thymus + ligandome: the mouse side, from deposits that needed no reprocessing
Browse files`thymus/SOURCES.md` carried a `## Not here` block saying a mouse thymic reference would
mean reprocessing raw spectra. That turned out to be wrong about two of the deposits.
PXD008733 ships five Trans-Proteomic Pipeline PSM tables (850,396 PSMs, 151 MB) beside its
raw spectra, with DECOY_ entries to recompute the FDR from and the immunoprecipitating
antibody encoded in every run name. So:
thymus/thymus_immunopeptidome_mmu.tsv.gz 4,969 rows / 3,835 peptides
ligandome/tissue_self_mmu.tsv.gz 46,334 rows / 17,256 peptides, 18 tissues
Peptide-level FDR recomputed at 1% (probability_ip >= 0.974142; 35,470 target against 354
decoy peptides). Requiring an sp| protein leaves 32,827 distinct peptides across 19 tissues
against the 28,448 the paper reports, so the cutoff is neither loose nor lossy.
`mhc_a` is as-reported, never predicted: Y3 -> H-2Kb, B22 -> H-2Db, M5/M15 -> I-Ab. The
mapping is checked, not assumed -- on 9-mers it yields H-2Kb P5=F 48%, P9=L 49% and H-2Db
P5=N 77%, P9=L/I/V 48/22/10%, the canonical anchor motifs. Spelling is the pmhc/+ligandome/
form H-2Kb / H-2Db / I-Ab, not the H2-Kb of the contaminated CEDAR rows.
`source_protein` is re-derived by exact lookup against proteome/mouse.fasta.gz rather than
trusted per deposit, because the deposits name proteins three incompatible ways. I and L are
not collapsed: MS cannot tell them apart, so an I/L-collapsed match would assert an
identification the data does not carry.
Two things this does NOT claim. The MHC class II (I-Ab) thymic arm, MSV000087031, ships raw
spectra only and its re-search is still running -- documented in thymus/SOURCES.md, absent
from the table. And PXD031966 stays out entirely: its runs are labelled NOD2_3/NOD4/NOD5,
which names no tissue, and its peptides will not be called thymic on a guess.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
- DESCRIPTION.md +19 -6
- ligandome/SOURCES.md +67 -3
- ligandome/tissue_self_mmu.tsv.gz +3 -0
- thymus/SOURCES.md +133 -8
- thymus/thymus_immunopeptidome_mmu.tsv.gz +3 -0
|
@@ -39,12 +39,23 @@ silently admits mouse pMHC. Pre-existing and left unfixed; `neoag_tested_mmu.tsv
|
|
| 39 |
correctly-labelled murine set.
|
| 40 |
|
| 41 |
The `thymus/` tables use the reference-peptide schema (`peptide, mhc_a, mhc_class, mhc_species,
|
| 42 |
-
source_protein, species, dataset_origin`
|
| 43 |
-
donor-level candidate alleles, not a per-peptide deconvolution, and the seqtree
|
| 44 |
-
use is peptide-level
|
| 45 |
-
|
| 46 |
-
|
| 47 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 48 |
|
| 49 |
## Public datasets (this repo)
|
| 50 |
|
|
@@ -85,10 +96,12 @@ Every tracked directory now carries one:
|
|
| 85 |
| `proteome/mouse.fasta.gz` | Mouse proteome (UP000000589) | C57BL/6 self-reference proteome |
|
| 86 |
| `proteome/*_UP*.fasta.gz` | 16 bacterial + viral reference proteomes | foreign-antigen references for molecular-mimicry scans and peptide-flank extraction; see `proteome/README.md` |
|
| 87 |
| `thymus/thymus_immunopeptidome.tsv.gz` | Thymus self-peptidome (human) | HLA Ligand Atlas thymus-eluted self peptides (25.9k MHC-I + 28.0k MHC-II) β central-tolerance "self" reference for seqtree; fills the mislabeled source #1 |
|
|
|
|
| 88 |
| `thymus/thymus_expression.tsv.gz` | Thymus expression (human) | thymically expressed self: HPA thymus-cluster genes (126) + atlas thymus source proteins (10.4k) |
|
| 89 |
| `ligandome/viral_foreign_iedb.tsv.gz` | Viral ligandome (IEDB) | viral-source presented peptides (foreign reference) |
|
| 90 |
| `ligandome/viral_orfs_gse272406.tsv.gz` | Pan-viral ORFs (GSE272406) | translated novel viral ORF proteins (foreign; *not* thymus self β spec mislabel) |
|
| 91 |
| `ligandome/cancer_targets_tsarina.tsv.gz` | Cancer-testis antigens | curated shared tumor-antigen genes (tsarina) |
|
|
|
|
| 92 |
| `summary.tsv` | Pipeline stats | row counts & extraction metrics |
|
| 93 |
|
| 94 |
## Private (gitignored β NOT in this repo)
|
|
|
|
| 39 |
correctly-labelled murine set.
|
| 40 |
|
| 41 |
The `thymus/` tables use the reference-peptide schema (`peptide, mhc_a, mhc_class, mhc_species,
|
| 42 |
+
source_protein, species, dataset_origin`). In the human file `mhc_a` is null β the HLA Ligand Atlas
|
| 43 |
+
gives donor-level candidate alleles, not a per-peptide deconvolution, and the seqtree
|
| 44 |
+
self-similarity use is peptide-level.
