA_ID722_onbead_dig_5per_sample_2A_SS106_WT_A proteomic profiling by mass spectrometry 20220512_E3_RSLC1_Jelenic_Saha_IMBA_ID722_onbead_dig_5per_sample_2A_SS106_WT_A.raw 1 4 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion;AC=MS:1002416 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=TurboID;AC=XLMOD:02251 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=invertebrates;VV=v1.1.0 |
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4. Distinct worm groups become fractions 📘 Rule violation ≡ Correctness
PXD062557.sdrf.tsv assigns all 42 control, wild-type, tagged, knockout, and targeted runs to PXD062557-sample and biological replicate 1, varying only comment[fraction identifier] from 1–42. Filenames distinguishing groups such as N2, SS106_WT, SS107b_3xFG, and SS200a_W4_KO, including A/B/C or 1/2/3 replicate suffixes, instead reach the table as fractions of one sample and lose their condition and replicate distinctions.
Agent Prompt
## Issue description
Distinct worm strains, controls, conditions, and biological replicates in PXD062557 are modeled as sequential fractions of one source sample.
## Fix Focus Areas
- datasets/PXD062557/PXD062557.sdrf.tsv[2-43]
## Recommended Fix
Derive distinct source names and strain, condition, and biological-replicate annotations from authoritative project metadata, assay groups, and filenames. Assign fraction identifiers only where files are true fractions of the same sample rather than using one sequential fraction series across independent experimental groups.
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| PXD062741-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available Seq87982_chymo_DIA_480Ex2 proteomic profiling by mass spectrometry Seq87982_chymo_DIA_480Ex2.raw 1 41 AC=MS:1002038;NT=label free sample NT=Q Exactive;AC=MS:1001911 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=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=vertebrates;VV=v1.1.0 | ||
| PXD062741-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available Seq87983_chymo_DIA_480Ex2 proteomic profiling by mass spectrometry Seq87983_chymo_DIA_480Ex2.raw 1 42 AC=MS:1002038;NT=label free sample NT=Q Exactive;AC=MS:1001911 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=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=vertebrates;VV=v1.1.0 | ||
| PXD062741-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available Seq87984_chymo_DIA_480Ex2 proteomic profiling by mass spectrometry Seq87984_chymo_DIA_480Ex2.raw 1 43 AC=MS:1002038;NT=label free sample NT=Q Exactive;AC=MS:1001911 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=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=vertebrates;VV=v1.1.0 | ||
| PXD062741-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available checksum.txt proteomic profiling by mass spectrometry checksum.txt 1 44 AC=MS:1002038;NT=label free sample NT=Q Exactive;AC=MS:1001911 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=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=vertebrates;VV=v1.1.0 |
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5. Mouse data records a checksum as a run 📘 Rule violation ≡ Correctness
Row 45 assigns checksum.txt to both assay name and comment[data file] while supplying Q Exactive, DDA, technical-replicate, and fraction 44 metadata. Unlike the preceding .raw acquisition rows, the archive integrity manifest is therefore included as another acquired measurement.
Agent Prompt
## Issue description
PXD062741 represents the archive checksum manifest as a Q Exactive mass-spectrometry acquisition and experimental fraction.
## Fix Focus Areas
- datasets/PXD062741/PXD062741.sdrf.tsv[45-45]
## Recommended Fix
Delete the `checksum.txt` assay row from the SDRF and retain only files that represent acquired mass-spectrometry measurements.
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| PXD065410-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available Light.rar proteomic profiling by mass spectrometry Light.rar 1 1 AC=MS:1002038;NT=label free sample NT=Q Exactive HF;AC=MS:1002523 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=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=vertebrates;VV=v1.1.0 | ||
| PXD065410-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available Light_HAPCN_1.rar proteomic profiling by mass spectrometry Light_HAPCN_1.rar 1 2 AC=MS:1002038;NT=label free sample NT=Q Exactive HF;AC=MS:1002523 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=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=vertebrates;VV=v1.1.0 | ||
| PXD065410-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available Light_HAPCN_2.rar proteomic profiling by mass spectrometry Light_HAPCN_2.rar 1 3 AC=MS:1002038;NT=label free sample NT=Q Exactive HF;AC=MS:1002523 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=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=vertebrates;VV=v1.1.0 | ||
| PXD065410-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available Light_omitPCN_1.rar proteomic profiling by mass spectrometry Light_omitPCN_1.rar 1 4 AC=MS:1002038;NT=label free sample NT=Q Exactive HF;AC=MS:1002523 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=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=vertebrates;VV=v1.1.0 |
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9. Archive bundles become instrument runs 📘 Rule violation ≡ Correctness
Every row in PXD065410.sdrf.tsv maps a .rar archive directly to assay name and `comment[data file]` while assigning Q Exactive acquisition metadata. The condition-specific bundles are therefore represented as ten individual measurements without identifying the raw files contained in each archive.
