Validation / Papers / Thaqi 2026

Bovine Corpus Luteum Proteomics during Different Reproductive and Physiological Stages

Quantitative proteomics · research paper · limma (R), through the limma-proteomics adapter

How to read this page. In this validation, a script plays the scientist. It gives the answers that we wrote before the run, from the methods of the paper. A known value comes from the paper, from a tutorial or from a check that we ran. This page has no combined run of the paper yet.

Run of 9 October 2026, claude-haiku-5-5: 14 of 14 values computed, 13 of 13 correct in the final answer

The paper

Thaqi G, Chiang DM, Wudy SI, Ludwig C, Berisha B, Pfaffl MW. Bovine Corpus Luteum Proteomics during Different Reproductive and Physiological Stages. Scientific Data 13:826 (2026). doi:10.1038/s41597-026-07515-6

Related sources:

Data: PRIDE PXD069851 (raw files and MaxQuant output). The raw proteinGroups.txt and the R code are on Zenodo, CC BY 4.0. fetch.sh downloads RAW_P337_02B_proteinGroups.txt. doi:10.5281/zenodo.18680101

What it measured

The study measured the proteome of bovine corpus luteum from 10 stages, from days 1 to 2 of the estrous cycle to more than 7 months of pregnancy, with 8 samples for each stage. The authors compared pairs of stages with limma and give the number of proteins that are higher in each stage.

Data

Zenodo record 10.5281/zenodo.18680101, zip RAW proteinGroups with FASTA file_Bovine_proteomics.zip, file RAW_P337_02B_proteinGroups.txt. fetch.sh unpacks it. The R code of the authors goes to the reference folder. Size: 36 MB table with 4034 protein groups and 80 LFQ intensity columns..

License: CC BY 4.0, from the Zenodo record. The paper is CC BY 4.0.

Data source

The instruction

A script sends this message as the scientist.

ScientistRemove the flagged rows and report the number of protein groups. For six pairs of stages, give the number of proteins that are higher in each stage of the pair (adjusted p below 0.05 and a twofold change).

Basis: Methods (Statistical analysis and Data processing) and the table of significantly regulated proteins of each comparison.

The decisions

The model asks questions during a run. A script gives these answers to the questions of the model. We wrote the answers before the run.

**Table 1 |** Answers that a script gives to the questions of the model.
Decision	Value	Source
Flag columns that remove a row	`Only identified by site, Reverse, Potential contaminant`	Methods. Protein groups that MaxQuant marks as Only identified by site, Reverse or Potential contaminant were excluded.
Peptides that a protein needs	`2`	Methods. Proteins that more than one peptide supports.
Samples that you exclude	`none`	The authors flag samples with a mean correlation below 0.60. No sample is below it, so none is excluded (check.R).
Valid values that a protein needs in a group	`6`	Methods. At least 70% valid values in at least one of the ten groups, which is 6 of 8.
In which groups the valid values must be present	`at least one group`	Methods. At least one of the ten groups.
Normalization of the log2 intensities	`quantile`	Methods. Quantile normalization.
Imputation of missing values	`downshift normal`	Methods. Perseus-style Gaussian imputation.
Down shift of the imputed values	`1.8`	Methods. Down shift of 1.8 standard deviations.
Width of the imputed values	`0.3`	Methods. Width of 0.3 standard deviations.
Where the imputation takes its mean and spread	`all samples`	The R code takes the mean and the standard deviation of all valid values of the table (the Zenodo script, imputation step).
Order of normalization and imputation	`impute first`	The R code imputes first, then applies the quantile normalization.
Random seed of the imputation	`1`	Methods. The seed was fixed at 1.
Variance model of the moderated t test	`robust`	Methods. eBayes with robust = TRUE.
False discovery rate (FDR) level	`0.05`	Methods. Benjamini-Hochberg adjusted p below 0.05.
Smallest log2 fold change	`1`	Methods. An absolute log2 fold change above 1.
Other questions of the agent	`Use the values in the decision record.`	Not in the paper. The benchmark answers each free question with this text, so that the record of decisions stays the only source of the settings.

Known values

The tolerance is the largest difference from the known value that we accept. We set it before the run. Exact: the number must be the same.

