Add crosslinking proteomics SDRF annotations (batch 08/15, 50 datasets) - #546
Merged
Merged
Conversation
|
Important Review skippedReview was skipped due to path filters ⛔ Files ignored due to path filters (50)
CodeRabbit blocks several paths by default. You can override this behavior by explicitly including those paths in the path filters. For example, including ⚙️ Run configurationConfiguration used: defaults Review profile: CHILL Plan: Advanced Run ID: You can disable this status message by setting the Use the checkbox below for a quick retry:
Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. Comment |
PR Summary by QodoAdd batch 08 crosslinking proteomics SDRF annotations
AI Description
Diagram
High-Level Assessment
Files changed (50)
|
Code Review by Qodo
1. Second biological replicates disappear
|
![qodo-code-review[bot]](https://avatars.githubusercontent.com/in/484649?s=60&v=4){kind=small}
| PXD030429-sample marchantia polymorpha not applicable not applicable not applicable 1 synthetic reference not available not available not available not available 210412_HN_KaMe_F_04 proteomic profiling by mass spectrometry 210412_HN_KaMe_F_04.raw 1 37 AC=MS:1002038;NT=label free sample NT=Q Exactive;AC=MS:1001911 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 | ||
| PXD030429-sample marchantia polymorpha not applicable not applicable not applicable 1 synthetic reference not available not available not available not available 210412_HN_KaMe_F_05 proteomic profiling by mass spectrometry 210412_HN_KaMe_F_05.raw 1 38 AC=MS:1002038;NT=label free sample NT=Q Exactive;AC=MS:1001911 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 | ||
| PXD030429-sample marchantia polymorpha not applicable not applicable not applicable 1 synthetic reference not available not available not available not available 210412_HN_KaMe_F_06 proteomic profiling by mass spectrometry 210412_HN_KaMe_F_06.raw 1 39 AC=MS:1002038;NT=label free sample NT=Q Exactive;AC=MS:1001911 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 | ||
| PXD030429-sample marchantia polymorpha not applicable not applicable not applicable 1 synthetic reference not available not available not available not available checksum.txt proteomic profiling by mass spectrometry checksum.txt 1 40 AC=MS:1002038;NT=label free sample NT=Q Exactive;AC=MS:1001911 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 |
There was a problem hiding this comment.
1. Metadata files appear as assays 📘 Rule violation ≡ Correctness
The assay name and comment[data file] fields map five checksum.txt manifests, three FASTA databases, and ProteomeXchange metadata as proteomic profiling by mass spectrometry assay rows. This occurs when deposited project files are converted into rows without excluding non-experimental support files, so consumers enumerating experimental runs reach nonexistent assays and replicate identifiers across at least six accessions and eight datasets.
Agent Prompt
## Issue description
Checksums, sequence databases, and ProteomeXchange project metadata are incorrectly represented as mass-spectrometry assays and data files, creating nonexistent experimental runs and replicate identifiers.