|
| 45 |
+
|
| 46 |
+
**Thymus peptides are no longer human-only.** `thymus_immunopeptidome_mmu.tsv.gz` (2026-08-21)
|
| 47 |
+
carries the mouse side, from three deposits: the thymus slice of the Schuster murine MHC-I tissue
|
| 48 |
+
atlas (PXD008733) and sorted cTEC/mTEC (PXD042241), with a third β a re-search of the Nanaware
|
| 49 |
+
I-Ab thymic raw spectra (MSV000087031), the only source of mouse **class II** thymic ligands β
|
| 50 |
+
still running and **not yet in this revision**. PXD008733 turned out **not** to require
|
| 51 |
+
reprocessing after all β it ships
|
| 52 |
+
Trans-Proteomic Pipeline PSM tables alongside the raw spectra, with `DECOY_` entries to recompute
|
| 53 |
+
the FDR from and the immunoprecipitating antibody encoded in the run name, so `mhc_a` is populated
|
| 54 |
+
there (`H-2Kb` / `H-2Db` / `I-Ab`, as-reported, never predicted). Its other 18 tissues are deposited
|
| 55 |
+
separately as `ligandome/tissue_self_mmu.tsv.gz`. `thymus_expression.tsv.gz` is still human-only:
|
| 56 |
+
the mouse thymus proteome (PXD007288) is a 12 GB MaxQuant archive and the mTEC-TRA gene list
|
| 57 |
+
(Sansom GSE53111) is journal-supplement-only. See `thymus/SOURCES.md` for the per-deposit FDR
|
| 58 |
+
regimes, which differ and are not interchangeable.
|
| 59 |
|
| 60 |
## Public datasets (this repo)
|
| 61 |
|
|
|
|
| 96 |
| `proteome/mouse.fasta.gz` | Mouse proteome (UP000000589) | C57BL/6 self-reference proteome |
|
| 97 |
| `proteome/*_UP*.fasta.gz` | 16 bacterial + viral reference proteomes | foreign-antigen references for molecular-mimicry scans and peptide-flank extraction; see `proteome/README.md` |
|
| 98 |
| `thymus/thymus_immunopeptidome.tsv.gz` | Thymus self-peptidome (human) | HLA Ligand Atlas thymus-eluted self peptides (25.9k MHC-I + 28.0k MHC-II) β central-tolerance "self" reference for seqtree; fills the mislabeled source #1 |
|
| 99 |
+
| `thymus/thymus_immunopeptidome_mmu.tsv.gz` | Thymus self-peptidome (mouse) | 4,969 rows / 3,835 distinct peptides, `mhc_species=MusMusculus`. Whole thymus H-2Kb (1,089) + H-2Db (1,574) from the Schuster atlas PSM tables at a recomputed 1% peptide FDR, plus 2,304 peptides from sorted cTEC/mTEC (PXD042241, PEAKS β10lgP β₯ 20). `mhc_a` is as-reported from the IP antibody, never predicted. The MHC-II (I-Ab) arm is pending β see `thymus/SOURCES.md` |
|
| 100 |
| `thymus/thymus_expression.tsv.gz` | Thymus expression (human) | thymically expressed self: HPA thymus-cluster genes (126) + atlas thymus source proteins (10.4k) |
|
| 101 |
| `ligandome/viral_foreign_iedb.tsv.gz` | Viral ligandome (IEDB) | viral-source presented peptides (foreign reference) |
|
| 102 |
| `ligandome/viral_orfs_gse272406.tsv.gz` | Pan-viral ORFs (GSE272406) | translated novel viral ORF proteins (foreign; *not* thymus self β spec mislabel) |
|
| 103 |
| `ligandome/cancer_targets_tsarina.tsv.gz` | Cancer-testis antigens | curated shared tumor-antigen genes (tsarina) |
|
| 104 |
+
| `ligandome/tissue_self_mmu.tsv.gz` | Tissue self-ligandome (mouse) | 46,334 rows / 17,256 distinct peptides across **18 non-thymic tissues**, Schuster murine MHC-I atlas (PXD008733) at a recomputed 1% peptide FDR. H-2Kb 8,829 + H-2Db 7,781 peptides (MHC-I) and 4,348 I-Ab (MHC-II); carries a `tissue` column. Tumour cell lines (EL4, B16F10, GL261, LLC) excluded β they are not normal tissue |
|
| 105 |
| `summary.tsv` | Pipeline stats | row counts & extraction metrics |
|
| 106 |
|
| 107 |
## Private (gitignored β NOT in this repo)
|
|
@@ -1,8 +1,8 @@
|
|
| 1 |
# `ligandome/` β sources, provenance and citations
|
| 2 |
|
| 3 |
-
|
| 4 |
-
peptide looks like, what a novel viral ORF looks like,
|
| 5 |
-
enough to be targeted safely.
|
| 6 |
|
| 7 |
Every citation below was resolved against **PubMed** and carries its PMID and DOI. Where a source
|
| 8 |
could not be resolved, that is stated as unresolved rather than filled in with a plausible guess.
|
|
@@ -145,6 +145,66 @@ not a verification).
|
|
| 145 |
|
| 146 |
---
|
| 147 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 148 |
## Re-fetch / regenerate
|
| 149 |
|
| 150 |
None of these three are regenerated by this repository β they are deposited as fetched.
|
|
@@ -155,6 +215,10 @@ None of these three are regenerated by this repository β they are deposited as
|
|
| 155 |
# https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE272406
|
| 156 |
# cancer_targets_tsarina:
|
| 157 |
# pip install tsarina # https://github.com/pirl-unc/tsarina (CTA table export)
|
|
|
|
|
|
|
|
|
|
|
|
|
| 158 |
|
| 159 |
## