PXD017740

[nithujohn]

Added SDRF PXD017740: label free, fractionated

[qodo-code-review]

Review Summary by Qodo

Add SDRF PXD017740 label-free fractionated dataset

✨ Enhancement

Walkthroughs

Description

• Added SDRF dataset PXD017740 (label-free, fractionated)
• New proteomics data resource configuration

Diagram

flowchart LR
  A["SDRF Repository"] -- "adds new dataset" --> B["PXD017740<br/>Label-free Fractionated"]

Loading

File Changes

1. sdrf/PXD017740 ✨ Enhancement +265/-0

Add PXD017740 SDRF dataset configuration

• New SDRF dataset configuration file added
• Contains label-free fractionated proteomics data specifications
• Extends SDRF repository with PXD017740 dataset metadata

sdrf/PXD017740

---

[qodo-code-review]

Code Review by Qodo

🐞 Bugs (3) 📘 Rule violations (0) 📎 Requirement gaps (0)

1. Biorep used as fraction 🐞 Bug ≡ Correctness

Description

In sdrf/PXD017740, characteristics[biological replicate] increments across fractions for the
same source name, so each fraction is represented as a different biological replicate/individual.
This will cause downstream consumers that treat biological replicate as the individual ID to
miscount and mis-group samples.

Code

sdrf/PXD017740[R2-5]

+PXD017740_Sample_1	Homo sapiens	intervertebral disc	L4-L5 Intervertebral Space	59	male	normal	1	L4-L5 Intervertebral Space_59_1	proteomic profiling by mass spectrometry	Data dependent acquistion	1	1	VT_1_Fr1.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/01/PXD017740/VT_1_Fr1.raw	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion Lumos;AC=MS:1002732	NT=Trypsin;AC=MS:1001251	NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed	NT=Oxidation;AC=UNIMOD:35;MT=Fixed;TA=M	20 ppm	0.02 Da
+PXD017740_Sample_1	Homo sapiens	intervertebral disc	L4-L5 Intervertebral Space	59	male	normal	2	L4-L5 Intervertebral Space_59_2	proteomic profiling by mass spectrometry	Data dependent acquistion	1	2	VT_1_Fr2.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/01/PXD017740/VT_1_Fr2.raw	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion Lumos;AC=MS:1002732	NT=Trypsin;AC=MS:1001251	NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed	NT=Oxidation;AC=UNIMOD:35;MT=Fixed;TA=M	20 ppm	0.02 Da
+PXD017740_Sample_1	Homo sapiens	intervertebral disc	L4-L5 Intervertebral Space	59	male	normal	3	L4-L5 Intervertebral Space_59_3	proteomic profiling by mass spectrometry	Data dependent acquistion	1	3	VT_1_Fr3.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/01/PXD017740/VT_1_Fr3.raw	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion Lumos;AC=MS:1002732	NT=Trypsin;AC=MS:1001251	NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed	NT=Oxidation;AC=UNIMOD:35;MT=Fixed;TA=M	20 ppm	0.02 Da
+PXD017740_Sample_1	Homo sapiens	intervertebral disc	L4-L5 Intervertebral Space	59	male	normal	4	L4-L5 Intervertebral Space_59_4	proteomic profiling by mass spectrometry	Data dependent acquistion	1	4	VT_1_Fr4.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/01/PXD017740/VT_1_Fr4.raw	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion Lumos;AC=MS:1002732	NT=Trypsin;AC=MS:1001251	NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed	NT=Oxidation;AC=UNIMOD:35;MT=Fixed;TA=M	20 ppm	0.02 Da

Evidence

The new file increments biological replicate alongside fraction identifier for the same `source
name`, while existing SDRFs keep biological replicate constant across fractions; repo scripts also
explicitly reinterpret biological replicate as individual, making this semantic mismatch
impactful.

sdrf/PXD017740[1-5]
sdrf/PXD016999.sdrf.tsv[1-5]
OpenTargets_dataset_Summary_reportfile.py[93-100]

Agent prompt

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

## Issue description
`characteristics[biological replicate]` changes with `comment[fraction identifier]` for the same sample, which encodes fractions as different biological replicates.
### Issue Context
Other SDRFs in this repo keep `characteristics[biological replicate]` constant across fractions and use `comment[fraction identifier]` to distinguish fractions.
### Fix
For each `source name` (e.g., `PXD017740_Sample_1`), set `characteristics[biological replicate]` to a single stable value across all its fraction rows (typically the sample’s replicate/individual ID), leaving `comment[fraction identifier]` as the only fraction-varying field.
### Fix Focus Areas
- sdrf/PXD017740[2-133]

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

---

2. Wrong modification column name ✓ Resolved 🐞 Bug ⚙ Maintainability

Description

The header uses comment[modification parameter] (singular) instead of the repo-standard
comment[modification parameters] (plural). Any tooling expecting the standard column name will
fail to detect modifications for this dataset.