## Fix Focus Areas
- datasets/PXD030429/PXD030429.sdrf.tsv[41-41]
- datasets/PXD030495/PXD030495.sdrf.tsv[5-5]
- datasets/PXD030849/PXD030849.sdrf.tsv[26-28]
- datasets/PXD031114/PXD031114.sdrf.tsv[5-5]
- datasets/PXD031643/PXD031643.sdrf.tsv[42-43]
- datasets/PXD031911/PXD031911.sdrf.tsv[31-31]
- datasets/PXD031911/PXD031911.sdrf.tsv[96-97]
## Recommended Fix
Remove rows for checksum manifests, FASTA databases, and ProteomeXchange metadata. Retain only files that represent experimental MS acquisitions or supported derived MS results, ensuring that `assay name` and `comment[data file]` mappings agree with archive evidence.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
| @@ -0,0 +1,3 @@ | |||
| source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[biological replicate] characteristics[material type] characteristics[sample type] characteristics[enrichment process] characteristics[crosslink distance] characteristics[crosslinking reaction time] characteristics[crosslinking temperature] assay name technology type comment[data file] comment[technical replicate] comment[fraction identifier] comment[label] comment[instrument] comment[proteomics data acquisition method] comment[cleavage agent details] comment[cleavage agent details] comment[modification parameters] comment[modification parameters] comment[dissociation method] comment[collision energy] comment[precursor mass tolerance] comment[fragment mass tolerance] comment[fractionation method] comment[chemical cross-linking coupled with ms] comment[cross-linker] comment[crosslink enrichment method] comment[crosslinker concentration] comment[quenching reagent] comment[reduction reagent] comment[alkylation reagent] comment[sdrf version] comment[sdrf template] comment[sdrf template] | |||
| PXD030209-sample escherichia coli not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available fbsaca_210814E_08.mgf proteomic profiling by mass spectrometry fbsaca_210814E_08.mgf 1 1 AC=MS:1002038;NT=label free sample NT=Orbitrap Exploris 240;AC=MS:1003094 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=DSBU;AC=XLMOD:02043;CL=yes;TA=K,S,T,Y,nterm;MH=85.05;ML=111.03 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 | |||
There was a problem hiding this comment.
2. Quenching fields contain stray words 📘 Rule violation ≡ Correctness
The comment[quenching reagent] column contains prose fragments such as by, for, the, and and, or the numeric value 0, instead of a reagent term or valid unavailable marker. Every affected row exposes these malformed values as reagent metadata to validation and downstream annotation consumers, which receive meaningless protocol metadata rather than a quenching reagent.
Agent Prompt
## Issue description
Quenching-reagent fields contain prose fragments such as `by`, `for`, `the`, or `and`, or a numeric zero, instead of reagent names or valid missing-value sentinels.
## Fix Focus Areas
- datasets/PXD030209/PXD030209.sdrf.tsv[2-3]
- datasets/PXD030299/PXD030299.sdrf.tsv[2-23]
- datasets/PXD030849/PXD030849.sdrf.tsv[2-28]
- datasets/PXD030864/PXD030864.sdrf.tsv[2-33]
- datasets/PXD031114/PXD031114.sdrf.tsv[2-101]
- datasets/PXD031519/PXD031519.sdrf.tsv[2-34]
- datasets/PXD033175/PXD033175.sdrf.tsv[2-7]
- datasets/PXD033446/PXD033446.sdrf.tsv[2-22]
- datasets/PXD033764/PXD033764.sdrf.tsv[2-88]
## Recommended Fix
Replace each malformed value with the actual quenching reagent supported by the public protocol. Where the reagent cannot be established, use `not available` rather than prose fragments or numeric placeholders.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
| PXD031114-sample escherichia coli not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available 3_stepped_HCD-MS2_allows_accurate_Quant_analysis.zip proteomic profiling by mass spectrometry 3_stepped_HCD-MS2_allows_accurate_Quant_analysis.zip 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 chemical cross-linking coupled with mass spectrometry proteomics NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98 not available not available by not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 | ||
| PXD031114-sample escherichia coli not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available 5812HEK.fasta proteomic profiling by mass spectrometry 5812HEK.fasta 1 4 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98 not available not available by not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 | ||
| PXD031114-sample escherichia coli not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available ECmix_TMT_before_spikein_linearpeptides_SPS proteomic profiling by mass spectrometry ECmix_TMT_before_spikein_linearpeptides_SPS.raw 1 5 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98 not available not available by not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 | ||
| PXD031114-sample escherichia coli not applicable not applicable not applicable 1 synthetic reference not available 26.4 Å not available not available HEK_DSSO_sampleA_MS2_MS3_top2_1 proteomic profiling by mass spectrometry HEK_DSSO_sampleA_MS2_MS3_top2_1.raw 1 6 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98 not available not available by not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 |
There was a problem hiding this comment.
