Add crosslinking proteomics SDRF annotations (batch 12/15, 50 datasets)

[ypriverol]

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: PXD046413,PXD046414,PXD046472,PXD046634,PXD046754,PXD046990,PXD047023,PXD047030,PXD047274,PXD047277,PXD047368,PXD047378,PXD047422,PXD047455,PXD047547,PXD047569,PXD047725,PXD047929,PXD048046,PXD048145,PXD048174,PXD048180,PXD048194,PXD048297,PXD048298,PXD048452,PXD048567,PXD048614,PXD048625,PXD048632,PXD048897,PXD048937,PXD048965,PXD049047,PXD049094,PXD049182,PXD049372,PXD049433,PXD049681,PXD049684,PXD049689,PXD049991,PXD050097,PXD050493,PXD050556,PXD050824,PXD050833,PXD050928,PXD050929,PXD050930

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⛔ Files ignored due to path filters (50)

• datasets/PXD046413/PXD046413.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD046414/PXD046414.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD046472/PXD046472.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD046634/PXD046634.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD046754/PXD046754.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD046990/PXD046990.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD047023/PXD047023.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD047030/PXD047030.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD047274/PXD047274.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD047277/PXD047277.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD047368/PXD047368.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD047378/PXD047378.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD047422/PXD047422.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD047455/PXD047455.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD047547/PXD047547.sdrf.tsv is excluded by !**/*.tsv
• datasets/PXD047569/PXD047569.sdrf.tsv is excluded by !**/*.tsv
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[qodo-code-review]

PR Summary by Qodo

Add batch 12 crosslinking proteomics SDRF annotations

✨ Enhancement 🐞 Bug fix 📝 Documentation 🕐 40+ Minutes

AI Description

• Adds SDRF annotations for 50 crosslinking proteomics datasets in flat accession directories.
• Supplies required organism-template fields using spec-compliant unavailable values.
• Corrects PXD047023 acquisition instrument metadata to Bruker timsTOF Pro.

Diagram

graph TD
  A["PRIDE datasets"] --> B["Accession directories"] --> C["SDRF annotations"] --> D["Crosslink template"] --> E["Metadata consumers"]
  C --> F["Organism templates"]

Loading

High-Level Assessment

The accession-local, flat-file approach matches the repository’s dataset organization and keeps each annotation independently reviewable. Splitting the larger annotation effort into 50-dataset batches is preferable to one monolithic change; generating shared metadata would reduce repetition but would obscure accession-specific provenance and complicate downstream consumption.

Files changed (50) +1209 / -0

Enhancement (49) +1183 / -0

PXD046413.sdrf.tsvAdd PXD046413 BioID SDRF annotation +11/-0

Add PXD046413 BioID SDRF annotation

• Adds 10 human BioID assay annotations with Q Exactive HF acquisition metadata and human, crosslinking, and proteomics template declarations.

datasets/PXD046413/PXD046413.sdrf.tsv

PXD046414.sdrf.tsvAdd PXD046414 BioID SDRF annotation +11/-0

Add PXD046414 BioID SDRF annotation

• Adds 10 human BioID assay annotations with source-file, instrument, digestion, modification, and template metadata.

datasets/PXD046414/PXD046414.sdrf.tsv

PXD046472.sdrf.tsvAdd PXD046472 TurboID SDRF annotation +8/-0

Add PXD046472 TurboID SDRF annotation

• Adds seven human TurboID assay annotations for Q Exactive HF data under the human and crosslinking templates.

datasets/PXD046472/PXD046472.sdrf.tsv

PXD046634.sdrf.tsvAdd PXD046634 DSSO SDRF annotation +23/-0

Add PXD046634 DSSO SDRF annotation

• Adds 22 Chlorobium tepidum entries describing Orbitrap Fusion acquisition and DSSO crosslinking metadata.

datasets/PXD046634/PXD046634.sdrf.tsv

PXD046754.sdrf.tsvAdd PXD046754 mouse SDRF annotation +21/-0

Add PXD046754 mouse SDRF annotation

• Adds 20 mouse assay and supporting-file entries with the required developmental-stage field and vertebrate template declaration.

datasets/PXD046754/PXD046754.sdrf.tsv

PXD046990.sdrf.tsvAdd PXD046990 DSBU SDRF annotation +4/-0

Add PXD046990 DSBU SDRF annotation

• Adds three human Orbitrap Eclipse assays annotated with the DSBU crosslinker and crosslinking distance.

datasets/PXD046990/PXD046990.sdrf.tsv

PXD047030.sdrf.tsvAdd PXD047030 mouse SDRF annotation +5/-0

Add PXD047030 mouse SDRF annotation

• Adds four mouse crosslinking entries with 6220 TOF acquisition metadata and the required vertebrate developmental-stage field.

datasets/PXD047030/PXD047030.sdrf.tsv

PXD047274.sdrf.tsvAdd PXD047274 bacterial SDRF annotation +71/-0

Add PXD047274 bacterial SDRF annotation

• Adds 70 Staphylococcus aureus assay and supporting-file entries with Orbitrap Fusion acquisition metadata.

datasets/PXD047274/PXD047274.sdrf.tsv

PXD047277.sdrf.tsvAdd PXD047277 APEX2 SDRF annotation +13/-0

Add PXD047277 APEX2 SDRF annotation

• Adds 12 human APEX2 assays acquired on an Orbitrap Exploris 480 with crosslinking template metadata.

datasets/PXD047277/PXD047277.sdrf.tsv

PXD047368.sdrf.tsvAdd PXD047368 BS3 SDRF annotation +11/-0

Add PXD047368 BS3 SDRF annotation

• Adds 10 Mycobacterium tuberculosis entries describing Orbitrap Fusion Lumos acquisition and BS3 crosslinking.

datasets/PXD047368/PXD047368.sdrf.tsv

PXD047378.sdrf.tsvAdd PXD047378 APEX2 SDRF annotation +6/-0

Add PXD047378 APEX2 SDRF annotation

• Adds five human APEX2 dataset entries with LTQ Orbitrap Elite acquisition and template metadata.

datasets/PXD047378/PXD047378.sdrf.tsv

PXD047422.sdrf.tsvAdd PXD047422 viral DSSO annotation +101/-0

Add PXD047422 viral DSSO annotation

• Adds 100 human alphaherpesvirus assay and supporting-file entries with Orbitrap Fusion Lumos and DSSO metadata.

datasets/PXD047422/PXD047422.sdrf.tsv

PXD047455.sdrf.tsvAdd PXD047455 BioID SDRF annotation +20/-0

Add PXD047455 BioID SDRF annotation

• Adds 19 human BioID entries for timsTOF Pro 2 acquisition, including raw runs and processed results.

datasets/PXD047455/PXD047455.sdrf.tsv

PXD047547.sdrf.tsvAdd PXD047547 human SDRF annotation +3/-0

Add PXD047547 human SDRF annotation

• Adds two human Q Exactive HF crosslinking assay annotations with source-file and template metadata.

datasets/PXD047547/PXD047547.sdrf.tsv

PXD047569.sdrf.tsvAdd PXD047569 mouse TurboID annotation +94/-0

Add PXD047569 mouse TurboID annotation

• Adds 93 mouse TurboID assay and archive entries and supplies the required developmental-stage field for the vertebrate template.

datasets/PXD047569/PXD047569.sdrf.tsv

PXD047725.sdrf.tsvAdd PXD047725 TurboID SDRF annotation +37/-0

Add PXD047725 TurboID SDRF annotation

• Adds 36 human TurboID assays covering multiple experimental conditions and Q Exactive acquisition.

datasets/PXD047725/PXD047725.sdrf.tsv

PXD047929.sdrf.tsvAdd PXD047929 BS3 SDRF annotation +13/-0

Add PXD047929 BS3 SDRF annotation

• Adds 12 human Orbitrap Fusion Lumos assays annotated with BS3 crosslinking and fraction identifiers.

datasets/PXD047929/PXD047929.sdrf.tsv

PXD048046.sdrf.tsvAdd PXD048046 TurboID SDRF annotation +28/-0

Add PXD048046 TurboID SDRF annotation

• Adds 27 human TurboID assays with LTQ Orbitrap Velos acquisition and standardized proteomics metadata.

datasets/PXD048046/PXD048046.sdrf.tsv

PXD048145.sdrf.tsvAdd PXD048145 bacterial SDRF annotation +12/-0

Add PXD048145 bacterial SDRF annotation

• Adds 11 Escherichia coli RNA-crosslinking assays acquired on an Orbitrap Exploris 480.

datasets/PXD048145/PXD048145.sdrf.tsv

PXD048174.sdrf.tsvAdd PXD048174 TurboID SDRF annotation +15/-0

Add PXD048174 TurboID SDRF annotation

• Adds 14 human TurboID assays acquired on an Orbitrap Fusion Lumos across RCC4 experimental groups.

datasets/PXD048174/PXD048174.sdrf.tsv

PXD048180.sdrf.tsvAdd PXD048180 BioID SDRF annotation +12/-0

Add PXD048180 BioID SDRF annotation

• Adds 11 human BioID assays and controls acquired on an Orbitrap Fusion Lumos.

datasets/PXD048180/PXD048180.sdrf.tsv

PXD048194.sdrf.tsvAdd PXD048194 yeast DSSO annotation +9/-0

Add PXD048194 yeast DSSO annotation

• Adds eight Saccharomyces cerevisiae DSSO assays and supplies required developmental-stage and strain-or-breed fields as not available.

datasets/PXD048194/PXD048194.sdrf.tsv

PXD048297.sdrf.tsvAdd PXD048297 DMP SDRF annotation +7/-0

Add PXD048297 DMP SDRF annotation

• Adds six human Q Exactive HF-X assays annotated with DMP crosslinking metadata.

datasets/PXD048297/PXD048297.sdrf.tsv

PXD048298.sdrf.tsvAdd PXD048298 DMP SDRF annotation +13/-0

Add PXD048298 DMP SDRF annotation

• Adds 12 human DMP crosslinking assays covering CAS9 and MAGE4 knockout conditions.