Agent Prompt
## Issue description
RAR bundles are represented as individual instrument acquisitions instead of mapping their contained raw measurements.
## Fix Focus Areas
- datasets/PXD065410/PXD065410.sdrf.tsv[2-11]
## Recommended Fix
Use the public archive inventory to enumerate the acquired raw files contained in each bundle and map those files to the correct samples and replicates; do not treat each `.rar` container as one assay.
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| PXD060638-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available GT_JM_F_Bin1_1_DIAod_90m_5th_4ul_Slot1-32_5-16-2023_5885.d.zip proteomic profiling by mass spectrometry GT_JM_F_Bin1_1_DIAod_90m_5th_4ul_Slot1-32_5-16-2023_5885.d.zip 1 3 AC=MS:1002038;NT=label free sample NT=timsTOF Pro;AC=MS:1003005 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=TurboID;AC=XLMOD:02251 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=vertebrates;VV=v1.1.0 | ||
| PXD060638-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available GT_JM_F_Bin1_2_DIAod_90m_5th_3pt3ul_Slot1-33_5-17-2023_5887.d.zip proteomic profiling by mass spectrometry GT_JM_F_Bin1_2_DIAod_90m_5th_3pt3ul_Slot1-33_5-17-2023_5887.d.zip 1 4 AC=MS:1002038;NT=label free sample NT=timsTOF Pro;AC=MS:1003005 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=TurboID;AC=XLMOD:02251 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=vertebrates;VV=v1.1.0 | ||
| PXD060638-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available GT_JM_F_Bin1_3_DIAod_90m_5th_3pt2ul_Slot1-34_5-17-2023_5889.d.zip proteomic profiling by mass spectrometry GT_JM_F_Bin1_3_DIAod_90m_5th_3pt2ul_Slot1-34_5-17-2023_5889.d.zip 1 5 AC=MS:1002038;NT=label free sample NT=timsTOF Pro;AC=MS:1003005 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=TurboID;AC=XLMOD:02251 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=vertebrates;VV=v1.1.0 | ||
| PXD060638-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available GT_JM_F_Bin1_4_DIAod_90m_5th_3pt2ul_Slot1-35_5-17-2023_5891.d.zip proteomic profiling by mass spectrometry GT_JM_F_Bin1_4_DIAod_90m_5th_3pt2ul_Slot1-35_5-17-2023_5891.d.zip 1 6 AC=MS:1002038;NT=label free sample NT=timsTOF Pro;AC=MS:1003005 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=TurboID;AC=XLMOD:02251 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=vertebrates;VV=v1.1.0 |
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10. Mouse groups collapse into fractions 🐞 Bug ≡ Correctness
PXD060638 gives female and male Bin1 and Cyto runs one source, biological replicate 1, and sequential fraction identifiers. The F, M, Bin1, and Cyto assay groups are consequently represented as fractions of one sample rather than distinct biological conditions or replicates.
Agent Prompt
## Issue description
PXD060638 collapses sex and experimental groups into one artificial fraction series.
## Fix Focus Areas
- datasets/PXD060638/PXD060638.sdrf.tsv[4-29]
## Recommended Fix
Assign distinct source names and appropriate biological-replicate or factor values for the female, male, Bin1, and Cyto groups; reserve fraction identifiers for actual fractions of one sample.
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| PXD063145-sample rattus norvegicus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available GLP1APPLE293T1Experimentalgroup proteomic profiling by mass spectrometry GLP1APPLE293T1Experimentalgroup.raw 1 2 AC=MS:1002038;NT=label free sample NT=Orbitrap Exploris 480;AC=MS:1003028 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=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=vertebrates;VV=v1.1.0 | ||
| PXD063145-sample rattus norvegicus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available GLP1APPLE293T2Experimentalgroup proteomic profiling by mass spectrometry GLP1APPLE293T2Experimentalgroup.raw 1 3 AC=MS:1002038;NT=label free sample NT=Orbitrap Exploris 480;AC=MS:1003028 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=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=vertebrates;VV=v1.1.0 | ||
| PXD063145-sample rattus norvegicus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available GLP1APPLE293T3Experimentalgroup proteomic profiling by mass spectrometry GLP1APPLE293T3Experimentalgroup.raw 1 4 AC=MS:1002038;NT=label free sample NT=Orbitrap Exploris 480;AC=MS:1003028 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=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=vertebrates;VV=v1.1.0 | ||
| PXD063145-sample rattus norvegicus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available GLP1APPLE293T4Controlgroup proteomic profiling by mass spectrometry GLP1APPLE293T4Controlgroup.raw 1 5 AC=MS:1002038;NT=label free sample NT=Orbitrap Exploris 480;AC=MS:1003028 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=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=vertebrates;VV=v1.1.0 |
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11. Controls collapse into rat fractions 🐞 Bug ≡ Correctness
PXD063145 assigns numerous experimental and control groups one source and biological replicate while numbering every file as a separate fraction. The GLP1, ORF9B, PIN1, time-course, experimental, and control series therefore lose their group and replicate structure.