4. Human runs are labeled as bacteria 📘 Rule violation ≡ Correctness
PXD031114 assigns escherichia coli in characteristics[organism] to rows whose assay and data-file names identify HEK-only or mixed HEK/E. coli material. When these runs are processed, the incorrect uniform value reaches their samples and associated replicate metadata, so both human-cell and mixed-species assays are represented as bacterial.
Agent Prompt
## Issue description
HEK-only and mixed HEK/E. coli assays in PXD031114 are uniformly annotated as Escherichia coli, causing their samples and replicate metadata to be represented inaccurately.
## Fix Focus Areas
- datasets/PXD031114/PXD031114.sdrf.tsv[5-5]
- datasets/PXD031114/PXD031114.sdrf.tsv[22-22]
- datasets/PXD031114/PXD031114.sdrf.tsv[48-55]
## Recommended Fix
Map HEK material to the appropriate human organism and represent mixed HEK/E. coli material according to SDRF multi-organism conventions. Verify all rows and their associated replicate metadata rather than applying one organism uniformly across the dataset.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
| @@ -0,0 +1,5 @@ | |||
| source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[age] characteristics[sex] characteristics[biological replicate] characteristics[material type] characteristics[sample type] characteristics[enrichment process] characteristics[crosslink distance] characteristics[crosslinking reaction time] characteristics[crosslinking temperature] assay name technology type comment[data file] comment[technical replicate] comment[fraction identifier] comment[label] comment[instrument] comment[proteomics data acquisition method] comment[cleavage agent details] comment[cleavage agent details] comment[modification parameters] comment[modification parameters] comment[dissociation method] comment[collision energy] comment[precursor mass tolerance] comment[fragment mass tolerance] comment[fractionation method] comment[chemical cross-linking coupled with ms] comment[cross-linker] comment[crosslink enrichment method] comment[crosslinker concentration] comment[quenching reagent] comment[reduction reagent] comment[alkylation reagent] comment[sdrf version] comment[sdrf template] comment[sdrf template] comment[sdrf template] | |||
| PXD033205-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 26.4 Å not available not available Day0_DSBU.zip proteomic profiling by mass spectrometry Day0_DSBU.zip 1 1 AC=MS:1002038;NT=label free sample NT=timsTOF Pro;AC=MS:1003005 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=DSBU;AC=XLMOD:02043;CL=yes;TA=K,S,T,Y,nterm;MH=85.05;ML=111.03 not available not available 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 | |||
| PXD033205-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 26.4 Å not available not available Day0_EDC.zip proteomic profiling by mass spectrometry Day0_EDC.zip 1 2 AC=MS:1002038;NT=label free sample NT=timsTOF Pro;AC=MS:1003005 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=DSBU;AC=XLMOD:02043;CL=yes;TA=K,S,T,Y,nterm;MH=85.05;ML=111.03 not available not available 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 | |||
There was a problem hiding this comment.
5. One reagent's runs get another label 📘 Rule violation ≡ Correctness
The comment[cross-linker] column assigns NT=BS3 to DMTMM-named assays and NT=DSBU;AC=XLMOD:02043 to Day0_EDC.zip and Day1_EDC.zip, despite adjacent, separately named DSBU runs. In experiments containing multiple reagents, the uniform dataset-level annotation reaches every condition regardless of its assay or archive filename and collapses the reagent distinctions encoded there.
Agent Prompt
## Issue description
Assay-specific reagent names conflict with uniformly copied cross-linker annotations: DMTMM-named assays are assigned BS3, while EDC-named archives are assigned DSBU even though adjacent rows separately identify DSBU runs.