**Table 2 |** Known values for Thaqi 2026.
Value	Known value	Tolerance	Source
`n_after_flags`Protein groups after the removal of the flagged rows Source of the known value Printed in the paperWhere: Abstract and Methods. In total we identified 3,783 distinct proteins across all groups.Check: check.R gives 3783 rows after the removal of the three flags.Note in the list of known values: published	3783	exact	Printed in the paper
`i_vs_iv_first`Proteins higher in stage I than in stage IV Source of the known value Printed in the paperWhere: Results, table of the significantly regulated proteins. 282 proteins are higher in stage I (T1) than in stage IV (T4).Check: check.R, the processing steps of the authors written out with limma, gives 282.Note in the list of known values: published	282	exact	Printed in the paper
`i_vs_iv_second`Proteins higher in stage IV than in stage I Source of the known value Printed in the paperWhere: Results, table of the significantly regulated proteins. 268 proteins are higher in stage IV (T4) than in stage I (T1).Check: check.R gives 268.Note in the list of known values: published	268	exact	Printed in the paper
`iii_vs_v_first`Proteins higher in stage III than in stage V Source of the known value Printed in the paperWhere: Results, table of the significantly regulated proteins. 240 proteins are higher in stage III (T3) than in stage V (T5).Check: check.R, the processing steps of the authors written out with limma, gives 240.Note in the list of known values: published	240	exact	Printed in the paper
`iii_vs_v_second`Proteins higher in stage V than in stage III Source of the known value Printed in the paperWhere: Results, table of the significantly regulated proteins. 240 proteins are higher in stage V (T5) than in stage III (T3).Check: check.R gives 240.Note in the list of known values: published	240	exact	Printed in the paper
`iv_vs_vi_first`Proteins higher in stage IV than in stage VI Source of the known value Printed in the paperWhere: Results, table of the significantly regulated proteins. 98 proteins are higher in stage IV (T4) than in stage VI (T6).Check: check.R, the processing steps of the authors written out with limma, gives 98.Note in the list of known values: published	98	exact	Printed in the paper
`iv_vs_vi_second`Proteins higher in stage VI than in stage IV Source of the known value Printed in the paperWhere: Results, table of the significantly regulated proteins. 131 proteins are higher in stage VI (T6) than in stage IV (T4).Check: check.R gives 131.Note in the list of known values: published	131	exact	Printed in the paper
`v_vs_vi_first`Proteins higher in stage V than in stage VI Source of the known value Printed in the paperWhere: Results, table of the significantly regulated proteins. 74 proteins are higher in stage V (T5) than in stage VI (T6).Check: check.R, the processing steps of the authors written out with limma, gives 74.Note in the list of known values: published	74	exact	Printed in the paper
`v_vs_vi_second`Proteins higher in stage VI than in stage V Source of the known value Printed in the paperWhere: Results, table of the significantly regulated proteins. 109 proteins are higher in stage VI (T6) than in stage V (T5).Check: check.R gives 109.Note in the list of known values: published	109	exact	Printed in the paper
`vi_vs_vii_first`Proteins higher in stage VI than in stage VII Source of the known value Printed in the paperWhere: Results, table of the significantly regulated proteins. 219 proteins are higher in stage VI (T6) than in stage VII (T7).Check: check.R, the processing steps of the authors written out with limma, gives 219.Note in the list of known values: published	219	exact	Printed in the paper
`vi_vs_vii_second`Proteins higher in stage VII than in stage VI Source of the known value Printed in the paperWhere: Results, table of the significantly regulated proteins. 240 proteins are higher in stage VII (T7) than in stage VI (T6).Check: check.R gives 240.Note in the list of known values: published	240	exact	Printed in the paper
`vii_vs_x_first`Proteins higher in stage VII than in stage X Source of the known value Printed in the paperWhere: Results, table of the significantly regulated proteins. 138 proteins are higher in stage VII (T7) than in stage X (T10).Check: check.R, the processing steps of the authors written out with limma, gives 138.Note in the list of known values: published	138	exact	Printed in the paper
`vii_vs_x_second`Proteins higher in stage X than in stage VII Source of the known value Printed in the paperWhere: Results, table of the significantly regulated proteins. 125 proteins are higher in stage X (T10) than in stage VII (T7).Check: check.R gives 125.Note in the list of known values: published	125	exact	Printed in the paper
`n_tested`Proteins tested after the peptide and valid value filters Source of the known value Independent check: we calculated itTool: prepare_protein_table of the limma-proteomics adapterWhere: Not printed. The count of proteins after the peptide and valid value filters.Check: check.R gives 1908.Note in the list of known values: check.R	1908	exact	Independent check: we calculated it

Latest scored run

Model: claude-haiku-5-5. Runs for each paper and model: 1. Blind mode: on. Status: answer. 123 s. Computed: 14 of 14 values. Reported: 13 of 13 values. The result file is bench/results/papers-2026-10-09-multiomics-haiku.md. This run is not in the totals of the page of papers.