datasets/PXD048298/PXD048298.sdrf.tsv

PXD048452.sdrf.tsvAdd PXD048452 sulfo-SDA annotation +55/-0

Add PXD048452 sulfo-SDA annotation

• Adds 54 Bos taurus assays with sulfo-SDA crosslinking, Orbitrap Fusion Lumos acquisition, and vertebrate developmental-stage metadata.

datasets/PXD048452/PXD048452.sdrf.tsv

PXD048567.sdrf.tsvAdd PXD048567 human SDRF annotation +92/-0

Add PXD048567 human SDRF annotation

• Adds 91 human Q Exactive HF crosslinking assay annotations with sequential fraction and source-file mappings.

datasets/PXD048567/PXD048567.sdrf.tsv

PXD048614.sdrf.tsvAdd PXD048614 mouse SDRF annotation +7/-0

Add PXD048614 mouse SDRF annotation

• Adds six mouse crosslinking entries for paired mzXML and raw Orbitrap Eclipse files, including the required developmental-stage field.

datasets/PXD048614/PXD048614.sdrf.tsv

PXD048625.sdrf.tsvAdd PXD048625 DSS SDRF annotation +3/-0

Add PXD048625 DSS SDRF annotation

• Adds two human Q Exactive assays annotated with DSS crosslinking and a 30 Å distance.

datasets/PXD048625/PXD048625.sdrf.tsv

PXD048632.sdrf.tsvAdd PXD048632 human SDRF annotation +65/-0

Add PXD048632 human SDRF annotation

• Adds 64 human Q Exactive HF assays spanning heat-stress, muscle, and neuron-specific experimental groups.

datasets/PXD048632/PXD048632.sdrf.tsv

PXD048897.sdrf.tsvAdd PXD048897 Cricetulus SDRF annotation +17/-0

Add PXD048897 Cricetulus SDRF annotation

• Adds 16 Cricetulus assay and result-file entries for multiple digestion conditions acquired on an LTQ XL.

datasets/PXD048897/PXD048897.sdrf.tsv

PXD048937.sdrf.tsvAdd PXD048937 TurboID SDRF annotation +7/-0

Add PXD048937 TurboID SDRF annotation

• Adds six human TurboID assays covering ACSS2 and control replicates on an LTQ Orbitrap Elite.

datasets/PXD048937/PXD048937.sdrf.tsv

PXD048965.sdrf.tsvAdd PXD048965 TurboID SDRF annotation +2/-0

Add PXD048965 TurboID SDRF annotation

• Adds one human TurboID assay annotation with LTQ Orbitrap Elite acquisition metadata.

datasets/PXD048965/PXD048965.sdrf.tsv

PXD049047.sdrf.tsvAdd PXD049047 diazirine annotation +10/-0

Add PXD049047 diazirine annotation

• Adds nine human Q Exactive assays annotated with diazirine crosslinking across UV and fraction conditions.

datasets/PXD049047/PXD049047.sdrf.tsv

PXD049094.sdrf.tsvAdd PXD049094 BS3 SDRF annotation +4/-0

Add PXD049094 BS3 SDRF annotation

• Adds three human Q Exactive HF assays with BS3 crosslinking and 30 Å distance metadata.

datasets/PXD049094/PXD049094.sdrf.tsv

PXD049182.sdrf.tsvAdd PXD049182 viral BioID annotation +16/-0

Add PXD049182 viral BioID annotation

• Adds 15 Hepacivirus BioID assay and supporting-file entries with Q Exactive acquisition metadata.

datasets/PXD049182/PXD049182.sdrf.tsv

PXD049372.sdrf.tsvAdd PXD049372 Drosophila TurboID annotation +30/-0

Add PXD049372 Drosophila TurboID annotation

• Adds 29 Drosophila melanogaster TurboID assay and supporting-file entries. Required developmental-stage and strain-or-breed values are recorded as not available.

datasets/PXD049372/PXD049372.sdrf.tsv

PXD049433.sdrf.tsvAdd PXD049433 TurboID SDRF annotation +19/-0

Add PXD049433 TurboID SDRF annotation

• Adds 18 human TurboID pool and immunoprecipitation assays acquired on a Q Exactive HF.

datasets/PXD049433/PXD049433.sdrf.tsv

PXD049681.sdrf.tsvAdd PXD049681 BioID SDRF annotation +17/-0

Add PXD049681 BioID SDRF annotation

• Adds 16 human BioID assays acquired on an Orbitrap Fusion Lumos with standardized digestion and modification metadata.

datasets/PXD049681/PXD049681.sdrf.tsv

PXD049684.sdrf.tsvAdd PXD049684 BioID SDRF annotation +58/-0

Add PXD049684 BioID SDRF annotation

• Adds 57 human BioID assays covering ADAR variants, controls, and treatment conditions on an Orbitrap Fusion Lumos.

datasets/PXD049684/PXD049684.sdrf.tsv

PXD049689.sdrf.tsvAdd PXD049689 BioID SDRF annotation +31/-0

Add PXD049689 BioID SDRF annotation

• Adds 30 human BioID assays covering ADAR variants and interferon conditions on an Orbitrap Fusion Lumos.

datasets/PXD049689/PXD049689.sdrf.tsv

PXD049991.sdrf.tsvAdd PXD049991 timsTOF BioID annotation +47/-0

Add PXD049991 timsTOF BioID annotation

• Adds 46 human BioID assay and supporting-file entries acquired on a timsTOF Pro.

datasets/PXD049991/PXD049991.sdrf.tsv

PXD050097.sdrf.tsvAdd PXD050097 Xenopus BS3 annotation +11/-0

Add PXD050097 Xenopus BS3 annotation

• Adds 10 Xenopus laevis BS3 assays and supplies the developmental-stage field required by the vertebrate template.

datasets/PXD050097/PXD050097.sdrf.tsv

PXD050493.sdrf.tsvAdd PXD050493 bacterial SDRF annotation +29/-0

Add PXD050493 bacterial SDRF annotation

• Adds 28 Escherichia coli crosslinking assays covering UV, pH, and oligomeric-state conditions on an Orbitrap Fusion Lumos.

datasets/PXD050493/PXD050493.sdrf.tsv

PXD050556.sdrf.tsvAdd PXD050556 TurboID SDRF annotation +5/-0

Add PXD050556 TurboID SDRF annotation

• Adds four human TurboID archive entries for in-vitro and in-vivo LTQ Orbitrap spectra.

datasets/PXD050556/PXD050556.sdrf.tsv

PXD050824.sdrf.tsvAdd PXD050824 BioID SDRF annotation +9/-0

Add PXD050824 BioID SDRF annotation

• Adds eight human BioID assays acquired on an Orbitrap Fusion with standardized crosslinking metadata.

datasets/PXD050824/PXD050824.sdrf.tsv

PXD050833.sdrf.tsvAdd PXD050833 PDAC SDRF annotation +61/-0

Add PXD050833 PDAC SDRF annotation

• Adds 60 human Q Exactive HF assays spanning normal and PDAC cellular and extracellular-matrix fractions.

datasets/PXD050833/PXD050833.sdrf.tsv

PXD050928.sdrf.tsvAdd PXD050928 yeast DSS annotation +40/-0

Add PXD050928 yeast DSS annotation

• Adds 39 Saccharomyces cerevisiae DSS assay and analysis-file entries with required developmental-stage and strain-or-breed placeholders.

datasets/PXD050928/PXD050928.sdrf.tsv

PXD050929.sdrf.tsvPopulate PXD050929 yeast DSS annotation +0/-0

Populate PXD050929 yeast DSS annotation

• Replaces the placeholder content with 101 Saccharomyces cerevisiae DSS assay and analysis-file annotations. The file includes required invertebrate-template developmental-stage and strain-or-breed fields.

datasets/PXD050929/PXD050929.sdrf.tsv

PXD050930.sdrf.tsvPopulate PXD050930 yeast DMTMM annotation +0/-0

Populate PXD050930 yeast DMTMM annotation

• Replaces the placeholder content with 101 Saccharomyces cerevisiae DMTMM assay and analysis-file annotations, including an 11.4 Å distance and required template fields.

datasets/PXD050930/PXD050930.sdrf.tsv

Bug fix (1) +26 / -0

PXD047023.sdrf.tsvAdd corrected PXD047023 timsTOF annotation +26/-0

Add corrected PXD047023 timsTOF annotation

• Adds 25 Schizosaccharomyces pombe TurboID entries. All runs are assigned to the Bruker timsTOF Pro instead of the previously inferred Q Exactive instrument.

datasets/PXD047023/PXD047023.sdrf.tsv

[qodo-code-review]

Code Review by Qodo

🐞 Bugs (9) 📘 Rule violations (6) 📜 Skill insights (0)

⚠️ 20 lower-priority findings omitted to fit the comment size limit; re-run the review or view the findings in the Qodo portal.

1. Converted files duplicate three runs 📘 Rule violation ≡ Correctness ⭐ New

Description

Rows 2–7 assign each of three run stems one .mzXML assay and one corresponding .raw assay, each
with a different fraction identifier. Treating a converted derivative and its source file as
separate measurements doubles the acquisition count from three to six.

Code

datasets/PXD048614/PXD048614.sdrf.tsv[R2-5]

+PXD048614-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	20231227_Buchner_Crosslink_01.mzXML	proteomic profiling by mass spectrometry	20231227_Buchner_Crosslink_01.mzXML	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	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=vertebrates;VV=v1.1.0
+PXD048614-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	20231227_Buchner_Crosslink_01	proteomic profiling by mass spectrometry	20231227_Buchner_Crosslink_01.raw	1	2	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	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=vertebrates;VV=v1.1.0
+PXD048614-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	20231227_Buchner_Crosslink_02.mzXML	proteomic profiling by mass spectrometry	20231227_Buchner_Crosslink_02.mzXML	1	3	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	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=vertebrates;VV=v1.1.0
+PXD048614-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	20231227_Buchner_Crosslink_02	proteomic profiling by mass spectrometry	20231227_Buchner_Crosslink_02.raw	1	4	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	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=vertebrates;VV=v1.1.0

Evidence

Rule 5 requires assay and replicate relationships to be supported rather than inferred. The cited
rows repeat the same three run stems in .mzXML and .raw form but assign every representation a
distinct assay and fraction.

AGENTS.md: Do Not Fabricate Dataset Relationships or Identifiers
datasets/PXD048614/PXD048614.sdrf.tsv[2-7]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
Three converted files and their corresponding source files are modeled as six independent fractions rather than three acquisitions.

## Fix Focus Areas
- datasets/PXD048614/PXD048614.sdrf.tsv[2-7]

## Recommended Fix
Model each `.mzXML` and matching `.raw` pair as one archive-supported acquisition relationship, avoiding separate assay or fraction identifiers for converted derivatives.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

2. Yeast samples carry an animal template ✓ Resolved 📘 Rule violation ≡ Correctness ⭐ New

Description

Each row identifies the organism as saccharomyces cerevisiae while selecting
NT=invertebrates;VV=v1.1.0 in the organism-specific template column. The mismatch applies across
the accession whenever fungal metadata is interpreted through that animal layer.

Code

datasets/PXD050929/PXD050929.sdrf.tsv[2]

+PXD050929-sample	saccharomyces cerevisiae	not applicable	not applicable	not applicable	not available	not available	1	synthetic	reference	not available	30 Å	not available	not available	221111_QE1_ulianaf_YB_03_01.c.mzXML	proteomic profiling by mass spectrometry	221111_QE1_ulianaf_YB_03_01.c.mzXML	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=DSS;AC=XLMOD:02001	not available	not available	NH3HCO3	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

Evidence

Rule 4 requires template layers to match the dataset. The cited row simultaneously declares
saccharomyces cerevisiae and the organism-specific invertebrates layer, demonstrating the
mismatch repeated throughout the file.

AGENTS.md: Use Template-Appropriate Ontology Terms and Columns
datasets/PXD050929/PXD050929.sdrf.tsv[1-2]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
A fungal dataset declares the organism-specific invertebrates template, which is intended for animal samples.

## Fix Focus Areas
- datasets/PXD050929/PXD050929.sdrf.tsv[2-102]

## Recommended Fix
Remove the invertebrates template from every row and retain only template layers appropriate for Saccharomyces cerevisiae and this crosslinking proteomics dataset.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

3. Six runs name the wrong labeling enzyme 🐞 Bug ≡ Correctness ⭐ New

Description

The first six assay and raw-file names identify BioID or BirA, while comment[cross-linker] assigns
TurboID. Those runs are consequently grouped under a different labeling enzyme from the one encoded
in their deposited identifiers.

Code

datasets/PXD049372/PXD049372.sdrf.tsv[R2-3]

+PXD049372-sample	drosophila melanogaster	not applicable	not applicable	not applicable	not available	not available	1	synthetic	reference	not available	not available	not available	not available	20160208_QexHF2_RSLC8_RumpfKienzl_Dammermann_MFPL_onbead_BioID_BirA_SDS_5per	proteomic profiling by mass spectrometry	20160208_QexHF2_RSLC8_RumpfKienzl_Dammermann_MFPL_onbead_BioID_BirA_SDS_5per.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=TurboID;AC=XLMOD:02251	not available	not available	1	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
+PXD049372-sample	drosophila melanogaster	not applicable	not applicable	not applicable	not available	not available	1	synthetic	reference	not available	not available	not available	not available	20160208_QexHF2_RSLC8_RumpfKienzl_Dammermann_MFPL_onbead_BioID_Sas4_SDS_5per	proteomic profiling by mass spectrometry	20160208_QexHF2_RSLC8_RumpfKienzl_Dammermann_MFPL_onbead_BioID_Sas4_SDS_5per.raw	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	cross-linking mass spectrometry	NT=TurboID;AC=XLMOD:02251	not available	not available	1	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

Evidence

Lines 2–3 explicitly contain BioID and BirA in both assay and data-file names but assign
NT=TurboID;AC=XLMOD:02251; additional BirA-named runs through line 7 receive the same assignment,
whereas lines 8 onward explicitly name TurboID.

datasets/PXD049372/PXD049372.sdrf.tsv[2-8]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
The first six BioID/BirA runs are annotated with the TurboID controlled term.

## Fix Focus Areas
- datasets/PXD049372/PXD049372.sdrf.tsv[2-7]

## Recommended Fix
Replace TurboID with the accession-supported BioID controlled term on the BioID/BirA rows, while retaining TurboID on runs whose identifiers and source metadata actually describe TurboID.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

View high (13)

4. Figure archives become fake assays 📘 Rule violation ≡ Correctness ⭐ New

Description

Rows 2–5 of PXD047030.sdrf.tsv map Fig1.zip, Fig2.zip, Fig3.zip, and Fig9.zip to distinct
assay names and fractions while supplying complete 6220 Time-of-Flight acquisition metadata. Because
these archives contain figures rather than acquired mass-spectrometry data, consumers counting the
declared measurements encounter four unsupported sample-to-assay and fraction relationships instead
of mappings to the deposited acquisition files.

Code

datasets/PXD047030/PXD047030.sdrf.tsv[R2-5]

+PXD047030-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	Fig1.zip	proteomic profiling by mass spectrometry	Fig1.zip	1	1	AC=MS:1002038;NT=label free sample	NT=6220 Time-of-Flight LC/MS;AC=MS:1000675	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
+PXD047030-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	Fig2.zip	proteomic profiling by mass spectrometry	Fig2.zip	1	2	AC=MS:1002038;NT=label free sample	NT=6220 Time-of-Flight LC/MS;AC=MS:1000675	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
+PXD047030-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	Fig3.zip	proteomic profiling by mass spectrometry	Fig3.zip	1	3	AC=MS:1002038;NT=label free sample	NT=6220 Time-of-Flight LC/MS;AC=MS:1000675	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
+PXD047030-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	Fig9.zip	proteomic profiling by mass spectrometry	Fig9.zip	1	4	AC=MS:1002038;NT=label free sample	NT=6220 Time-of-Flight LC/MS;AC=MS:1000675	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

Evidence

Every cited data row names a Fig*.zip archive in both the assay and data-file columns, assigns it
a separate fraction, and supplies instrument and data-dependent acquisition metadata. This conflicts
with Rule 5 and the repository instructions, which require raw filenames and sample-to-assay
relationships to be supported by archive evidence and prohibit fabricated filenames or
relationships.

AGENTS.md: Do Not Fabricate Dataset Relationships or Identifiers
datasets/PXD047030/PXD047030.sdrf.tsv[2-5]
datasets/PXD047030/PXD047030.sdrf.tsv[1-5]
AGENTS.md[24-31]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
Figure archives are annotated as acquisition data files and assigned assay, instrument, and fraction metadata, exposing them as measured mass-spectrometry runs with unsupported relationships.

## Fix Focus Areas
- datasets/PXD047030/PXD047030.sdrf.tsv[2-5]

## Recommended Fix
Remove the `Fig*.zip` rows and replace them with mappings for the accession's actual acquired mass-spectrometry files, using only archive-supported assay and fraction relationships. If the acquisition files cannot be identified, do not invent assay coordinates from figure archives; keep the accession out of the canonical dataset directory until valid mappings can be established.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

5. Three sample groups become one sample 🐞 Bug ≡ Correctness ⭐ New

Description

Heat-stress, muscle, and neuron assays all use PXD048632-sample, biological replicate 1, and no
characteristic or factor that records the group. Their explicitly named replicate groups are
therefore represented as fractions of one source rather than distinct experimental samples.

Code

datasets/PXD048632/PXD048632.sdrf.tsv[14]

+PXD048632-sample	homo sapiens	not applicable	not applicable	not applicable	not available	not applicable	1	synthetic	reference	not available	not available	not available	not available	HSP90-muscle-replicate1-1	proteomic profiling by mass spectrometry	HSP90-muscle-replicate1-1.raw	1	13	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=human;VV=v1.1.0

Evidence

Lines 2, 14, and 24 identify heat-stress, muscle, and neuron runs respectively, but each has the
same source and biological-replicate metadata. The run names also explicitly distinguish replicate 1
and replicate 2 while the biological-replicate column never changes.

datasets/PXD048632/PXD048632.sdrf.tsv[2-14]
datasets/PXD048632/PXD048632.sdrf.tsv[24-25]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
Heat-stress, muscle, and neuron assay groups are all assigned to one source and biological replicate.

## Fix Focus Areas
- datasets/PXD048632/PXD048632.sdrf.tsv[2-65]

## Recommended Fix
Create source names and biological-replicate mappings for each documented heat-stress, muscle, and neuron sample, and encode the group in the appropriate characteristic or factor column while retaining true fractions under each source.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

6. Runs name the wrong instrument model 🐞 Bug ≡ Correctness ⭐ New

Description

Rows whose assay and data-file names contain Exploris1 assign Orbitrap Fusion ETD as the
instrument. This mismatch affects every Exploris-identified run from line 47 onward, causing
instrument-based searches and analyses to classify those acquisitions incorrectly.

Code

datasets/PXD047569/PXD047569.sdrf.tsv[47]

+PXD047569-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	20201009_Exploris1_SA_DZ028_MR10_E-T_T5C1_1	proteomic profiling by mass spectrometry	20201009_Exploris1_SA_DZ028_MR10_E-T_T5C1_1.raw	1	46	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion ETD;AC=MS:1002417	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

Evidence

The first affected row names both the assay and raw file 20201009_Exploris1... while assigning the
distinct Orbitrap Fusion ETD controlled term; the same pairing continues through later Exploris
runs.

datasets/PXD047569/PXD047569.sdrf.tsv[47-55]
datasets/PXD047569/PXD047569.sdrf.tsv[80-88]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
Runs whose assay and data-file names identify an Exploris instrument are annotated as Orbitrap Fusion ETD.

## Fix Focus Areas
- datasets/PXD047569/PXD047569.sdrf.tsv[47-94]

## Recommended Fix
Determine the exact Exploris model from the accession's public acquisition metadata and replace the Orbitrap Fusion ETD term on all Exploris-identified rows, preserving any genuinely Fusion-acquired rows.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

7. Knockout and control become one sample 🐞 Bug ≡ Correctness ⭐ New

Description

source name and characteristics[biological replicate] remain PXD048297-sample and 1 for both
CAS9_MAGE4 and MAGEKO_MAGE4 assays. The two cell conditions and their A–C replicates therefore
have no sample-level field by which consumers can distinguish them.

Code

datasets/PXD048297/PXD048297.sdrf.tsv[5]

+PXD048297-sample	homo sapiens	not applicable	not applicable	not applicable	not available	not applicable	1	synthetic	reference	not available	not available	not available	not available	HFX1445_IPP251_AN_A375_MAGEKO_MAGE4_A	proteomic profiling by mass spectrometry	HFX1445_IPP251_AN_A375_MAGEKO_MAGE4_A.raw	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	cross-linking mass spectrometry	NT=DMP;AC=XLMOD:02003	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

Evidence

Lines 2–4 identify CAS9 assays and lines 5–7 identify MAGEKO assays, but all six rows use the
identical source name and biological-replicate value. Repository instructions explicitly prohibit
fabricated sample relationships and require alignment with archive metadata.

datasets/PXD048297/PXD048297.sdrf.tsv[2-7]
AGENTS.md[37-40]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
Distinct CAS9 and MAGE knockout conditions are mapped to one source and biological replicate.

## Fix Focus Areas
- datasets/PXD048297/PXD048297.sdrf.tsv[2-7]

## Recommended Fix
Create condition-specific source names and map the A–C runs to their correct biological replicates, adding an appropriate factor or characteristic column for the CAS9 versus knockout condition when supported by the accession metadata.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

8. A number replaces the quench reagent 🐞 Bug ≡ Correctness ⭐ New

Description

comment[quenching reagent] contains the bare value 1 on every PXD049372 row rather than a
reagent or an unavailable sentinel. The malformed protocol value reaches all raw acquisitions as
well as the already-reported auxiliary-file rows.

Code

datasets/PXD049372/PXD049372.sdrf.tsv[2]

+PXD049372-sample	drosophila melanogaster	not applicable	not applicable	not applicable	not available	not available	1	synthetic	reference	not available	not available	not available	not available	20160208_QexHF2_RSLC8_RumpfKienzl_Dammermann_MFPL_onbead_BioID_BirA_SDS_5per	proteomic profiling by mass spectrometry	20160208_QexHF2_RSLC8_RumpfKienzl_Dammermann_MFPL_onbead_BioID_BirA_SDS_5per.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=TurboID;AC=XLMOD:02251	not available	not available	1	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

Evidence

The header orders crosslink enrichment, crosslinker concentration, quenching reagent, reduction
reagent, and alkylation reagent in that sequence. Each data row supplies not available, `not
available, 1, not available, and not available, placing 1` specifically in the
quenching-reagent field.

datasets/PXD049372/PXD049372.sdrf.tsv[1-3]
datasets/PXD049372/PXD049372.sdrf.tsv[24-30]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
Every row places the numeric value `1` in the quenching-reagent column.

## Fix Focus Areas
- datasets/PXD049372/PXD049372.sdrf.tsv[2-30]

## Recommended Fix
Replace `1` with the accession-supported quenching reagent, or use the specification-compliant unavailable sentinel when no quenching reagent is documented.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

9. Data-independent runs use wrong method 🐞 Bug ≡ Correctness ⭐ New

Description

PXD049689.sdrf.tsv declares NT=Data-dependent acquisition for every file whose assay and
data-file name explicitly contains DIA. All thirty records will consequently be classified as
data-dependent rather than data-independent acquisitions by users of the acquisition-method field.

Code

datasets/PXD049689/PXD049689.sdrf.tsv[R2-4]

+PXD049689-sample	homo sapiens	not applicable	not applicable	not applicable	not available	not applicable	1	synthetic	reference	not available	not available	not available	not available	4834_Lumos1_DIA_74min-400_850_20W_01_GFP_R1_NT_01	proteomic profiling by mass spectrometry	4834_Lumos1_DIA_74min-400_850_20W_01_GFP_R1_NT_01.raw	1	1	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion Lumos;AC=MS:1002732	NT=Data-dependent acquisition;AC=PRIDE:0000449	NT=Trypsin;AC=MS:1001251	NT=Lys-C;AC=MS:1001309	NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed	NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable	NT=HCD;AC=PRIDE:0000590	not available	not available	not available	not available	cross-linking mass spectrometry	NT=BioID;AC=XLMOD:02250	not available	not available	not available	not available	not available	v1.1.0	NT=ms-proteomics;VV=v1.1.0	NT=crosslinking;VV=v1.0.0	NT=human;VV=v1.1.0
+PXD049689-sample	homo sapiens	not applicable	not applicable	not applicable	not available	not applicable	1	synthetic	reference	not available	not available	not available	not available	4834_Lumos1_DIA_74min-400_850_20W_02_GFP_R2_NT_01	proteomic profiling by mass spectrometry	4834_Lumos1_DIA_74min-400_850_20W_02_GFP_R2_NT_01.raw	1	2	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion Lumos;AC=MS:1002732	NT=Data-dependent acquisition;AC=PRIDE:0000449	NT=Trypsin;AC=MS:1001251	NT=Lys-C;AC=MS:1001309	NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed	NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable	NT=HCD;AC=PRIDE:0000590	not available	not available	not available	not available	cross-linking mass spectrometry	NT=BioID;AC=XLMOD:02250	not available	not available	not available	not available	not available	v1.1.0	NT=ms-proteomics;VV=v1.1.0	NT=crosslinking;VV=v1.0.0	NT=human;VV=v1.1.0
+PXD049689-sample	homo sapiens	not applicable	not applicable	not applicable	not available	not applicable	1	synthetic	reference	not available	not available	not available	not available	4834_Lumos1_DIA_74min-400_850_20W_03_GFP_R3_NT_01	proteomic profiling by mass spectrometry	4834_Lumos1_DIA_74min-400_850_20W_03_GFP_R3_NT_01.raw	1	3	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion Lumos;AC=MS:1002732	NT=Data-dependent acquisition;AC=PRIDE:0000449	NT=Trypsin;AC=MS:1001251	NT=Lys-C;AC=MS:1001309	NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed	NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable	NT=HCD;AC=PRIDE:0000590	not available	not available	not available	not available	cross-linking mass spectrometry	NT=BioID;AC=XLMOD:02250	not available	not available	not available	not available	not available	v1.1.0	NT=ms-proteomics;VV=v1.1.0	NT=crosslinking;VV=v1.0.0	NT=human;VV=v1.1.0

Evidence

Each row uses DIA in both its assay and raw-file identifier while the method column consistently
declares Data-dependent acquisition. This is a direct contradiction within the newly added SDRF
rather than an inference from an external source.

datasets/PXD049689/PXD049689.sdrf.tsv[1-31]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
All run names explicitly identify DIA acquisition, but their `comment[proteomics data acquisition method]` values declare data-dependent acquisition.

## Fix Focus Areas
- datasets/PXD049689/PXD049689.sdrf.tsv[2-31]

## Recommended Fix
Replace the data-dependent acquisition annotation on every DIA row with the correct data-independent acquisition ontology annotation, preserving the existing assay and raw-file mappings.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

10. Treatment and control become one sample 🐞 Bug ≡ Correctness ⭐ New

Description

The ACSS2 and control runs all share PXD048937-sample, biological replicate 1, and no factor
column describing treatment status. The six assays are consequently modeled only as fractions of one
source, losing the treatment/control comparison and the replicate identities encoded in their names.

Code

datasets/PXD048937/PXD048937.sdrf.tsv[5]

+PXD048937-sample	homo sapiens	not applicable	not applicable	not applicable	not available	not applicable	1	synthetic	reference	not available	not available	not available	not available	ctrl-1	proteomic profiling by mass spectrometry	ctrl-1.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	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=human;VV=v1.1.0

Evidence

Lines 2–4 name ACSS2-1 through ACSS2-3 and lines 5–7 name ctrl-1 through ctrl-3, while all rows
retain the same source and biological replicate and differ only by fraction identifier.

datasets/PXD048937/PXD048937.sdrf.tsv[2-7]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
Three ACSS2 runs and three control runs are represented as fractions of one source with one biological-replicate value.

## Fix Focus Areas
- datasets/PXD048937/PXD048937.sdrf.tsv[2-7]

## Recommended Fix
Map ACSS2-1 through ACSS2-3 and ctrl-1 through ctrl-3 to their actual source and biological-replicate identities, and add the accession-supported treatment factor so consumers can recover the comparison.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

11. A modifier replaces the quench reagent 📘 Rule violation ≡ Correctness ⭐ New

Description

The comment[quenching reagent] column in PXD048145.sdrf.tsv contains only the incomplete
modifier final rather than an identifiable reagent or an allowed unavailable sentinel. This
affects every listed acquisition, including the RNA UV rows, leaving consumers with unusable
quenching-protocol metadata.