## Fix Focus Areas
- datasets/PXD030299/PXD030299.sdrf.tsv[17-17]
- datasets/PXD030299/PXD030299.sdrf.tsv[20-23]
- datasets/PXD033205/PXD033205.sdrf.tsv[3-3]
- datasets/PXD033205/PXD033205.sdrf.tsv[5-5]
## Recommended Fix
Assign the correct controlled cross-linker term to each DMTMM and EDC assay using the public experiment metadata. Apply annotations per condition or file rather than uniformly at the dataset level, and do not reuse the BS3 or DSBU annotation for conditions using another reagent.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
Comment on lines
+2
to
+3
| PXD033244-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available JWK_Cal-ID_HEK_TMT proteomic profiling by mass spectrometry JWK_Cal-ID_HEK_TMT.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=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 | ||
| PXD033244-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available JWK_Cal-ID_mCN_TMT proteomic profiling by mass spectrometry JWK_Cal-ID_mCN_TMT.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=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 |
There was a problem hiding this comment.
6. Labeled assays appear label-free 🐞 Bug ≡ Correctness
The comment[label] value is label free sample for filenames explicitly identifying TMT, SILAC, N14/N15, or four-plex experiments. The contradiction affects five datasets and causes labeled channels or isotopic conditions to be collapsed into a label-free design.
Agent Prompt
## Issue description
Assays whose filenames explicitly identify TMT, SILAC, N14/N15, or four-plex labeling are incorrectly declared label-free.
## Fix Focus Areas
- datasets/PXD030299/PXD030299.sdrf.tsv[4-23]
- datasets/PXD031114/PXD031114.sdrf.tsv[3-3]
- datasets/PXD031114/PXD031114.sdrf.tsv[22-97]
- datasets/PXD031911/PXD031911.sdrf.tsv[4-7]
- datasets/PXD031911/PXD031911.sdrf.tsv[100-101]
- datasets/PXD033244/PXD033244.sdrf.tsv[2-3]
- datasets/PXD033764/PXD033764.sdrf.tsv[2-88]
## Recommended Fix
Replace the label-free value with the appropriate controlled labeling term and represent multiplexed channels as required by the SDRF template. Verify each mapping against the archive metadata and publication.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
Comment on lines
+9
to
+10
| PXD031411-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 26.4 Å not available not available DMSO-ingel proteomic profiling by mass spectrometry DMSO-ingel.raw 1 8 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0 | ||
| PXD031411-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 26.4 Å not available not available DMSO-insolution proteomic profiling by mass spectrometry DMSO-insolution.raw 1 9 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=DSSO;AC=XLMOD:02010;CL=yes;TA=K,S,T,Y,nterm;MH=54.01;ML=85.98 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0 |
There was a problem hiding this comment.
7. Controls appear cross-linked 🐞 Bug ≡ Correctness
DMSO and explicitly unXlink assay rows still declare chemical cross-linking and assign DSSO or an unknown cross-linker. The error occurs where condition-specific controls inherit the same cross-linking fields as treated rows, making controls indistinguishable downstream.
Agent Prompt
## Issue description
Control and explicitly uncross-linked assays inherit cross-linking metadata from treated rows.
## Fix Focus Areas
- datasets/PXD031411/PXD031411.sdrf.tsv[9-10]
- datasets/PXD033175/PXD033175.sdrf.tsv[5-7]
## Recommended Fix
Mark the DMSO and `unXlink` rows as non-cross-linked and use the appropriate sentinel for cross-linker-specific fields. Preserve DSSO or other cross-linker terms only on genuinely treated assays.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
…lumns Required by the vertebrates/invertebrates/plants SDRF templates; value set to the spec-compliant reserved word 'not available' where the field was not previously populated. human-only files are unaffected (field optional in that template).
Contributor
SDRF change report50 new · 0 modified · 0 deleted · highest risk: none External reviewer notesQuoted from AI review bots on this PR. Not verified by this report unless marked as also flagged.
New datasets (50)parse_sdrf validation of new datasets is reported by the SDRF review gate check.