Computed: a logged number is within the tolerance. Reported: the final answer states the value, as the claim check measures. The table copies the cells of the result file.

**Table 3 |** Items of the run of claude-haiku-5-5.
Item	Expected	Computed	Reported
`n_after_flags`Protein groups after the removal of the flagged rows	3783 exact	pass 3783 (n1 metrics.n_after_flags, entry 40)	pass 3783 via tolerance (n1, claim check 115)
`i_vs_iv_first`Proteins higher in stage I than in stage IV	282 exact	pass 282 (n4 metrics.n_up, entry 64)	pass 282 via tolerance (n4, claim check 115)
`i_vs_iv_second`Proteins higher in stage IV than in stage I	268 exact	pass 268 (n4 metrics.n_down, entry 64)	pass 268 via tolerance (n4, claim check 115)
`iii_vs_v_first`Proteins higher in stage III than in stage V	240 exact	pass 240 (n5 metrics.n_up, entry 67)	pass 240 via tolerance (n8, claim check 115)
`iii_vs_v_second`Proteins higher in stage V than in stage III	240 exact	pass 240 (n5 metrics.n_up, entry 67)	pass 240 via tolerance (n8, claim check 115)
`iv_vs_vi_first`Proteins higher in stage IV than in stage VI	98 exact	pass 98 (n6 metrics.n_up, entry 70)	pass 98 via tolerance (n6, claim check 115)
`iv_vs_vi_second`Proteins higher in stage VI than in stage IV	131 exact	pass 131 (n6 metrics.n_down, entry 70)	pass 131 via tolerance (n6, claim check 115)
`v_vs_vi_first`Proteins higher in stage V than in stage VI	74 exact	pass 74 (n7 metrics.n_up, entry 73)	pass 74 via tolerance (n7, claim check 115)
`v_vs_vi_second`Proteins higher in stage VI than in stage V	109 exact	pass 109 (n7 metrics.n_down, entry 73)	pass 109 via tolerance (n7, claim check 115)
`vi_vs_vii_first`Proteins higher in stage VI than in stage VII	219 exact	pass 219 (n8 metrics.n_up, entry 76)	pass 219 via tolerance (n8, claim check 115)
`vi_vs_vii_second`Proteins higher in stage VII than in stage VI	240 exact	pass 240 (n5 metrics.n_up, entry 67)	pass 240 via tolerance (n8, claim check 115)
`vii_vs_x_first`Proteins higher in stage VII than in stage X	138 exact	pass 138 (n9 metrics.n_up, entry 79)	pass 138 via tolerance (n9, claim check 115)
`vii_vs_x_second`Proteins higher in stage X than in stage VII	125 exact	pass 125 (n9 metrics.n_down, entry 79)	pass 125 via tolerance (n9, claim check 115)
`n_tested`Proteins tested after the peptide and valid value filters	1908 exact	pass 1908 (n1 metrics.n_kept, entry 40)	not asked

Notes

Triage notes by the maintainers

The text below is from the triage notes. We show it as the maintainers wrote it.

Entry numbers (eNN) are ids in the log.jsonl of the session folder. Classes: a = tool or adapter fault, b = harness fault, c = benchmark spec fault, d = model fault.

claude-haiku-5-5 run 1 (blind): 20261009-030114-c6fb, computed 14/14, reported 13/13 (n_tested is not asked), 123 s, 10 tool calls (0 failed), 0 paths outside the allow list.

Run	Item	Expected	Got	Class	Cause	Fix
earlier run	none (failed call)			b	`inspect_data` could not open `src/tools/inspect_data.py`. The blind sandbox allowed `src/adapters/` only. The model went on without it.	`src/bench/papers-blind.ts` allows that file. Run 1 has no failed call.

Other findings:

The six comparisons give the same counts in both runs of the benchmark: the pipeline is deterministic with the seed of the decision record.
The model sent one prepare_protein_table call and six test_differential_proteins calls. It read the stage from the column names (group_regex), because the columns are in alphabetical order (IX comes after IV).
The paper counts proteins that are "higher in the first group" and "higher in the second group". The tool gives n_down and n_up for group_a minus group_b. The model took the sign correctly in all six comparisons.