Code

datasets/PXD048145/PXD048145.sdrf.tsv[2]

+PXD048145-sample	escherichia coli	not applicable	not applicable	not applicable	1	synthetic	reference	not available	not available	not available	not available	RNA_DEB_Ecoli_S30_LB_bRPfrac_8.mzML	proteomic profiling by mass spectrometry	RNA_DEB_Ecoli_S30_LB_bRPfrac_8.mzML	1	1	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	chemical cross-linking coupled with mass spectrometry proteomics	NT=unknown crosslinker;AC=XLMOD:00000	not available	not available	final	not available	not available	v1.1.0	NT=ms-proteomics;VV=v1.1.0	NT=crosslinking;VV=v1.0.0

Evidence

Rule 4 requires values compatible with the selected template, and the header places
comment[quenching reagent] after the crosslinker concentration column. Every cited row contains
final in that exact position, which does not identify a reagent, while other repository SDRFs use
an actual reagent such as Tris-HCl in the same column.

AGENTS.md: Use Template-Appropriate Ontology Terms and Columns
datasets/PXD048145/PXD048145.sdrf.tsv[1-12]
datasets/PXD020859/PXD020859-sv-only-bs3.sdrf.tsv[1-2]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
The `comment[quenching reagent]` column contains the prose fragment `final` in every row rather than a reagent or a valid unavailable sentinel.

## Fix Focus Areas
- datasets/PXD048145/PXD048145.sdrf.tsv[2-12]

## Recommended Fix
Replace `final` with the documented, archive-supported quenching reagent using the template-supported representation. If the archive does not establish the reagent, use the spec-compliant `not available` sentinel consistently.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

12. Four conditions become one sample 🐞 Bug ≡ Correctness ⭐ New

Description

source name and characteristics[biological replicate] are identical across the CAS9/MAGE4,
CAS9/WT1, knockout/MAGE4, and knockout/WT1 assay groups. Consumers consequently cannot recover
either experimental dimension or associate the a–c runs with their correct condition-specific
samples.

Code

datasets/PXD048298/PXD048298.sdrf.tsv[5]

+PXD048298-sample	homo sapiens	not applicable	not applicable	not applicable	not available	not applicable	1	synthetic	reference	not available	not available	not available	not available	HFX0109b_IPP222_ROCHE_A375_CAS9_WT1_a	proteomic profiling by mass spectrometry	HFX0109b_IPP222_ROCHE_A375_CAS9_WT1_a.raw	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	cross-linking mass spectrometry	NT=DMP;AC=XLMOD:02003	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

Evidence

Representative rows at lines 2, 5, 8, and 11 identify four different assay groups, yet every row
carries PXD048298-sample and biological replicate 1.

datasets/PXD048298/PXD048298.sdrf.tsv[2-5]
datasets/PXD048298/PXD048298.sdrf.tsv[8-13]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
Four distinct knockout/control and target groups are collapsed into one source and one biological replicate.

## Fix Focus Areas
- datasets/PXD048298/PXD048298.sdrf.tsv[2-13]

## Recommended Fix
Assign condition-specific source names, map the a–c runs to their actual biological replicates, and add supported factor or characteristic columns that preserve both the cell condition and MAGE4/WT1 grouping.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

13. Result archives become fake assays 📘 Rule violation ≡ Correctness ⭐ New

Description

Rows 89–94 assign six .rar result and proximity archives separate assay names, fraction
identifiers, and Orbitrap acquisition metadata. When archive bundles are enumerated alongside the
preceding raw files, the dataset gains six unsupported instrument measurements.

Code

datasets/PXD047569/PXD047569.sdrf.tsv[R89-92]

+PXD047569-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	DZ013-EZH2_lines_whole_proteome.rar	proteomic profiling by mass spectrometry	DZ013-EZH2_lines_whole_proteome.rar	1	88	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion ETD;AC=MS:1002417	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
+PXD047569-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	DZ016-RNF2_proximity.rar	proteomic profiling by mass spectrometry	DZ016-RNF2_proximity.rar	1	89	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion ETD;AC=MS:1002417	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
+PXD047569-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	DZ028-EZH2_proximity_EB.rar	proteomic profiling by mass spectrometry	DZ028-EZH2_proximity_EB.rar	1	90	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion ETD;AC=MS:1002417	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
+PXD047569-sample	mus musculus	not applicable	not applicable	not applicable	not available	1	synthetic	reference	not available	not available	not available	not available	DZ030-EZH2_GFP.rar	proteomic profiling by mass spectrometry	DZ030-EZH2_GFP.rar	1	91	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion ETD;AC=MS:1002417	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

Evidence

Rule 5 prohibits unsupported raw-file and sample relationships. The cited rows use .rar bundles
such as DZ013-EZH2_lines_whole_proteome.rar and DZ016-RNF2_proximity.rar as assays while copying
full acquisition metadata onto them.

AGENTS.md: Do Not Fabricate Dataset Relationships or Identifiers
datasets/PXD047569/PXD047569.sdrf.tsv[89-94]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
Result and proximity archives are represented as independent instrument assays with fabricated fraction relationships.

## Fix Focus Areas
- datasets/PXD047569/PXD047569.sdrf.tsv[89-94]

## Recommended Fix
Remove the archive-bundle rows and retain only archive-supported acquired mass-spectrometry files as assays, preserving only relationships established by the source metadata.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

14. Result archives appear as instrument runs 🐞 Bug ≡ Correctness ⭐ New

Description

PXD047023.sdrf.tsv places Rep*_result_*.zip archives in both assay name and `comment[data
file]` while copying timsTOF acquisition, digestion, and fragmentation metadata onto them. Whenever
consumers enumerate the SDRF data files, these six processed-result packages are counted alongside
the actual .d.zip raw acquisitions.

Code

datasets/PXD047023/PXD047023.sdrf.tsv[6]

+PXD047023-sample	schizosaccharomyces pombe strain spy73 975 h+	not applicable	not applicable	not applicable	1	synthetic	reference	not available	not available	not available	not available	Rep1_result_01-03-2022.zip	proteomic profiling by mass spectrometry	Rep1_result_01-03-2022.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

Evidence

The file explicitly distinguishes raw acquisition archives by raw_data and Bruker .d.zip names,
but assigns the same full acquisition metadata to the intervening result archives. Repository
guidance requires file mappings to align with archive metadata and prohibits fabricated sample/file
relationships.

datasets/PXD047023/PXD047023.sdrf.tsv[2-26]
AGENTS.md[24-31]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
Processed `Rep*_result_*.zip` archives are represented as mass-spectrometry assay/data-file rows even though the file names distinguish them from the neighboring `raw_data` acquisitions.

## Fix Focus Areas
- datasets/PXD047023/PXD047023.sdrf.tsv[6-26]

## Recommended Fix
Remove the rows whose `comment[data file]` values are `Rep*_result_*.zip`. Retain only the rows that map actual acquired raw files, and derive assay coordinates from those raw acquisitions.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

15. A fragment replaces all quench data 📘 Rule violation ≡ Correctness ⭐ New

Description

The comment[quenching reagent] field contains the isolated preposition by throughout the assay
table. All records therefore omit the actual reagent while appearing to provide
crosslinking-protocol metadata.

Code

datasets/PXD050930/PXD050930.sdrf.tsv[2]

+PXD050930-sample	saccharomyces cerevisiae	not applicable	not applicable	not applicable	not available	not available	1	synthetic	reference	not available	11.4 Å	not available	not available	230322_QE1_ulianaf_YB_03_02.c.mzXML	proteomic profiling by mass spectrometry	230322_QE1_ulianaf_YB_03_02.c.mzXML	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=DMTMM;AC=XLMOD:02015	not available	not available	by	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

Evidence

Rule 4 requires template-appropriate annotation values. The cited row places by in the
comment[quenching reagent] position, and the malformed value is repeated throughout the file.

AGENTS.md: Use Template-Appropriate Ontology Terms and Columns
datasets/PXD050930/PXD050930.sdrf.tsv[1-2]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
The quenching-reagent field contains the sentence fragment `by` instead of a reagent or reserved missing-value term.

## Fix Focus Areas
- datasets/PXD050930/PXD050930.sdrf.tsv[2-102]

## Recommended Fix
Replace `by` with the quenching reagent supported by the archive metadata, or use `not available` if no reagent can be established.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

16. An action replaces the quench reagent 📘 Rule violation ≡ Correctness ⭐ New

Description

The comment[quenching reagent] column contains the bare action word adding in every assay row.
All 27 records therefore expose a sentence fragment where consumers expect the reagent used by the
crosslinking protocol.

Code

datasets/PXD048046/PXD048046.sdrf.tsv[2]

+PXD048046-sample	homo sapiens	not applicable	not applicable	not applicable	not available	not applicable	1	synthetic	reference	not available	not available	not available	not available	02fev22_DaniG_PGK1-6_diluicao1_10	proteomic profiling by mass spectrometry	02fev22_DaniG_PGK1-6_diluicao1_10.raw	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=TurboID;AC=XLMOD:02251	not available	not available	adding	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

Evidence

Rule 4 requires template-appropriate annotation values. The cited assay rows place adding in
comment[quenching reagent], which neither identifies a reagent nor uses the reserved unavailable
value.

AGENTS.md: Use Template-Appropriate Ontology Terms and Columns
datasets/PXD048046/PXD048046.sdrf.tsv[1-28]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
The quenching-reagent column contains `adding`, which is an action fragment rather than a reagent or reserved missing-value term.

## Fix Focus Areas
- datasets/PXD048046/PXD048046.sdrf.tsv[2-28]

## Recommended Fix
Replace `adding` with the archive-supported quenching reagent using the template-supported representation, or use `not available` when the reagent cannot be established.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

---

Context sources

Review mode: 🧠 Deep: This batch adds 50 independently edited SDRF datasets with substantial metadata variation and an already demonstrated high density of subtle, easy-to-miss annotation defects.