Advisory report built from db00376. Risk labels do not block merging. |
| PXD030299-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available 2020_09_14_06_aSync_14N_14N_BS3_TRP_XL proteomic profiling by mass spectrometry 2020_09_14_06_aSync_14N_14N_BS3_TRP_XL.raw 1 15 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 chemical cross-linking coupled with mass spectrometry proteomics NT=BS3;AC=XLMOD:02000 not available not available the not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0 | ||
| PXD030299-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available 2020_09_15_04_aSync_14N_15N_DMTMM_TRP_XL proteomic profiling by mass spectrometry 2020_09_15_04_aSync_14N_15N_DMTMM_TRP_XL.raw 1 16 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 chemical cross-linking coupled with mass spectrometry proteomics NT=BS3;AC=XLMOD:02000 not available not available the not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0 | ||
| PXD030299-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available 2020_09_15_07_aSync_14N_15N_BS3_TRP_XL proteomic profiling by mass spectrometry 2020_09_15_07_aSync_14N_15N_BS3_TRP_XL.raw 1 17 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 chemical cross-linking coupled with mass spectrometry proteomics NT=BS3;AC=XLMOD:02000 not available not available the not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0 | ||
| PXD030299-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available 2020_09_16_01_aSync_15N_15N_BS3_TRP_XL proteomic profiling by mass spectrometry 2020_09_16_01_aSync_15N_15N_BS3_TRP_XL.raw 1 18 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 chemical cross-linking coupled with mass spectrometry proteomics NT=BS3;AC=XLMOD:02000 not available not available the not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0 |
There was a problem hiding this comment.
1. Gluc assays get wrong enzymes 🐞 Bug ≡ Correctness
comment[cleavage agent details] remains Trypsin and Lys-C on PXD030299 rows whose assay and raw-file names explicitly say GluC. The mismatch occurs on rows 19, 21, and 22, so consumers receive the wrong digestion enzyme for those assays.
Agent Prompt
## Issue description
PXD030299 rows explicitly named for GluC digestion are annotated with Trypsin and Lys-C instead of glutamyl endopeptidase.
## Fix Focus Areas
- datasets/PXD030299/PXD030299.sdrf.tsv[19-22]
## Recommended Fix
For the GluC-named rows, replace the incorrect cleavage-agent values with the verified GluC annotation, using `NT=glutamyl endopeptidase;AC=MS:1001917` where supported by the source metadata.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
| PXD033167-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 18 Å not available not available MT_DCX-HeavyLight_LCSDA_BioRep1_SEC-frac5 proteomic profiling by mass spectrometry MT_DCX-HeavyLight_LCSDA_BioRep1_SEC-frac5.raw 1 5 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=SDA;AC=XLMOD:02171 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 | ||
| PXD033167-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 18 Å not available not available MT_DCX-HeavyLight_LCSDA_BioRep1_SEC-frac6 proteomic profiling by mass spectrometry MT_DCX-HeavyLight_LCSDA_BioRep1_SEC-frac6.raw 1 6 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=SDA;AC=XLMOD:02171 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 | ||
| PXD033167-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 18 Å not available not available MT_DCX-HeavyLight_LCSDA_BioRep1_SPE proteomic profiling by mass spectrometry MT_DCX-HeavyLight_LCSDA_BioRep1_SPE.raw 1 7 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=SDA;AC=XLMOD:02171 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 | ||
| PXD033167-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 18 Å not available not available MT_DCX-HeavyLight_LCSDA_BioRep2_SEC-frac1 proteomic profiling by mass spectrometry MT_DCX-HeavyLight_LCSDA_BioRep2_SEC-frac1.raw 1 8 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=SDA;AC=XLMOD:02171 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 |
There was a problem hiding this comment.
2. Second biological replicates disappear 🐞 Bug ≡ Correctness
characteristics[biological replicate] remains 1 for PXD033167 BioRep2 rows and PXD031644 biorep_2 rows. These explicit second biological replicates are therefore grouped with replicate 1 throughout downstream analysis.
