thymus/SOURCES.md

thymus/ — sources

The central-tolerance reference: what a developing T-cell repertoire was negatively selected against. All three files are experimental (mass spectrometry / antibody-based expression); the harmonisation into this schema, and every FDR cutoff, is computed.

Human and mouse are separate files rather than one two-species table, matching the _mmu / _hsa convention in neoantigens/. Every consumer already filters on mhc_species, and the human deposit is an LFS object all of them read.

thymus_immunopeptidome.tsv.gz — 53,878 rows

Thymus-eluted self peptides, HLA Ligand Atlas (dataset_origin = hla_ligand_atlas_thymus).

mhc_class	rows
MHCII	27,987
MHCI	25,891

Schema: peptide, mhc_a, mhc_class, mhc_species, source_protein, species, dataset_origin. Human only. mhc_a is empty throughout — the atlas gives donor-level candidate alleles, not a per-peptide deconvolution.

A hit here is a tolerance argument and an autoimmunity flag, and those are the same fact read two ways: a neoantigen resembling a thymically presented peptide had its reactive clones plausibly deleted (lower expected immunogenicity), and a vaccine built on it risks cross-reacting with self. mhcmatch.mimics keeps it as its own category for exactly that reason and never sums it with the foreign ones — see mhcmatch.mimics.KINDS.

thymus_immunopeptidome_mmu.tsv.gz — the mouse counterpart

Same schema, column for column. mhc_species = species = MusMusculus throughout. Added 2026-08-21; this file is what the ## Not here block of this document used to say was impossible.

8,151 rows / 6,791 distinct peptides as deposited here.

dataset_origin	mhc_class	mhc_a	peptides
massive_msv000087031_thymus	MHCII	I-Ab	1,488
pride_pxd008733_thymus	MHCI	H-2Db	1,574
pride_pxd008733_thymus	MHCI	H-2Kb	1,089
pride_pxd008733_thymus	MHCII	I-Ab	2
pride_pxd031966_thymus	MHCI	(empty)	1,694
pride_pxd042241_tec	MHCI	(empty)	2,304

1,490 class-II and 5,301 class-I distinct peptides. 148 rows carry an empty source_protein.

MHC-I lengths run 8–11 with a median of 9. The two MHC-II rows are all that survive the 11–25 window from PXD008733's 16 thymic anti-I-A/I-E PSMs — that immunoprecipitation returned mostly 9–10mers, which is the class-I-length contamination the Nanaware paper is about. 121 rows carry an empty source_protein; they are PXD042241 peptides from non-canonical ORFs that are not in UP000000589.

Unlike the human file, mhc_a is populated where the deposit records an immunoprecipitating antibody, in the pmhc/+ligandome/ spelling H-2Kb / H-2Db / I-Ab — not the H2-Kb form found in the contaminated CEDAR rows of neoantigens/neoag_tested.tsv.gz. It is as-reported attribution; nothing is predicted, and it is empty where the immunoprecipitation was pan-H-2.

pride_pxd008733_thymus — whole thymus, H-2Kb and H-2Db

The thymus slice of the murine MHC-I tissue atlas; the other 18 tissues are in ligandome/tissue_self_mmu.tsv.gz, which carries the full provenance and the FDR derivation.

Schuster H, Shao W, Weiss T, Pedrioli PGA, Roth P, Weller M, Campbell DS, Deutsch EW, Moritz RL, Planz O, Rammensee HG, Aebersold R, Caron E. A tissue-based draft map of the murine MHC class I immunopeptidome. Sci Data 2018;5:180157. PMID 30084848 · doi:10.1038/sdata.2018.157

Taken from the deposit's own Trans-Proteomic Pipeline PSM tables, not its raw spectra. Peptide-level FDR recomputed from the deposit's DECOY_ entries at 1%: probability_ip ≥ 0.974142, 35,470 target against 354 decoy peptides.

pride_pxd042241_tec — sorted cortical and medullary thymic epithelial cells

The cells that actually induce central tolerance, which whole thymus dilutes.

Larouche JD, Laumont CM, Trofimov A, Vincent K, Hesnard L, Brochu S, Côté C, Humeau JF, Bonneil É, Lanoix J, Durette C, Gendron P, Laverdure JP, Richie ER, Lemieux S, Thibault P, Perreault C. Transposable elements regulate thymus development and function. eLife 2024;12:e91037. PMID 38635416 · doi:10.7554/eLife.91037

mhc_a is empty: the deposit does not name the immunoprecipitating antibody.

Its FDR is not recomputable, and the cutoff is a stated convention. The mzid declares no threshold at protocol level and carries no decoy entries, and its passThreshold attribute is not a quality filter — it passes PSMs down to −10lgP = 5.00 while rejecting others up to 35.62. The retained set is rank-1 PSMs at PEAKS −10lgP ≥ 20. That cutoff is doing real work: 8–11mers rise from 67.2% to 82.0% of distinct peptides and 9-mers from 28.0% to 38.1%. It is not a measured 1% FDR and must not be described as one.