Tip of the day

💡 Did you know, you can enable the Remediation agent and Qodo fixes findings in a dedicated fix PR

More tips ↗ | Customize Qodo ↗ | Qodo docs ↗

[qodo-code-review]

1. Ancillary files become fake assays 📘 Rule violation ≡ Correctness

The new SDRFs misuse comment[data file] by assigning checksums, sequence databases, archives,
spreadsheets, reports, documentation, and processed-result bundles their own assay and fraction
identifiers; in PXD047378, every row is such an auxiliary artifact labeled as an LTQ Orbitrap Elite
acquisition. Across the affected accessions, recognizable non-acquisition filenames trigger
unsupported sample-to-assay, technical-replicate, and fraction relationships, while PXD047378
exposes no individual acquired raw file and instead creates five assay coordinates for auxiliary
files.

Agent Prompt

## Issue description
Several new SDRFs represent checksum manifests, reference databases, documentation, spreadsheets, archives, and processed-result files as mass-spectrometry assays. PXD047378 consists entirely of auxiliary files represented as LTQ Orbitrap Elite acquisitions, and these artifacts do not support the sample-to-assay, replicate, and fraction relationships assigned to them.

## Fix Focus Areas
- datasets/PXD046634/PXD046634.sdrf.tsv[22-23]
- datasets/PXD046754/PXD046754.sdrf.tsv[18-21]
- datasets/PXD047274/PXD047274.sdrf.tsv[55-55]
- datasets/PXD047274/PXD047274.sdrf.tsv[66-67]
- datasets/PXD047368/PXD047368.sdrf.tsv[10-11]
- datasets/PXD047378/PXD047378.sdrf.tsv[2-6]
- datasets/PXD047422/PXD047422.sdrf.tsv[97-101]
- datasets/PXD047455/PXD047455.sdrf.tsv[20-20]
- datasets/PXD049182/PXD049182.sdrf.tsv[14-16]
- datasets/PXD049372/PXD049372.sdrf.tsv[26-30]

## Recommended Fix
Remove rows whose `comment[data file]` value is an ancillary, reference, documentation, checksum, archive, or processed-result artifact. Replace the PXD047378 rows with one row per actual raw acquisition contained in the deposit, retain only supported acquisition or accepted peak-list files elsewhere, and derive assay, replicate, and fraction relationships for those files from authoritative archive metadata.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

2. Database files become fake assays 🐞 Bug ≡ Correctness

Rows 22–23 assign a checksum and FASTA sequence database their own assay names, technical
coordinates, instrument, acquisition method, and digestion protocol. Consumers enumerating the
dataset's measurements therefore receive two nonexistent Orbitrap acquisitions alongside the real
raw runs.

Agent Prompt

## Issue description
Checksum and FASTA database files are represented as mass-spectrometry assays even though they are auxiliary dataset artifacts.

## Fix Focus Areas
- datasets/PXD046634/PXD046634.sdrf.tsv[22-23]

## Recommended Fix
Delete these auxiliary-file rows from the SDRF and retain only rows representing actual acquired mass-spectrometry runs.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

3. Analysis artifacts become fake runs 🐞 Bug ≡ Correctness

Rows 18–21 encode a MaxQuant archive, sample spreadsheet, checksum, and FASTA database as Q Exactive
acquisitions with digestion and fragmentation metadata. These four auxiliary artifacts consequently
appear as measured fractions and inflate the dataset's run count.

Agent Prompt

## Issue description
Four analysis and metadata artifacts are incorrectly represented as acquired mass-spectrometry runs.

## Fix Focus Areas
- datasets/PXD046754/PXD046754.sdrf.tsv[18-21]

## Recommended Fix
Remove the archive, spreadsheet, checksum, and FASTA rows, leaving only rows whose data files are actual acquired spectra.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

13. A fragment replaces the quench reagent 🐞 Bug ≡ Correctness

The comment[quenching reagent] value is the isolated word by in every PXD046990 row rather than
a reagent or an unavailable sentinel. All three runs therefore publish malformed
crosslinking-protocol metadata.

Agent Prompt

## Issue description
Every quenching-reagent cell contains the prose fragment `by` rather than valid protocol metadata.

## Fix Focus Areas
- datasets/PXD046990/PXD046990.sdrf.tsv[2-4]

## Recommended Fix
Replace `by` with the actual quenching reagent when known, otherwise use the repository's `not available` sentinel.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

4. Documents become measured acquisitions 🐞 Bug ≡ Correctness

Rows 66–67 encode a PDF document and a FASTA sequence database as Orbitrap acquisitions with
data-dependent acquisition and cleavage metadata. Downstream run inventories consequently include
documentation and a search database as measured samples.

Agent Prompt

## Issue description
A PDF and FASTA database are incorrectly represented as mass-spectrometry assay rows.

## Fix Focus Areas
- datasets/PXD047274/PXD047274.sdrf.tsv[66-67]

## Recommended Fix
Delete the auxiliary-file rows from the SDRF and keep only actual acquired spectral data files as assays.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

10. Reference files become extra runs 🐞 Bug ≡ Correctness

Rows 26–30 encode FASTA databases, a checksum, an experimental-design spreadsheet, and a FragPipe
output archive as Q Exactive HF-X acquisitions. Downstream users therefore receive five auxiliary
artifacts as measured assay fractions.

Agent Prompt

## Issue description
Reference databases, metadata, and result artifacts are represented as mass-spectrometry acquisitions.

## Fix Focus Areas
- datasets/PXD049372/PXD049372.sdrf.tsv[26-30]

## Recommended Fix
Remove rows 26–30 and keep only rows corresponding to actual acquired raw files.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

11. A spreadsheet becomes an extra run 🐞 Bug ≡ Correctness

Row 47 registers Search.file.xlsx as a timsTOF Pro acquisition with DDA, cleavage, and
fragmentation metadata. The search spreadsheet consequently appears as a forty-sixth measured
fraction.

Agent Prompt

## Issue description
A search spreadsheet is incorrectly represented as an acquired timsTOF run.

## Fix Focus Areas
- datasets/PXD049991/PXD049991.sdrf.tsv[47-47]

## Recommended Fix
Delete the spreadsheet row and retain only actual `.d.zip` acquisition rows.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

18. A fragment replaces the quench reagent 🐞 Bug ≡ Correctness

The comment[quenching reagent] field contains by in every PXD050824 row rather than a reagent or
unavailable sentinel. All eight BioID runs therefore publish malformed crosslinking-protocol
metadata.

Agent Prompt

## Issue description
Every quenching-reagent cell contains the prose fragment `by` instead of valid protocol metadata.

## Fix Focus Areas
- datasets/PXD050824/PXD050824.sdrf.tsv[2-9]

## Recommended Fix
Replace `by` with the actual quenching reagent when known, otherwise use `not available` in every row.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

12. Twenty-three artifacts become assays 🐞 Bug ≡ Correctness

Rows 18–40 represent a FASTA database, spreadsheets, CSV results, checksum, analysis script,
definition files, and search-result XML files as Q Exactive acquisitions. These auxiliary files
create 23 nonexistent measured fractions and carry copied digestion and fragmentation metadata.

Agent Prompt

## Issue description
Twenty-three database, result, script, and configuration artifacts are represented as acquired Q Exactive runs.

## Fix Focus Areas
- datasets/PXD050928/PXD050928.sdrf.tsv[18-40]

## Recommended Fix
Delete rows 18–40 and retain only the sixteen actual `.mzXML` acquisition rows.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[github-actions]

SDRF change report

50 new · 0 modified · 0 deleted · highest risk: none

⚠️ Needs attention

Backed by this report's own checks of the SDRF data: high-risk changes and AI reviewer findings the data confirms.

• PXD047023 · Result archives appear as instrument runs: non-acquisition data files: Rep1_result_01-03-2022.zip, Rep2_result_05-04-2022.zip, Rep3_result_25-04-2022.zip (qodo-code-review[bot])
• PXD047368 · Results files become measured runs: non-acquisition data files: Bpa-HspR_BS3_XLs.xlsx, checksum.txt (qodo-code-review[bot])
• PXD047422 · Result tables become extra assays: non-acquisition data files: APMS_HA_UL12_MAPK8mut_txt.7z, APMS_HA_UL47_DDB1mut_txt.7z, APMS_HA_UL49_PP1mut_txt.7z (qodo-code-review[bot])
• PXD047455 · A result table becomes an assay: non-acquisition data files: wp-esf_537_esf4_diann_directdia_20231130_psms_filt.csv (qodo-code-review[bot])
• PXD048897 · Text results become extra acquisitions: non-acquisition data files: DTpreFchymotrypsin.txt, DTpreFpepsin.txt, DTpreFtrypsin.txt (qodo-code-review[bot])
• PXD049182 · Search outputs become fake acquisitions: non-acquisition data files: 180824_CK_HB_BioID2_HCV.pdResult, BioID2_181212.blib, checksum.txt (qodo-code-review[bot])
• PXD049991 · A spreadsheet becomes an extra run: non-acquisition data files: Search.file.xlsx (qodo-code-review[bot])

External reviewer notes

Quoted from AI review bots on this PR. Not verified by this report unless marked as also flagged.