Agent Prompt
## Issue description
Rows explicitly identifying biological replicate 2 are assigned biological replicate 1, collapsing distinct samples.
## Fix Focus Areas
- datasets/PXD033167/PXD033167.sdrf.tsv[9-31]
- datasets/PXD031644/PXD031644.sdrf.tsv[12-21]
## Recommended Fix
Assign biological replicate 2 to every `BioRep2` or `biorep_2` row and use source names that distinguish the separate biological samples.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
Comment on lines
+2
to
+3
| PXD031643-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available 071521_AB_mito_old_young_1_fr_10_rep1 proteomic profiling by mass spectrometry 071521_AB_mito_old_young_1_fr_10_rep1.raw 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 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 | ||
| PXD031643-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available 071521_AB_mito_old_young_1_fr_10_rep2 proteomic profiling by mass spectrometry 071521_AB_mito_old_young_1_fr_10_rep2.raw 1 2 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 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 |
There was a problem hiding this comment.
3. Technical replicates become fractions 🐞 Bug ≡ Correctness
comment[technical replicate] remains 1 on paired _rep1 and _rep2 raw files, while each pair receives different sequential fraction identifiers in PXD031643 and PXD031644. The second acquisition of each physical fraction is consequently represented as a new fraction rather than technical replicate 2.
Agent Prompt
## Issue description
Paired technical replicates are assigned the same technical-replicate value and different fraction identifiers.
## Fix Focus Areas
- datasets/PXD031643/PXD031643.sdrf.tsv[2-49]
- datasets/PXD031644/PXD031644.sdrf.tsv[2-21]
## Recommended Fix
Assign technical replicate 1 and 2 according to each filename pair, and give both members of a pair the same fraction identifier derived from their shared `fr_*` token.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
Comment on lines
+4
to
+5
| PXD031827-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available 20211209_QExHFX2_RSLC10_Levina_Leonard_MPL_MUW_XL_dimer_30p proteomic profiling by mass spectrometry 20211209_QExHFX2_RSLC10_Levina_Leonard_MPL_MUW_XL_dimer_30p.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 chemical cross-linking coupled with mass spectrometry proteomics NT=BS3;AC=XLMOD:02000 not available not available Tris 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 | ||
| PXD031827-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available 30 Å not available not available 20211209_QExHFX2_RSLC10_Levina_Leonard_MPL_MUW_XL_monomer_2p proteomic profiling by mass spectrometry 20211209_QExHFX2_RSLC10_Levina_Leonard_MPL_MUW_XL_monomer_2p.raw 1 4 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion Lumos;AC=MS:1002732 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=BS3;AC=XLMOD:02000 not available not available Tris 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 |
There was a problem hiding this comment.
4. Two runs report wrong instrument 🐞 Bug ≡ Correctness
PXD031827 rows 4–5 use QExHFX2 assay and raw-file names but declare the instrument as Orbitrap Fusion Lumos. Other repository rows using the same QExHFX naming convention identify a Q Exactive HF-family instrument, so these two runs carry incorrect instrument metadata.
Agent Prompt
## Issue description
Two QExHFX2 acquisitions are incorrectly annotated as Orbitrap Fusion Lumos runs.
