Add crosslinking proteomics SDRF annotations (batch 13/15, 50 datasets) - #551
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PR Summary by QodoAdd batch 13 crosslinking proteomics SDRF annotations
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Code Review by Qodo
1. Cattle samples omit required breed
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![qodo-code-review[bot]](https://avatars.githubusercontent.com/in/484649?s=60&v=4){kind=small}
| PXD051971-sample saccharomyces cerevisiae not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available 20210519_H2A_H2B_Ubp10_DSBU_Trp_1.zhrm proteomic profiling by mass spectrometry 20210519_H2A_H2B_Ubp10_DSBU_Trp_1.zhrm 1 2 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSBU;AC=XLMOD:02043;CL=yes;TA=K,S,T,Y,nterm;MH=85.05;ML=111.03 not available not available the 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 | ||
| PXD051971-sample saccharomyces cerevisiae not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available 20210519_H2A_H2B_Ubp10_DSBU_Trp_2 proteomic profiling by mass spectrometry 20210519_H2A_H2B_Ubp10_DSBU_Trp_2.raw 1 3 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSBU;AC=XLMOD:02043;CL=yes;TA=K,S,T,Y,nterm;MH=85.05;ML=111.03 not available not available the 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 | ||
| PXD051971-sample saccharomyces cerevisiae not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available 20210519_H2A_H2B_Ubp10_DSBU_Trp_2.zhrm proteomic profiling by mass spectrometry 20210519_H2A_H2B_Ubp10_DSBU_Trp_2.zhrm 1 4 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSBU;AC=XLMOD:02043;CL=yes;TA=K,S,T,Y,nterm;MH=85.05;ML=111.03 not available not available the 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 | ||
| PXD051971-sample saccharomyces cerevisiae not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available 20210519_H2A_H2B_Ubp10_EDC_Trp_1 proteomic profiling by mass spectrometry 20210519_H2A_H2B_Ubp10_EDC_Trp_1.raw 1 5 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSBU;AC=XLMOD:02043;CL=yes;TA=K,S,T,Y,nterm;MH=85.05;ML=111.03 not available not available the 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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2. Edc assays are annotated as dsbu 📘 Rule violation ≡ Correctness
The EDC-named assay rows in PXD051971 assign the DSBU term NT=DSBU;AC=XLMOD:02043, target residues, and mass values as their cross-linker parameters. This mismatch affects EDC Trp, Ubiq, GluC, and GC assays and their associated files, exposing parameters for a different cross-linking reaction to downstream searches.
Agent Prompt
## Issue description
PXD051971 assigns DSBU chemistry, including its ontology term, target residues, and mass values, to runs explicitly identified as EDC experiments.
## Fix Focus Areas
- datasets/PXD051971/PXD051971.sdrf.tsv[6-67]
## Recommended Fix
Identify every EDC row and replace the DSBU cross-linker term, DSBU-specific mass values, and target attributes with the correct EDC annotation supported by the study metadata. Retain DSBU only for assays whose archive names and evidence identify DSBU.
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| source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] 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] | |||
| PXD051971-sample saccharomyces cerevisiae not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available 20210519_H2A_H2B_Ubp10_DSBU_Trp_1 proteomic profiling by mass spectrometry 20210519_H2A_H2B_Ubp10_DSBU_Trp_1.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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSBU;AC=XLMOD:02043;CL=yes;TA=K,S,T,Y,nterm;MH=85.05;ML=111.03 not available not available the 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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3. Yeast assay rows have invalid metadata 📘 Rule violation ≡ Correctness
Eight added SDRFs populate comment[quenching reagent] with unsupported fragments or generic terms such as the, by, of, solution, and media, while PXD051971 and PXD053636 also pair Saccharomyces cerevisiae with the animal-specific invertebrates template. The malformed annotations repeat across the affected assays—including APEX2, PhoX, and DSSO runs—and, for the two yeast accessions, their associated result-file rows, with the sole PXD053607 assay reaching the canonical dataset unchanged.
Agent Prompt
## Issue description
Eight datasets place sentence fragments or generic terms such as `the`, `by`, `of`, `solution`, and `media` in `comment[quenching reagent]`; PXD051971 and PXD053636 additionally assign yeast samples to the invertebrates template.
