Skip to content

Add crosslinking proteomics SDRF annotations (batch 15/15, 50 datasets) #553

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ypriverol merged 4 commits into from
Sep 17, 2026
Merged

Add crosslinking proteomics SDRF annotations (batch 15/15, 50 datasets) #553

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
1197edf
Add crosslinking proteomics SDRF annotations (batch 15, 50 data…
ypriverol Sep 17, 2026
125e015
Add missing characteristics[developmental stage]/[strain or breed] co…
ypriverol Sep 17, 2026
f4d908f
Fix instrument assignment for PXD062293 timsTOF Pro 2 runs
ypriverol Sep 17, 2026
9d493af
Remove invertebrates organism template layer from yeast SDRFs
ypriverol Sep 17, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
64 changes: 64 additions & 0 deletions datasets/PXD060322/PXD060322.sdrf.tsv
View file
Open in desktop

Large diffs are not rendered by default.

30 changes: 30 additions & 0 deletions datasets/PXD060638/PXD060638.sdrf.tsv
View file
Open in desktop

Large diffs are not rendered by default.

19 changes: 19 additions & 0 deletions datasets/PXD060825/PXD060825.sdrf.tsv
View file
Open in desktop

Large diffs are not rendered by default.

32 changes: 32 additions & 0 deletions datasets/PXD061125/PXD061125.sdrf.tsv
View file
Open in desktop

Large diffs are not rendered by default.

15 changes: 15 additions & 0 deletions datasets/PXD061317/PXD061317.sdrf.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[developmental stage] characteristics[biological replicate] characteristics[material type] characteristics[sample type] characteristics[enrichment process] characteristics[crosslink distance] characteristics[crosslinking reaction time] characteristics[crosslinking temperature] assay name technology type comment[data file] comment[technical replicate] comment[fraction identifier] comment[label] comment[instrument] comment[proteomics data acquisition method] comment[cleavage agent details] comment[cleavage agent details] comment[modification parameters] comment[modification parameters] comment[dissociation method] comment[collision energy] comment[precursor mass tolerance] comment[fragment mass tolerance] comment[fractionation method] comment[chemical cross-linking coupled with ms] comment[cross-linker] comment[crosslink enrichment method] comment[crosslinker concentration] comment[quenching reagent] comment[reduction reagent] comment[alkylation reagent] comment[sdrf version] comment[sdrf template] comment[sdrf template] comment[sdrf template]
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available 241203_DC2p4_membrane_PD_DMSO-post_Slot2-12_1_8506.d.zip proteomic profiling by mass spectrometry 241203_DC2p4_membrane_PD_DMSO-post_Slot2-12_1_8506.d.zip 1 1 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available 241203_DC2p4_membrane_PD_DMSO-post_Slot2-12_1_8507.d.zip proteomic profiling by mass spectrometry 241203_DC2p4_membrane_PD_DMSO-post_Slot2-12_1_8507.d.zip 1 2 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available 241203_DC2p4_membrane_PD_DMSO-post_Slot2-12_1_8508.d.zip proteomic profiling by mass spectrometry 241203_DC2p4_membrane_PD_DMSO-post_Slot2-12_1_8508.d.zip 1 3 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available 241203_DC2p4_membrane_PD_NHS-biotin-post_Slot2-13_1_8503.d.zip proteomic profiling by mass spectrometry 241203_DC2p4_membrane_PD_NHS-biotin-post_Slot2-13_1_8503.d.zip 1 4 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available 241203_DC2p4_membrane_PD_NHS-biotin-post_Slot2-13_1_8504.d.zip proteomic profiling by mass spectrometry 241203_DC2p4_membrane_PD_NHS-biotin-post_Slot2-13_1_8504.d.zip 1 5 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available 241203_DC2p4_membrane_PD_NHS-biotin-post_Slot2-13_1_8505.d.zip proteomic profiling by mass spectrometry 241203_DC2p4_membrane_PD_NHS-biotin-post_Slot2-13_1_8505.d.zip 1 6 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available 241203_DC2p4_membrane_global_CMW_Slot2-15_1_8516.d.zip proteomic profiling by mass spectrometry 241203_DC2p4_membrane_global_CMW_Slot2-15_1_8516.d.zip 1 7 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available 241203_DC2p4_membrane_global_CMW_Slot2-15_1_8518.d.zip proteomic profiling by mass spectrometry 241203_DC2p4_membrane_global_CMW_Slot2-15_1_8518.d.zip 1 8 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available 241203_DC2p4_membrane_global_CMW_Slot2-15_1_8520.d.zip proteomic profiling by mass spectrometry 241203_DC2p4_membrane_global_CMW_Slot2-15_1_8520.d.zip 1 9 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available combined.prot.xml proteomic profiling by mass spectrometry combined.prot.xml 1 10 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available combined_peptide.tsv proteomic profiling by mass spectrometry combined_peptide.tsv 1 11 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available combined_protein.tsv proteomic profiling by mass spectrometry combined_protein.tsv 1 12 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available fragger.params proteomic profiling by mass spectrometry fragger.params 1 13 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
Comment on lines +11 to +14

@qodo-code-review qodo-code-review Bot Sep 17, 2026

Copy link
Copy Markdown

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Action required

2. Analysis outputs become instrument runs 📘 Rule violation ≡ Correctness

Rows 11–15 assign combined.prot.xml, combined peptide and protein tables, fragger.params, and
fragpipe.workflow to assay name and comment[data file] with a timsTOF HT instrument and
data-dependent acquisition method. These processed outputs and settings are consequently represented
as five additional acquisition fractions after the nine actual .d.zip runs.
Agent Prompt 
## Issue description
PXD061317 incorrectly represents processed reports, result tables, and FragPipe configuration files as mass-spectrometry acquisitions.

## Fix Focus Areas
- datasets/PXD061317/PXD061317.sdrf.tsv[11-15]

## Recommended Fix
Delete rows 11–15 containing `combined.prot.xml`, the combined peptide and protein TSV reports, `fragger.params`, and `fragpipe.workflow`, so the SDRF retains only the acquired `.d.zip` files as assays. Ensure the retained fraction identifiers remain consistent.

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

PXD061317-sample mus musculus not applicable not applicable not applicable not available 1 synthetic reference not available not available not available not available fragpipe.workflow proteomic profiling by mass spectrometry fragpipe.workflow 1 14 AC=MS:1002038;NT=label free sample NT=timsTOF HT;AC=MS:1003404 NT=Data-dependent acquisition;AC=PRIDE:0000449 NT=Trypsin;AC=MS:1001251 NT=Lys-C;AC=MS:1001309 NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable NT=HCD;AC=PRIDE:0000590 not available not available not available not available cross-linking mass spectrometry NT=unknown crosslinker;AC=XLMOD:00000 not available not available not available not available not available v1.1.0 NT=ms-proteomics;VV=v1.1.0 NT=crosslinking;VV=v1.0.0 NT=vertebrates;VV=v1.1.0
Loading
Loading