## Fix Focus Areas
- datasets/PXD031827/PXD031827.sdrf.tsv[4-5]
## Recommended Fix
Verify the exact Q Exactive model from the source metadata and replace the Orbitrap Fusion Lumos name and accession on rows 4 and 5.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
| @@ -0,0 +1,21 @@ | |||
| source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[age] characteristics[sex] characteristics[biological replicate] characteristics[material type] characteristics[sample type] characteristics[enrichment process] characteristics[crosslink distance] characteristics[crosslinking reaction time] characteristics[crosslinking temperature] assay name technology type comment[data file] comment[technical replicate] comment[fraction identifier] comment[label] comment[instrument] comment[proteomics data acquisition method] comment[cleavage agent details] comment[cleavage agent details] comment[modification parameters] comment[modification parameters] comment[dissociation method] comment[collision energy] comment[precursor mass tolerance] comment[fragment mass tolerance] comment[fractionation method] comment[chemical cross-linking coupled with ms] comment[cross-linker] comment[crosslink enrichment method] comment[crosslinker concentration] comment[quenching reagent] comment[reduction reagent] comment[alkylation reagent] comment[sdrf version] comment[sdrf template] comment[sdrf template] comment[sdrf template] | |||
| PXD031644-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 080921_AB_HEK_mito_ADP_fr_10 proteomic profiling by mass spectrometry 080921_AB_HEK_mito_ADP_fr_10.raw 1 1 AC=MS:1002038;NT=label free sample NT=Q Exactive Plus;AC=MS:1002634 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=BDP-NHP;AC=XLMOD:02014 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0 | |||
There was a problem hiding this comment.
5. Cell-derived samples appear synthetic 🐞 Bug ≡ Correctness
PXD031644 HEK_mito runs and PXD033593 SH_cells runs set characteristics[material type] to synthetic. These filenames explicitly identify cell-derived biological preparations, so searches and analyses by material type classify them as synthetic standards instead of biological material.
Agent Prompt
## Issue description
Cell-derived mitochondrial and SH-cell samples are incorrectly classified as synthetic material.
## Fix Focus Areas
- datasets/PXD031644/PXD031644.sdrf.tsv[2-21]
- datasets/PXD033593/PXD033593.sdrf.tsv[2-6]
## Recommended Fix
Replace `synthetic` with the biologically appropriate material type and populate the available cell-line or cell-type metadata from the dataset source.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
Comment on lines
+2
to
+4
| PXD030578-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 220119_GKokic_BS3_pSEC_11_NCE26-30 proteomic profiling by mass spectrometry 220119_GKokic_BS3_pSEC_11_NCE26-30.raw 1 1 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion;AC=MS:1002416 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=BS3;AC=XLMOD:02000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0 | ||
| PXD030578-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 220119_GKokic_BS3_pSEC_11_NCE28 proteomic profiling by mass spectrometry 220119_GKokic_BS3_pSEC_11_NCE28.raw 1 2 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion;AC=MS:1002416 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=BS3;AC=XLMOD:02000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0 | ||
| PXD030578-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 220119_GKokic_BS3_pSEC_11_NCE30 proteomic profiling by mass spectrometry 220119_GKokic_BS3_pSEC_11_NCE30.raw 1 3 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion;AC=MS:1002416 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available chemical cross-linking coupled with mass spectrometry proteomics NT=BS3;AC=XLMOD:02000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0 |
There was a problem hiding this comment.
14. Recorded collision energies disappear 🐞 Bug ≡ Correctness
Every PXD030578 filename records normalized collision energy as NCE26-30, NCE28, or NCE30, but comment[collision energy] is not available. The added annotation therefore discards acquisition parameters already encoded for all 33 assays.
Agent Prompt
## Issue description
PXD030578 omits collision-energy metadata even though each assay filename explicitly supplies it.