## Fix Focus Areas
- datasets/PXD051971/PXD051971.sdrf.tsv[2-71]
- datasets/PXD052310/PXD052310.sdrf.tsv[2-52]
- datasets/PXD052930/PXD052930.sdrf.tsv[2-49]
- datasets/PXD053578/PXD053578.sdrf.tsv[2-47]
- datasets/PXD053607/PXD053607.sdrf.tsv[2-2]
- datasets/PXD053636/PXD053636.sdrf.tsv[2-35]
- datasets/PXD053984/PXD053984.sdrf.tsv[2-23]
- datasets/PXD054551/PXD054551.sdrf.tsv[2-36]
## Recommended Fix
Replace every malformed quenching-reagent value with the actual archive-supported reagent and applicable ontology mapping based on study evidence, or use `not available` when no reagent can be established. For PXD051971 and PXD053636, remove the invertebrates template and select the repository-supported fungal or yeast template when applicable, then validate every SDRF row and associated result-file row.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
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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] | |||
| PXD052801-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 062123_cell_lines_DIA_24mz_HEK293_1.mzML proteomic profiling by mass spectrometry 062123_cell_lines_DIA_24mz_HEK293_1.mzML 1 1 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=PIR;AC=XLMOD:02014 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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4. Cell-line acquisitions are mislabeled 📘 Rule violation ≡ Correctness
The comment[proteomics data acquisition method] values in PXD052801, PXD052821, PXD052867, and PXD053509 declare Data-dependent acquisition even though the corresponding assay, raw-file, or quantitative-file names identify DIA or SpDIA runs. The conflict affects the HEK293, HeLa, Lumos, and added quantitative-file rows, causing consumers of the acquisition-method field to classify independent-acquisition experiments as dependent-acquisition data.
Agent Prompt
## Issue description
Four datasets contain files identified by assay, raw-file, or quantitative-file names as DIA or SpDIA runs, but their SDRF acquisition-method fields annotate them as data-dependent acquisitions.
## Fix Focus Areas
- datasets/PXD052801/PXD052801.sdrf.tsv[2-16]
- datasets/PXD052821/PXD052821.sdrf.tsv[2-19]
- datasets/PXD052867/PXD052867.sdrf.tsv[3-40]
- datasets/PXD053509/PXD053509.sdrf.tsv[2-35]
## Recommended Fix
Replace the data-dependent acquisition mapping with the repository's supported data-independent acquisition ontology mapping for each row confirmed by its filename as a DIA or SpDIA run. Limit the update to confirmed DIA or SpDIA rows and verify every changed mapping against the public archive metadata.
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| PXD054720-sample escherichia coli not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available ABRF_iPRG_XL_2023.fasta proteomic profiling by mass spectrometry ABRF_iPRG_XL_2023.fasta 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98 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 | ||
| PXD054720-sample escherichia coli not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available F001234.mzid.gz proteomic profiling by mass spectrometry F001234.mzid.gz 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98 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 | ||
| PXD054720-sample escherichia coli not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available F001235.mzid.gz proteomic profiling by mass spectrometry F001235.mzid.gz 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98 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 | ||
| PXD054720-sample escherichia coli not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available F001236.mzid.gz proteomic profiling by mass spectrometry F001236.mzid.gz 1 7 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98 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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5. Ancillary files become acquisition assays 📘 Rule violation ≡ Correctness
Multiple SDRFs map FASTA databases, identification results, checksums, spreadsheets, archives, and documents into both assay name and comment[data file] instead of limiting those fields to deposited raw-category runs. Whenever these ancillary files are included, each is treated as a separate proteomics acquisition assay, creating nonexistent experimental runs and incorrect sample-to-run relationships alongside the actual raw files.
Agent Prompt
## Issue description
Several SDRFs incorrectly represent support, database, result, checksum, spreadsheet, archive, and document files as independent mass-spectrometry acquisition assays rather than limiting assay rows to deposited experimental run files.
## Fix Focus Areas
- datasets/PXD051047/PXD051047.sdrf.tsv[71-71]
- datasets/PXD051348/PXD051348.sdrf.tsv[47-47]
- datasets/PXD051971/PXD051971.sdrf.tsv[66-71]
- datasets/PXD052310/PXD052310.sdrf.tsv[50-52]
- datasets/PXD052694/PXD052694.sdrf.tsv[3-24]
- datasets/PXD052926/PXD052926.sdrf.tsv[26-26]
- datasets/PXD053636/PXD053636.sdrf.tsv[3-34]
- datasets/PXD054720/PXD054720.sdrf.tsv[5-10]
## Recommended Fix
Remove rows whose data-file values are ancillary files rather than deposited experimental runs. Retain one row per valid selected-format run, preserve the correct relationships to the raw acquisitions, and verify that every retained run maps to its correct sample.