Code

sdrf/PXD017740[1]

+source name	characteristics[organism]	characteristics[organism part]	characteristics[organism part]	characteristics[age]	characteristics[sex]	characteristics[disease]	characteristics[biological replicate]	assay name	technology type	comment[proteomics data acquisition method]	comment[technical replicate]	comment[fraction identifier]	comment[data file]	comment[file uri]	comment[label]	comment[instrument]	comment[cleavage agent details]	comment[modification parameter]	comment[modification parameter]	comment[precursor mass tolerance]	comment[fragment mass tolerance]

Evidence

The added file’s header uses the singular form, while existing SDRFs use the plural form, indicating
a schema mismatch within this repo.

sdrf/PXD017740[1-1]
sdrf/PXD016999.sdrf.tsv[1-1]

Agent prompt

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

## Issue description
Header column name uses `comment[modification parameter]` (singular), which is inconsistent with other SDRFs in this repo.
### Issue Context
Existing SDRFs consistently use repeated `comment[modification parameters]` columns.
### Fix
Rename the two `comment[modification parameter]` columns to `comment[modification parameters]` to match the repository convention.
### Fix Focus Areas
- sdrf/PXD017740[1-1]

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

---

3. Oxidation set as fixed 🐞 Bug ≡ Correctness

Description

The SDRF marks Oxidation (UNIMOD:35) as MT=Fixed, which conflicts with the repo’s other SDRFs that
record Oxidation as MT=Variable. This misstates the modification search settings in metadata
exports/validation.

Code

sdrf/PXD017740[2]

+PXD017740_Sample_1	Homo sapiens	intervertebral disc	L4-L5 Intervertebral Space	59	male	normal	1	L4-L5 Intervertebral Space_59_1	proteomic profiling by mass spectrometry	Data dependent acquistion	1	1	VT_1_Fr1.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/01/PXD017740/VT_1_Fr1.raw	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion Lumos;AC=MS:1002732	NT=Trypsin;AC=MS:1001251	NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed	NT=Oxidation;AC=UNIMOD:35;MT=Fixed;TA=M	20 ppm	0.02 Da

Evidence

The added file encodes Oxidation with MT=Fixed, while multiple existing SDRFs in this repo encode
Oxidation as MT=Variable.

sdrf/PXD017740[2-4]
sdrf/PXD000427.sdrf.tsv[2-2]
sdrf/PXD033060-dia.sdrf.tsv[2-2]

Agent prompt

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

## Issue description
Oxidation (UNIMOD:35) is recorded with `MT=Fixed`.
### Issue Context
Across SDRFs in this repo, Oxidation is consistently represented as a variable modification.
### Fix
If Oxidation was not intentionally fixed for this dataset’s search, change `MT=Fixed` to `MT=Variable` for the Oxidation entries.
### Fix Focus Areas
- sdrf/PXD017740[2-265]

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

---

4. Acquisition method misspelled 🐞 Bug ⚙ Maintainability

Description

comment[proteomics data acquisition method] is set to Data dependent acquistion (misspelled),
which can break controlled matching/validation and makes the SDRF inconsistent with other repo files
that use CV-formatted acquisition method values. This will reduce interoperability of the metadata.

Code

sdrf/PXD017740[2]

+PXD017740_Sample_1	Homo sapiens	intervertebral disc	L4-L5 Intervertebral Space	59	male	normal	1	L4-L5 Intervertebral Space_59_1	proteomic profiling by mass spectrometry	Data dependent acquistion	1	1	VT_1_Fr1.raw	https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/01/PXD017740/VT_1_Fr1.raw	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion Lumos;AC=MS:1002732	NT=Trypsin;AC=MS:1001251	NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed	NT=Oxidation;AC=UNIMOD:35;MT=Fixed;TA=M	20 ppm	0.02 Da

Evidence

The new file contains a spelling error in the acquisition method field; other SDRFs demonstrate
consistent CV-style encoding for the same column.

sdrf/PXD017740[2-2]
sdrf/PXD033060-dia.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 acquisition method value is misspelled as `Data dependent acquistion`.
### Issue Context
Other SDRFs in this repo encode acquisition method values in a controlled `NT=...;AC=...` style.
### Fix
Correct the spelling to `Data dependent acquisition` and, if required by your SDRF conventions/validator, encode it as a CV term (e.g., `NT=...;AC=...`).
### Fix Focus Areas
- sdrf/PXD017740[2-265]

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

---

[coderabbitai]

Warning

Rate limit exceeded

@nithujohn has exceeded the limit for the number of commits that can be reviewed per hour. Please wait 39 minutes and 59 seconds before requesting another review.

You’ve run out of usage credits. Purchase more in the billing tab.

⌛ How to resolve this issue?

After the wait time has elapsed, a review can be triggered using the @coderabbitai review command as a PR comment. Alternatively, push new commits to this PR.

We recommend that you space out your commits to avoid hitting the rate limit.

🚦 How do rate limits work?

CodeRabbit enforces hourly rate limits for each developer per organization.

Our paid plans have higher rate limits than the trial, open-source and free plans. In all cases, we re-allow further reviews after a brief timeout.

Please see our FAQ for further information.

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 7cc6ea46-587a-4b8c-bfc0-f6c6cc101c72

📥 Commits

Reviewing files that changed from the base of the PR and between ea48cff and 4834f4d.

📒 Files selected for processing (1)

• sdrf/PXD017740

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

---

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.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands and usage tips.}