## Fix Focus Areas
- datasets/PXD030578/PXD030578.sdrf.tsv[2-34]
## Recommended Fix
Populate `comment[collision energy]` from each filename, preserving the stepped `26-30 NCE` value and the individual `28 NCE` and `30 NCE` values.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
| @@ -0,0 +1,25 @@ | |||
| source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[age] characteristics[sex] characteristics[biological replicate] characteristics[material type] characteristics[sample type] characteristics[enrichment process] characteristics[crosslink distance] characteristics[crosslinking reaction time] characteristics[crosslinking temperature] assay name technology type comment[data file] comment[technical replicate] comment[fraction identifier] comment[label] comment[instrument] comment[proteomics data acquisition method] comment[cleavage agent details] comment[cleavage agent details] comment[modification parameters] comment[modification parameters] comment[dissociation method] comment[collision energy] comment[precursor mass tolerance] comment[fragment mass tolerance] comment[fractionation method] comment[chemical cross-linking coupled with ms] comment[cross-linker] comment[crosslink enrichment method] comment[crosslinker concentration] comment[quenching reagent] comment[reduction reagent] comment[alkylation reagent] comment[sdrf version] comment[sdrf template] comment[sdrf template] comment[sdrf template] | |||
| PXD032297-sample homo sapiens not applicable not applicable not applicable not available not applicable 1 synthetic reference not available not available not available not available 2207_RR_E_01 proteomic profiling by mass spectrometry 2207_RR_E_01.raw 1 1 AC=MS:1002038;NT=label free sample NT=Orbitrap Fusion;AC=MS:1002416 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=BioID;AC=XLMOD:02250 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=human;VV=v1.1.0 | |||
There was a problem hiding this comment.
6. Proximity labels masquerade as crosslinks 🐞 Bug ≡ Correctness
The new rows put BioID or TurboID in comment[cross-linker] and set `comment[chemical cross-linking coupled with ms] to cross-linking mass spectrometry`, although these are proximity-labeling biotin ligases rather than chemical cross-linkers. This occurs throughout PXD032297, PXD032952, PXD033026, PXD033043, PXD033044, PXD033062, PXD033063, and PXD033066, so downstream crosslinking queries classify every affected run incorrectly.
Agent Prompt
Issue description
BioID and TurboID runs are proximity-labeling experiments, but the added SDRFs classify them as chemical cross-linking mass spectrometry and store the ligases as cross-linkers. This makes crosslinking-specific consumers retrieve and interpret these runs as covalent crosslinking data.
Fix Focus Areas
- datasets/PXD032297/PXD032297.sdrf.tsv[2-25]
- datasets/PXD032952/PXD032952.sdrf.tsv[2-25]
- datasets/PXD033026/PXD033026.sdrf.tsv[2-18]
- datasets/PXD033043/PXD033043.sdrf.tsv[2-18]
- datasets/PXD033044/PXD033044.sdrf.tsv[2-18]
- datasets/PXD033062/PXD033062.sdrf.tsv[2-19]
- datasets/PXD033063/PXD033063.sdrf.tsv[2-19]
- datasets/PXD033066/PXD033066.sdrf.tsv[2-19]
Recommended Fix
Replace the cross-linking-specific assay classification and cross-linker values in these rows with the repository-supported proximity-labeling/biotinylation annotations. If the SDRF schema cannot represent that experiment type, omit these datasets from the crosslinking annotation batch rather than labeling the ligases as chemical cross-linkers.
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
|
Code review by qodo was updated up to the latest commit b8f17f5 |
comment[sdrf template] declared NT=invertebrates;VV=v1.1.0 (an animal-only template) for 3 Saccharomyces cerevisiae datasets. Removing the mismatched template column; ms-proteomics and crosslinking layers are unaffected. Confirmed by qodo-code-review[bot] and this report's own data check.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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: PXD030209,PXD030274,PXD030299,PXD030429,PXD030495,PXD030543,PXD030578,PXD030590,PXD030619,PXD030849,PXD030864,PXD030970,PXD031033,PXD031096,PXD031114,PXD031197,PXD031214,PXD031215,PXD031345,PXD031381,PXD031411,PXD031415,PXD031519,PXD031601,PXD031643,PXD031644,PXD031827,PXD031845,PXD031911,PXD031997,PXD032222,PXD032297,PXD032952,PXD033004,PXD033026,PXD033043,PXD033044,PXD033062,PXD033063,PXD033066,PXD033167,PXD033175,PXD033181,PXD033205,PXD033244,PXD033391,PXD033446,PXD033593,PXD033633,PXD033764