Source proteins in this deposit are Ensembl and transposable-element identifiers from a personalized mTEC/cTEC database, so peptides derived from non-canonical ORFs carry an empty source_protein after re-mapping.

pride_pxd031966_thymus — NOD mouse, whole thymus

The NOD-mouse MHC-I deposit covers thymus and pancreas, and its run labels name neither: NOD2_3, NOD4, NOD5. PMID 36210013 is closed-access with no PMC copy, and the deposited tables give only 30–50 peptides per run, far too few to tell the two apart. This was recorded here as an open labelling problem, and its peptides were deliberately withheld rather than guessed.

The re-search settled it. Searching the nine raw files against the whole mouse proteome (rather than the deposit's own predicted-binder FASTA) gives 1,700–5,800 peptides per run — enough for the source proteins to speak:

run	thymus-exclusive proteins	acinar zymogen peptides	call
NOD2_3	Prss16 ×3, Psmb11 ×1	4	thymus
NOD4	none	160	pancreas
NOD5	none	145	pancreas

The call is made on presence, not on a ratio. Prss16 is the thymus-specific serine protease and Psmb11 the thymoproteasome subunit β5t, confined to cortical thymic epithelium; neither has a tissue of expression outside thymus in the mouse, so a peptide from either cannot have been eluted from pancreas. The converse holds for the exocrine zymogen program. A ratio is the wrong instrument and would have got this wrong — on a 3× rule NOD2_3 reads "unresolved" at 11 thymic against 4 pancreatic markers, while carrying three Prss16 peptides and a Psmb11 one.

An earlier, looser marker set inflated the thymic signal in both pancreas runs, because it counted Krt5/Krt8/Krt14 — thymic-epithelium markers in a thymus context but generic epithelial keratins elsewhere — and Lck/Zap70/Tcf7, which mark the T-cell infiltrate that is the defining lesion of the NOD pancreas. Those genes are now explicitly excluded; the rule is in src/assign_pxd031966_tissue.py.

Only NOD2_3 is deposited here. NOD4 and NOD5 are in ligandome/tissue_self_mmu.tsv.gz as pancreas.

Wang L, Li X, Yang S, Chen X, Li J, Wang S, Zhang M, Zheng Z, Zhou J, Wang L, Wu Y. Proteomic identification of MHC class I-associated peptidome derived from non-obese diabetic mouse thymus and pancreas. J Proteomics 2022;270:104746. PMID 36210013 · doi:10.1016/j.jprot.2022.104746

mhc_a is empty: the immunoprecipitation used the pan-H-2 antibody M1/42.3.9.8, which resolves no allele. NOD is H-2^g7 (K^d, D^b), so these peptides are not C57BL/6 K^b/D^b ligands — read dataset_origin before pooling them with the PXD008733 rows.

Re-searched, not taken as deposited. The authors searched a predicted-MHC-binder FASTA at 5% PSM FDR; a database of peptides someone already predicted to bind can only return peptides someone already predicted to bind. This is nf-core/mhcquant 3.2.0 against UP000000589 at 1% peptide-level FDR.

massive_msv000087031_thymus — I-Ab, the MHC class II arm

1,488 distinct peptides — the only mouse class-II thymic ligands in the compendium. No identifications were deposited, so this is a re-search of the raw spectra with nf-core/mhcquant 3.2.0: unspecific cleavage, Comet, MS²Rescore (DeepLC + MS²PIP Immuno-HCD), Percolator, 1% peptide-level FDR, against UP000000589 plus contaminants.

Checked as class-II ligands rather than assumed. Median length 16 aa (mean 16.0, range 11–25), matching the ~16 aa thymic peak the source paper reports. 49% of the peptides (733 of 1,488) share a nested core with another peptide in the set — ragged N- and C-termini around a common binding core is the defining signature of MHC class-II processing and does not arise for class I, where the termini are trimmed to the closed groove.

The deposit's 11–25 window removes a peak the paper itself flags. That paper is titled for this problem: the thymic I-Ab length distribution is bimodal, with a second mode near 10 aa that is class-I-length material co-purifying with a limiting-abundance class-II preparation. The window applied here (mhcmatch.mimics._LEN["mhc2"]) drops it by construction — 1,303 rows fell outside the per-class windows across all arms. That is a filter, not a measurement, and it is why the distribution here is unimodal where the paper's is not.