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| PXD051261-sample streptococcus pyogenes mgas315 not applicable not applicable not applicable 1 synthetic reference not available not available not available not available DT_M2109_366 proteomic profiling by mass spectrometry DT_M2109_366.raw 1 64 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 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 | ||
| PXD051261-sample streptococcus pyogenes mgas315 not applicable not applicable not applicable 1 synthetic reference not available not available not available not available DT_M2109_367 proteomic profiling by mass spectrometry DT_M2109_367.raw 1 65 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 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 | ||
| PXD051261-sample streptococcus pyogenes mgas315 not applicable not applicable not applicable 1 synthetic reference not available not available not available not available MSinjection_rawfile_to_biological_sample_information.csv proteomic profiling by mass spectrometry MSinjection_rawfile_to_biological_sample_information.csv 1 66 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 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 | ||
| PXD051261-sample streptococcus pyogenes mgas315 not applicable not applicable not applicable 1 synthetic reference not available not available not available not available P_2S_tPA_1mM_DSS_1_DT_C2203_101 proteomic profiling by mass spectrometry P_2S_tPA_1mM_DSS_1_DT_C2203_101.raw 1 67 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 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 |
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6. Known crosslinkers become unknown 🐞 Bug ≡ Correctness
PXD051261 assigns NT=unknown crosslinker;AC=XLMOD:00000 to files whose names explicitly identify DSS and DSG. The mismatch affects both reagent groups and prevents consumers from selecting the corresponding crosslinking chemistry.
Agent Prompt
## Issue description
PXD051261 marks DSS and DSG runs as using an unknown crosslinker even though their filenames identify the reagents.
## Fix Focus Areas
- datasets/PXD051261/PXD051261.sdrf.tsv[68-99]
## Recommended Fix
Replace the unknown-crosslinker values on DSS and DSG rows with the appropriate XLMOD terms and reagent-specific metadata, using archive evidence to separate the two groups.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
…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).
Contributor
SDRF change report50 new · 0 modified · 0 deleted · highest risk: none External reviewer notesQuoted from AI review bots on this PR. Not verified by this report unless marked as also flagged.
New datasets (50)parse_sdrf validation of new datasets is reported by the SDRF review gate check.
Advisory report built from 4311088. Risk labels do not block merging. |
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| source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[developmental stage] 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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1. Cattle samples omit required breed 🐞 Bug ≡ Correctness
The PXD052552 and PXD052694 headers declare the vertebrates template but omit characteristics[strain or breed] between their sample characteristics. Every added Bos taurus and Mus musculus row therefore lacks the required field and cannot record breed or strain information, even with the reserved not available value.
Agent Prompt
## Issue description
The PXD052552 and PXD052694 vertebrate SDRFs omit the required `characteristics[strain or breed]` column and corresponding row values.
## Fix Focus Areas
- datasets/PXD052552/PXD052552.sdrf.tsv[1-21]
- datasets/PXD052694/PXD052694.sdrf.tsv[1-25]
## Recommended Fix
Add `characteristics[strain or breed]` to each header alongside the other organism characteristics and add a value to every row. Use `not available` when the cattle breed or mouse strain is unknown.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
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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] | |||
| PXD053010-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 11.4 Å not available not available Zou_Rappsilber_AC_NF90-NF45-RNA_EDC_S1_R1 proteomic profiling by mass spectrometry Zou_Rappsilber_AC_NF90-NF45-RNA_EDC_S1_R1.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=EDC;AC=XLMOD:02009;CL=no;TA=K,D,E not available not available using 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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2. Edc runs are indexed as diazirine 🐞 Bug ≡ Correctness
PXD053010 labels every EDC-named assay as NT=EDC but assigns AC=XLMOD:02009, an accession the repository associates with NT=diazirine. All 19 added EDC assay rows therefore expose diazirine chemistry to consumers filtering or interpreting cross-linker annotations.
Agent Prompt
## Issue description
PXD053010 assigns the diazirine accession `XLMOD:02009` to assays explicitly identified as EDC, so downstream consumers receive the wrong cross-linker identity.
## Fix Focus Areas
- datasets/PXD053010/PXD053010.sdrf.tsv[2-20]
## Recommended Fix
Replace the cross-linker annotation in every PXD053010 row with the validated XLMOD accession and associated attributes for EDC. Recheck the linked cross-link distance and target-residue metadata so they describe the corrected reagent consistently.
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Code review by qodo was updated up to the latest commit 2f4ccff |
comment[sdrf template] declared NT=invertebrates;VV=v1.1.0 (an animal-only template) for 3 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: PXD051014,PXD051047,PXD051143,PXD051261,PXD051348,PXD051405,PXD051493,PXD051557,PXD051602,PXD051693,PXD051742,PXD051886,PXD051971,PXD052310,PXD052552,PXD052623,PXD052624,PXD052637,PXD052687,PXD052694,PXD052745,PXD052746,PXD052801,PXD052821,PXD052825,PXD052867,PXD052917,PXD052923,PXD052926,PXD052930,PXD053010,PXD053341,PXD053452,PXD053489,PXD053494,PXD053509,PXD053578,PXD053607,PXD053636,PXD053760,PXD053832,PXD053924,PXD053984,PXD054003,PXD054140,PXD054141,PXD054249,PXD054551,PXD054616,PXD054720