• PXD047023 · qodo-code-review[bot]: Result archives appear as instrument runs. PXD047023.sdrf.tsv places Rep*result*.zip archives in both assay name and comment[data file] while copying timsTOF acquisition, digestion, and fragmentation metadata onto them. (source) · ✓ confirmed by data: non-acquisition data files: Rep1_result_01-03-2022.zip, Rep2_result_05-04-2022.zip, Rep3_result_25-04-2022.zip
• PXD047368 · qodo-code-review[bot]: Results files become measured runs. Rows 10–11 register a crosslink-results spreadsheet and checksum as Orbitrap Fusion Lumos acquisitions with complete MS protocol metadata. Consumers consequently see two additional measurements that were never instrument acquisitions. (source) · ✓ confirmed by data: non-acquisition data files: Bpa-HspR_BS3_XLs.xlsx, checksum.txt
• PXD047422 · qodo-code-review[bot]: Result tables become extra assays. Rows 96–100 encode a text-results archive, raw-file key, and crosslink result CSVs as Orbitrap Fusion Lumos acquisitions. The dataset's assay list is therefore inflated by five analysis outputs carrying copied acquisition metadata. (source) · ✓ confirmed by data: non-acquisition data files: APMS_HA_UL12_MAPK8mut_txt.7z, APMS_HA_UL47_DDB1mut_txt.7z, APMS_HA_UL49_PP1mut_txt.7z
• PXD047455 · qodo-code-review[bot]: A result table becomes an assay. Row 20 registers a filtered peptide-spectrum-match CSV as a timsTOF acquisition with DDA and digestion metadata. Consumers consequently receive an analysis table as a nineteenth measured run. (source) · ✓ confirmed by data: non-acquisition data files: wp-esf_537_esf4_diann_directdia_20231130_psms_filt.csv
• PXD048897 · qodo-code-review[bot]: Text results become extra acquisitions. PXD048897 creates assay rows for each .txt result file and assigns them distinct fraction identifiers plus copied LTQ XL acquisition metadata. These rows duplicate the underlying experiments as nonexistent instrument runs and distort the dataset's run count. (source) · ✓ confirmed by data: non-acquisition data files: DTpreFchymotrypsin.txt, DTpreFpepsin.txt, DTpreFtrypsin.txt
• PXD049182 · qodo-code-review[bot]: Search outputs become fake acquisitions. Rows 14–16 register a Proteome Discoverer result, spectral library, and checksum as Q Exactive assays with copied acquisition metadata. These analysis artifacts consequently appear as three additional measured fractions. (source) · ✓ confirmed by data: non-acquisition data files: 180824_CK_HB_BioID2_HCV.pdResult, BioID2_181212.blib, checksum.txt
• PXD049991 · qodo-code-review[bot]: A spreadsheet becomes an extra run. Row 47 registers Search.file.xlsx as a timsTOF Pro acquisition with DDA, cleavage, and fragmentation metadata. The search spreadsheet consequently appears as a forty-sixth measured fraction. (source) · ✓ confirmed by data: non-acquisition data files: Search.file.xlsx
• PXD046634 · qodo-code-review[bot]: Database files become fake assays. Rows 22–23 assign a checksum and FASTA sequence database their own assay names, technical coordinates, instrument, acquisition method, and digestion protocol. (source)
• PXD046754 · qodo-code-review[bot]: Analysis artifacts become fake runs. Rows 18–21 encode a MaxQuant archive, sample spreadsheet, checksum, and FASTA database as Q Exactive acquisitions with digestion and fragmentation metadata. (source)
• PXD046990 · qodo-code-review[bot]: A fragment replaces the quench reagent. The comment[quenching reagent] value is the isolated word by in every PXD046990 row rather than a reagent or an unavailable sentinel. All three runs therefore publish malformed crosslinking-protocol metadata. (source)
• PXD047030 · qodo-code-review[bot]: Figure archives become fake assays. Rows 2–5 of PXD047030.sdrf.tsv map Fig1.zip , Fig2.zip , Fig3.zip , and Fig9.zip to distinct assay names and fractions while supplying complete 6220 Time-of-Flight acquisition metadata. (source)
• PXD047274 · qodo-code-review[bot]: Documents become measured acquisitions. Rows 66–67 encode a PDF document and a FASTA sequence database as Orbitrap acquisitions with data-dependent acquisition and cleavage metadata. Downstream run inventories consequently include documentation and a search database as measured samples. (source)
• PXD047378 · qodo-code-review[bot]: Ancillary files become fake assays. The new SDRFs misuse comment[data file] by assigning checksums, sequence databases, archives, spreadsheets, reports, documentation, and processed-result bundles their own assay and fraction identifiers; in PXD047378, every row is such an auxiliary artifact la… (source)
• PXD047569 · qodo-code-review[bot]: Runs name the wrong instrument model. Rows whose assay and data-file names contain Exploris1 assign Orbitrap Fusion ETD as the instrument. This mismatch affects every Exploris-identified run from line 47 onward, causing instrument-based searches and analyses to classify those acquisitions incorre… (source)
• PXD047569 · qodo-code-review[bot]: Result archives become fake assays. Rows 89–94 assign six .rar result and proximity archives separate assay names, fraction identifiers, and Orbitrap acquisition metadata. (source)
• PXD047725 · qodo-code-review[bot]: A fragment replaces all quench data. The comment[quenching reagent] field contains the isolated word using throughout PXD047725 rather than a reagent or sentinel. Every run in this dataset therefore carries malformed crosslinking-protocol metadata. (source)
• PXD048046 · qodo-code-review[bot]: An action replaces the quench reagent. The comment[quenching reagent] column contains the bare action word adding in every assay row. All 27 records therefore expose a sentence fragment where consumers expect the reagent used by the crosslinking protocol. (source)
• PXD048145 · qodo-code-review[bot]: A modifier replaces the quench reagent. The comment[quenching reagent] column in PXD048145.sdrf.tsv contains only the incomplete modifier final rather than an identifiable reagent or an allowed unavailable sentinel. (source)
• PXD048194 · qodo-code-review[bot]: Yeast is classified as an animal. PXD048194 identifies the organism as saccharomyces cerevisiae but declares the organism-specific SDRF template as invertebrates . All runs consequently advertise a taxonomic template that does not apply to their fungal source. (source)
• PXD048297 · qodo-code-review[bot]: Knockout and control become one sample. source name and characteristics[biological replicate] remain PXD048297-sample and 1 for both CAS9_MAGE4 and MAGEKO_MAGE4 assays. The two cell conditions and their A–C replicates therefore have no sample-level field by which consumers can distinguish them. (source)
• PXD048298 · qodo-code-review[bot]: Four conditions become one sample. source name and characteristics[biological replicate] are identical across the CAS9/MAGE4, CAS9/WT1, knockout/MAGE4, and knockout/WT1 assay groups. (source)
• PXD048614 · qodo-code-review[bot]: Converted files duplicate three runs. Rows 2–7 assign each of three run stems one .mzXML assay and one corresponding .raw assay, each with a different fraction identifier. Treating a converted derivative and its source file as separate measurements doubles the acquisition count from three to six. (source)
• PXD048632 · qodo-code-review[bot]: Three sample groups become one sample. Heat-stress, muscle, and neuron assays all use PXD048632-sample , biological replicate 1 , and no characteristic or factor that records the group. (source)
• PXD048897 · qodo-code-review[bot]: Enzyme metadata contradicts run names. PXD048897 declares Trypsin and Lys-C for runs whose assay and data-file names explicitly identify chymotrypsin or pepsin digestion. The incorrect cleavage metadata reaches both raw acquisitions and their paired result-file rows. (source)
• PXD048937 · qodo-code-review[bot]: Treatment and control become one sample. The ACSS2 and control runs all share PXD048937-sample , biological replicate 1 , and no factor column describing treatment status. The six assays are consequently modeled only as fractions of one source, losing the treatment/control comparison and the replica… (source)
• PXD048965 · qodo-code-review[bot]: An exploris run names the wrong model. The sole assay and raw-file identifier starts with Exploris04267 , but comment[instrument] declares an LTQ Orbitrap Elite. The dataset therefore publishes a different instrument family from the one explicitly encoded in its run identifier. (source)
• PXD049372 · qodo-code-review[bot]: Six runs name the wrong labeling enzyme. The first six assay and raw-file names identify BioID or BirA, while comment[cross-linker] assigns TurboID. Those runs are consequently grouped under a different labeling enzyme from the one encoded in their deposited identifiers. (source)
• PXD049372 · qodo-code-review[bot]: A number replaces the quench reagent. comment[quenching reagent] contains the bare value 1 on every PXD049372 row rather than a reagent or an unavailable sentinel. The malformed protocol value reaches all raw acquisitions as well as the already-reported auxiliary-file rows. (source)
• PXD049372 · qodo-code-review[bot]: Reference files become extra runs. Rows 26–30 encode FASTA databases, a checksum, an experimental-design spreadsheet, and a FragPipe output archive as Q Exactive HF-X acquisitions. Downstream users therefore receive five auxiliary artifacts as measured assay fractions. (source)
• PXD049689 · qodo-code-review[bot]: Data-independent runs use wrong method. PXD049689.sdrf.tsv declares NT=Data-dependent acquisition for every file whose assay and data-file name explicitly contains DIA . All thirty records will consequently be classified as data-dependent rather than data-independent acquisitions by users of the ac… (source)
• PXD050824 · qodo-code-review[bot]: A fragment replaces the quench reagent. The comment[quenching reagent] field contains by in every PXD050824 row rather than a reagent or unavailable sentinel. All eight BioID runs therefore publish malformed crosslinking-protocol metadata. (source)
• PXD050928 · qodo-code-review[bot]: Yeast is classified as an animal. PXD050928 identifies every source as saccharomyces cerevisiae while declaring the organism-specific template as invertebrates . The complete dataset consequently advertises an animal template for fungal samples. (source)
• PXD050928 · qodo-code-review[bot]: Twenty-three artifacts become assays. Rows 18–40 represent a FASTA database, spreadsheets, CSV results, checksum, analysis script, definition files, and search-result XML files as Q Exactive acquisitions. (source)
• PXD050930 · qodo-code-review[bot]: A fragment replaces all quench data. The comment[quenching reagent] field contains the isolated preposition by throughout the assay table. All records therefore omit the actual reagent while appearing to provide crosslinking-protocol metadata. (source)
• PXD050930 · qodo-code-review[bot]: Fungal runs declare an animal template. The dataset annotates saccharomyces cerevisiae but ends each record with the invertebrates organism-specific template. Every fungal run is consequently presented with a template layer intended for an animal taxonomic group. (source)

New datasets (50)

parse_sdrf validation of new datasets is reported by the SDRF review gate check.

Dataset	Rows	Defects
PXD046413	10	no_factor_value: 1
PXD046414	10	no_factor_value: 1
PXD046472	7	no_factor_value: 1
PXD046634	22	no_factor_value: 1, peak_list_data_file: 4
PXD046754	20	no_factor_value: 1
PXD046990	3	no_factor_value: 1
PXD047023	25	no_factor_value: 1
PXD047030	4	no_factor_value: 1
PXD047274	70	no_factor_value: 1
PXD047277	12	no_factor_value: 1
PXD047368	10	no_factor_value: 1
PXD047378	5	no_factor_value: 1
PXD047422	100	no_factor_value: 1
PXD047455	19	no_factor_value: 1
PXD047547	2	no_factor_value: 1
PXD047569	93	no_factor_value: 1
PXD047725	36	no_factor_value: 1
PXD047929	12	no_factor_value: 1
PXD048046	27	no_factor_value: 1
PXD048145	11	no_factor_value: 1, peak_list_data_file: 11
PXD048174	14	no_factor_value: 1
PXD048180	11	no_factor_value: 1
PXD048194	8	no_factor_value: 1
PXD048297	6	no_factor_value: 1
PXD048298	12	no_factor_value: 1
PXD048452	54	no_factor_value: 1
PXD048567	91	no_factor_value: 1
PXD048614	6	no_factor_value: 1, peak_list_data_file: 3
PXD048625	2	no_factor_value: 1
PXD048632	64	no_factor_value: 1
PXD048897	16	no_factor_value: 1
PXD048937	6	no_factor_value: 1
PXD048965	1	no_factor_value: 1
PXD049047	9	no_factor_value: 1
PXD049094	3	no_factor_value: 1
PXD049182	15	no_factor_value: 1
PXD049372	29	no_factor_value: 1
PXD049433	18	no_factor_value: 1
PXD049681	16	no_factor_value: 1
PXD049684	57	no_factor_value: 1
PXD049689	30	no_factor_value: 1
PXD049991	46	no_factor_value: 1
PXD050097	10	no_factor_value: 1
PXD050493	28	no_factor_value: 1
PXD050556	4	no_factor_value: 1
PXD050824	8	no_factor_value: 1
PXD050833	60	no_factor_value: 1
PXD050928	39	no_factor_value: 1, peak_list_data_file: 16
PXD050929	100	no_factor_value: 1, peak_list_data_file: 48
PXD050930	100	no_factor_value: 1, peak_list_data_file: 34

_{Advisory report built from de53b36. Risk labels do not block merging.}

[qodo-code-review]

1. Figure archives become fake assays 📘 Rule violation ≡ Correctness

Rows 2–5 of PXD047030.sdrf.tsv map Fig1.zip, Fig2.zip, Fig3.zip, and Fig9.zip to distinct
assay names and fractions while supplying complete 6220 Time-of-Flight acquisition metadata. Because
these archives contain figures rather than acquired mass-spectrometry data, consumers counting the
declared measurements encounter four unsupported sample-to-assay and fraction relationships instead
of mappings to the deposited acquisition files.

Agent Prompt

## Issue description
Figure archives are annotated as acquisition data files and assigned assay, instrument, and fraction metadata, exposing them as measured mass-spectrometry runs with unsupported relationships.

## Fix Focus Areas
- datasets/PXD047030/PXD047030.sdrf.tsv[2-5]

## Recommended Fix
Remove the `Fig*.zip` rows and replace them with mappings for the accession's actual acquired mass-spectrometry files, using only archive-supported assay and fraction relationships. If the acquisition files cannot be identified, do not invent assay coordinates from figure archives; keep the accession out of the canonical dataset directory until valid mappings can be established.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

2. Result archives become fake assays 📘 Rule violation ≡ Correctness

Rows 89–94 assign six .rar result and proximity archives separate assay names, fraction
identifiers, and Orbitrap acquisition metadata. When archive bundles are enumerated alongside the
preceding raw files, the dataset gains six unsupported instrument measurements.

Agent Prompt

## Issue description
Result and proximity archives are represented as independent instrument assays with fabricated fraction relationships.

## Fix Focus Areas
- datasets/PXD047569/PXD047569.sdrf.tsv[89-94]

## Recommended Fix
Remove the archive-bundle rows and retain only archive-supported acquired mass-spectrometry files as assays, preserving only relationships established by the source metadata.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

3. An action replaces the quench reagent 📘 Rule violation ≡ Correctness

The comment[quenching reagent] column contains the bare action word adding in every assay row.
All 27 records therefore expose a sentence fragment where consumers expect the reagent used by the
crosslinking protocol.

Agent Prompt

## Issue description
The quenching-reagent column contains `adding`, which is an action fragment rather than a reagent or reserved missing-value term.

## Fix Focus Areas
- datasets/PXD048046/PXD048046.sdrf.tsv[2-28]

## Recommended Fix
Replace `adding` with the archive-supported quenching reagent using the template-supported representation, or use `not available` when the reagent cannot be established.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

4. A modifier replaces the quench reagent 📘 Rule violation ≡ Correctness

The comment[quenching reagent] column in PXD048145.sdrf.tsv contains only the incomplete
modifier final rather than an identifiable reagent or an allowed unavailable sentinel. This
affects every listed acquisition, including the RNA UV rows, leaving consumers with unusable
quenching-protocol metadata.

Agent Prompt

## Issue description
The `comment[quenching reagent]` column contains the prose fragment `final` in every row rather than a reagent or a valid unavailable sentinel.

## Fix Focus Areas
- datasets/PXD048145/PXD048145.sdrf.tsv[2-12]

## Recommended Fix
Replace `final` with the documented, archive-supported quenching reagent using the template-supported representation. If the archive does not establish the reagent, use the spec-compliant `not available` sentinel consistently.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

5. Converted files duplicate three runs 📘 Rule violation ≡ Correctness

Rows 2–7 assign each of three run stems one .mzXML assay and one corresponding .raw assay, each
with a different fraction identifier. Treating a converted derivative and its source file as
separate measurements doubles the acquisition count from three to six.

Agent Prompt

## Issue description
Three converted files and their corresponding source files are modeled as six independent fractions rather than three acquisitions.

## Fix Focus Areas
- datasets/PXD048614/PXD048614.sdrf.tsv[2-7]

## Recommended Fix
Model each `.mzXML` and matching `.raw` pair as one archive-supported acquisition relationship, avoiding separate assay or fraction identifiers for converted derivatives.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

13. Treatment and control become one sample 🐞 Bug ≡ Correctness

The ACSS2 and control runs all share PXD048937-sample, biological replicate 1, and no factor
column describing treatment status. The six assays are consequently modeled only as fractions of one
source, losing the treatment/control comparison and the replicate identities encoded in their names.

Agent Prompt

## Issue description
Three ACSS2 runs and three control runs are represented as fractions of one source with one biological-replicate value.

## Fix Focus Areas
- datasets/PXD048937/PXD048937.sdrf.tsv[2-7]

## Recommended Fix
Map ACSS2-1 through ACSS2-3 and ctrl-1 through ctrl-3 to their actual source and biological-replicate identities, and add the accession-supported treatment factor so consumers can recover the comparison.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

14. Six runs name the wrong labeling enzyme 🐞 Bug ≡ Correctness

The first six assay and raw-file names identify BioID or BirA, while comment[cross-linker] assigns
TurboID. Those runs are consequently grouped under a different labeling enzyme from the one encoded
in their deposited identifiers.

Agent Prompt

## Issue description
The first six BioID/BirA runs are annotated with the TurboID controlled term.

## Fix Focus Areas
- datasets/PXD049372/PXD049372.sdrf.tsv[2-7]

## Recommended Fix
Replace TurboID with the accession-supported BioID controlled term on the BioID/BirA rows, while retaining TurboID on runs whose identifiers and source metadata actually describe TurboID.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

15. A number replaces the quench reagent 🐞 Bug ≡ Correctness

comment[quenching reagent] contains the bare value 1 on every PXD049372 row rather than a
reagent or an unavailable sentinel. The malformed protocol value reaches all raw acquisitions as
well as the already-reported auxiliary-file rows.

Agent Prompt

## Issue description
Every row places the numeric value `1` in the quenching-reagent column.

## Fix Focus Areas
- datasets/PXD049372/PXD049372.sdrf.tsv[2-30]

## Recommended Fix
Replace `1` with the accession-supported quenching reagent, or use the specification-compliant unavailable sentinel when no quenching reagent is documented.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

16. Result archives appear as instrument runs 🐞 Bug ≡ Correctness

PXD047023.sdrf.tsv places Rep*_result_*.zip archives in both assay name and `comment[data
file]` while copying timsTOF acquisition, digestion, and fragmentation metadata onto them. Whenever
consumers enumerate the SDRF data files, these six processed-result packages are counted alongside
the actual .d.zip raw acquisitions.

Agent Prompt

## Issue description
Processed `Rep*_result_*.zip` archives are represented as mass-spectrometry assay/data-file rows even though the file names distinguish them from the neighboring `raw_data` acquisitions.

## Fix Focus Areas
- datasets/PXD047023/PXD047023.sdrf.tsv[6-26]

## Recommended Fix
Remove the rows whose `comment[data file]` values are `Rep*_result_*.zip`. Retain only the rows that map actual acquired raw files, and derive assay coordinates from those raw acquisitions.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

[qodo-code-review]

17. Data-independent runs use wrong method 🐞 Bug ≡ Correctness

PXD049689.sdrf.tsv declares NT=Data-dependent acquisition for every file whose assay and
data-file name explicitly contains DIA. All thirty records will consequently be classified as
data-dependent rather than data-independent acquisitions by users of the acquisition-method field.

Agent Prompt

## Issue description
All run names explicitly identify DIA acquisition, but their `comment[proteomics data acquisition method]` values declare data-dependent acquisition.

## Fix Focus Areas
- datasets/PXD049689/PXD049689.sdrf.tsv[2-31]

## Recommended Fix
Replace the data-dependent acquisition annotation on every DIA row with the correct data-independent acquisition ontology annotation, preserving the existing assay and raw-file mappings.

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[qodo-code-review]

Code review by qodo was updated up to the latest commit 39284aa