Agent Prompt
## Issue description
PXD063145 collapses multiple experiments, controls, and replicate series into fractions of one source.
## Fix Focus Areas
- datasets/PXD063145/PXD063145.sdrf.tsv[3-57]
## Recommended Fix
Assign source names, biological replicates, and factor values that preserve each GLP1, ORF9B, PIN1, treatment, time-point, experimental, and control group; do not use sequential fractions to distinguish independent samples.
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| PXD063145-sample rattus norvegicus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available PIN1APPLE4Controlgroup proteomic profiling by mass spectrometry PIN1APPLE4Controlgroup.raw 1 54 AC=MS:1002038;NT=label free sample NT=Orbitrap Exploris 480;AC=MS:1003028 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=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=vertebrates;VV=v1.1.0 | ||
| PXD063145-sample rattus norvegicus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available PIN1APPLE5Controlgroup proteomic profiling by mass spectrometry PIN1APPLE5Controlgroup.raw 1 55 AC=MS:1002038;NT=label free sample NT=Orbitrap Exploris 480;AC=MS:1003028 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=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=vertebrates;VV=v1.1.0 | ||
| PXD063145-sample rattus norvegicus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available PIN1APPLE6Controlgroup proteomic profiling by mass spectrometry PIN1APPLE6Controlgroup.raw 1 56 AC=MS:1002038;NT=label free sample NT=Orbitrap Exploris 480;AC=MS:1003028 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=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=vertebrates;VV=v1.1.0 | ||
| PXD063145-sample rattus norvegicus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available checksum.txt proteomic profiling by mass spectrometry checksum.txt 1 57 AC=MS:1002038;NT=label free sample NT=Orbitrap Exploris 480;AC=MS:1003028 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=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=vertebrates;VV=v1.1.0 |
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12. Checksum becomes a rat assay 🐞 Bug ≡ Correctness
PXD063145 assigns checksum.txt as an Orbitrap assay with fraction identifier 57. The checksum manifest is consequently exposed as a proteomics acquisition alongside the actual .raw files.
Agent Prompt
## Issue description
PXD063145 represents the checksum manifest as a mass-spectrometry acquisition.
## Fix Focus Areas
- datasets/PXD063145/PXD063145.sdrf.tsv[58-58]
## Recommended Fix
Remove the `checksum.txt` row from the SDRF.
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| PXD064792-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available 2 Å not available not available r1_BCOR_A_ITD_INPUT.mzXML proteomic profiling by mass spectrometry r1_BCOR_A_ITD_INPUT.mzXML 1 1 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Velos;AC=MS:1001742 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=formaldehyde;AC=XLMOD:02006 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=vertebrates;VV=v1.1.0 | ||
| PXD064792-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available 2 Å not available not available r1_BCOR_A_ITD_INPUT proteomic profiling by mass spectrometry r1_BCOR_A_ITD_INPUT.raw 1 2 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Velos;AC=MS:1001742 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=formaldehyde;AC=XLMOD:02006 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=vertebrates;VV=v1.1.0 | ||
| PXD064792-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available 2 Å not available not available r1_BCOR_A_ITD_IP.mzXML proteomic profiling by mass spectrometry r1_BCOR_A_ITD_IP.mzXML 1 3 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Velos;AC=MS:1001742 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=formaldehyde;AC=XLMOD:02006 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=vertebrates;VV=v1.1.0 | ||
| PXD064792-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available 2 Å not available not available r1_BCOR_A_ITD_IP proteomic profiling by mass spectrometry r1_BCOR_A_ITD_IP.raw 1 4 AC=MS:1002038;NT=label free sample NT=LTQ Orbitrap Velos;AC=MS:1001742 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=formaldehyde;AC=XLMOD:02006 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=vertebrates;VV=v1.1.0 |
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13. Mouse conditions collapse into fractions 🐞 Bug ≡ Correctness
PXD064792 gives the A/C, mutant/wild-type, input/IP, and run-1/run-2 groups one source and biological replicate while changing only fraction identifiers. Those experimental conditions and replicates are therefore represented as fractions of one mouse sample.
Agent Prompt
## Issue description
PXD064792 collapses distinct experimental conditions and runs into one artificial fraction series.