Nanaware PP, Jurewicz MM, Clement CC, Lu L, Santambrogio L, Stern LJ. Distinguishing Signal From Noise in Immunopeptidome Studies of Limiting-Abundance Biological Samples: Peptides Presented by I-A^b in C57BL/6 Mouse Thymus. Front Immunol 2021;12:658601. PMID 33995376 · doi:10.3389/fimmu.2021.658601

Twelve of the deposit's 37 runs — the four thymus samples (120116WTII, 020617WT_MHCII, 061417MHCII_WT1, 061417MHCII_WT2) in three technical replicates each — of which eleven were usable. 061417MHCII_WT1_1.raw is unreadable: it carries the size MassIVE declares (757,890,890 bytes) and a valid Thermo 01a1 "Finnigan" header, but ThermoRawFileParser fails on it with RAW file cannot be processed, so the damage is mid-file. The other eleven convert cleanly. It costs one of three technical replicates of Thymus 3 — not a sample and not a condition. The splenic B-cell and dendritic-cell arms and the human LCL runs are deliberately not included: this is a thymic reference, and pooling peripheral APCs into it would destroy the distinction the file exists to make.

thymus_expression_mmu.tsv.gz — 15,306 rows

The mouse side of the table below, added 2026-08-21. Schema gene, species, evidence, value; species = MusMusculus throughout, and unlike the human file value is populated — it carries the measurement, so a caller can threshold rather than take mere presence as evidence.

evidence	rows	what it is
fantom5_mouse_thymus_tpm	11,862	adult-thymus CAGE median TPM > 0 (E-MTAB-3579)
geiger_silac_thymus_ppb	3,444	thymus SILAC protein abundance > 0 (E-PROT-11)

12,646 distinct genes. The two lines of evidence are kept in a column rather than pooled, exactly as in the human file: one says the gene is transcribed in thymus, the other that its protein was detected there. Full provenance, citations and caveats — including why Aire reads zero — are in expression/SOURCES.md.

thymus_expression.tsv.gz — 10,493 rows

Thymically expressed self, by gene. Schema: gene, species, evidence, value.

evidence	rows	what it is
hpa_thymus_ntpm	16,279	HPA thymus nTPM > 0 — the measured value, added 2026-08-21
hla_ligand_atlas_thymus_source	10,367	source proteins of the peptides above
hpa_thymus_cluster	126	Human Protein Atlas thymus-cluster genes

26,772 rows. The evidence lines are kept in a column rather than pooled, because they are three different statements: a gene is transcribed in thymus, a peptide from its protein was eluted from thymus, and it is thymus-enriched by cluster assignment. They support each other; they are not interchangeable.

Why the hpa_thymus_ntpm line was added. Before it, this table was not quantitative: 10,367 of its 10,493 rows carried an empty value — they record which proteins peptides came from, which is not an expression measurement — and the only rows with content held a text cluster label. The mouse table had numbers and the human one did not. Note also that GTEx has no thymus at all, so the compendium's main safety read cannot answer thymic questions; expression/SOURCES.md records what was searched and why HPA is the source that works.

Caveats on the mouse file

• It is not the human file's equal in size, and cannot be. The human deposit is one large multi-donor atlas; the mouse side is assembled from three smaller studies with different antibodies, instruments and search pipelines. Read the dataset_origin column before pooling.
• Three different FDR regimes are present, one per dataset_origin — a recomputed 1% peptide-level FDR (PXD008733), a stated PEAKS score convention (PXD042241), and mhcquant's 1% peptide-level FDR (MSV000087031). They are not interchangeable; the column is the handle.
• source_protein is re-derived by exact lookup against proteome/mouse.fasta.gz, not taken from the deposits, because the three name their proteins in three incompatible ways. I and L are not collapsed — MS cannot distinguish them, so an I/L-collapsed match would assert an identification the data does not carry.
• Lengths are clipped to mhcmatch.mimics._LEN (MHC-I 8–11, MHC-II 11–25) because every consumer drops the rest silently.

Not here

The mouse thymus expression gap is closed — see thymus_expression_mmu.tsv.gz above. What is still absent is a promiscuous-expression (AIRE-driven TRA) table: the Sansom mTEC-TRA gene list (GSE53111) is journal-supplement-only and the mouse thymus proteome (PXD007288) is a 12 GB MaxQuant archive. Bulk data cannot substitute — Aire itself reads 0 TPM in whole thymus because it is confined to a rare mTEC subset, so the promiscuous-expression question needs sorted mTEC, not this file. Absent, not overlooked.

PXD031966 is now here, and the tissue labels were settled by measurement. See the pride_pxd031966_thymus section above.

Re-fetch / regenerate

cd ~/vcs/projects/2026-mouse-thymus
# results-only deposits (671 MB); verify every file against PRIDE's SHA-1 `checksum` field
aria2c -i src/urls_results.txt -d ~/hf/pmhc_data/raw/thymus_mouse -x4 -j3 --continue
./src/ingest_pxd008733.py
./src/ingest_pxd042241.py
# MSV000087031 raw spectra + re-search, on aldan3
aldan3 slurm submit src/fetch_raw.sbatch -- <srcdir> <destdir>
aldan3 slurm submit src/mhcquant.sbatch -- mhc2 /projects/hla_epitope/mouse_thymus
./src/build_thymus_mmu.py