## Fix Focus Areas
- datasets/PXD064792/PXD064792.sdrf.tsv[2-33]
## Recommended Fix
Assign source names, biological replicates, and factor values that distinguish A/C, ITD/WT, INPUT/IP, and r1/r2 groups; reserve fraction identifiers for actual fractions of one sample.
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Code review by qodo was updated up to the latest commit f4d908f |
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SDRF change report50 new · 0 modified · 0 deleted · highest risk: none
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| Dataset | Rows | Defects |
|---|---|---|
| PXD060322 | 63 | no_factor_value: 1 |
| PXD060638 | 29 | no_factor_value: 1 |
| PXD060825 | 18 | no_factor_value: 1 |
| PXD061125 | 31 | no_factor_value: 1 |
| PXD061317 | 14 | no_factor_value: 1 |
| PXD061540 | 27 | no_factor_value: 1 |
| PXD061541 | 43 | no_factor_value: 1 |
| PXD061560 | 35 | no_factor_value: 1 |
| PXD061563 | 50 | no_factor_value: 1 |
| PXD061564 | 27 | no_factor_value: 1 |
| PXD061566 | 27 | no_factor_value: 1 |
| PXD061687 | 16 | no_factor_value: 1 |
| PXD061691 | 32 | no_factor_value: 1 |
| PXD061712 | 37 | no_factor_value: 1 |
| PXD061752 | 11 | no_factor_value: 1 |
| PXD062101 | 15 | no_factor_value: 1 |
| PXD062203 | 4 | no_factor_value: 1 |
| PXD062293 | 10 | no_factor_value: 1 |
| PXD062479 | 40 | no_factor_value: 1 |
| PXD062557 | 42 | no_factor_value: 1 |
| PXD062741 | 44 | no_factor_value: 1 |
| PXD062870 | 8 | no_factor_value: 1 |
| PXD063033 | 28 | no_factor_value: 1 |
| PXD063145 | 57 | no_factor_value: 1 |
| PXD063191 | 21 | no_factor_value: 1 |
| PXD063192 | 12 | no_factor_value: 1 |
| PXD063709 | 1 | no_factor_value: 1 |
| PXD063736 | 10 | no_factor_value: 1 |
| PXD063825 | 37 | no_factor_value: 1 |
| PXD063839 | 18 | no_factor_value: 1 |
| PXD063858 | 12 | no_factor_value: 1 |
| PXD063968 | 1 | no_factor_value: 1 |
| PXD064535 | 18 | no_factor_value: 1 |
| PXD064557 | 29 | no_factor_value: 1 |
| PXD064792 | 32 | no_factor_value: 1, peak_list_data_file: 16 |
| PXD064931 | 5 | no_factor_value: 1 |
| PXD064932 | 5 | no_factor_value: 1 |
| PXD065410 | 10 | no_factor_value: 1 |
| PXD065739 | 16 | no_factor_value: 1 |
| PXD065858 | 18 | no_factor_value: 1 |
| PXD065859 | 9 | no_factor_value: 1 |
| PXD065869 | 24 | no_factor_value: 1 |
| PXD065870 | 11 | no_factor_value: 1 |
| PXD065871 | 18 | no_factor_value: 1 |
| PXD066067 | 1 | no_factor_value: 1 |
| PXD066251 | 3 | no_factor_value: 1 |
| PXD066655 | 12 | no_factor_value: 1 |
| PXD069219 | 2 | no_factor_value: 1 |
| PXD069360 | 2 | no_factor_value: 1 |
| PXD069844 | 33 | no_factor_value: 1 |
Advisory report built from 9d493af. Risk labels do not block merging.
4 tasks
comment[sdrf template] declared NT=invertebrates;VV=v1.1.0 (an animal-only template) for 2 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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Part of the crosslinking proteomics SDRF annotation effort (splits PR #537 into batches of 50). Adds 50 new datasets in flat
datasets/<accession>/layout. Accessions: PXD060322,PXD060638,PXD060825,PXD061125,PXD061317,PXD061540,PXD061541,PXD061560,PXD061563,PXD061564,PXD061566,PXD061687,PXD061691,PXD061712,PXD061752,PXD062101,PXD062203,PXD062293,PXD062479,PXD062557,PXD062741,PXD062870,PXD063033,PXD063145,PXD063191,PXD063192,PXD063709,PXD063736,PXD063825,PXD063839,PXD063858,PXD063968,PXD064535,PXD064557,PXD064792,PXD064931,PXD064932,PXD065410,PXD065739,PXD065858,PXD065859,PXD065869,PXD065870,PXD065871,PXD066067,PXD066251,PXD066655,PXD069219,PXD069360,PXD069844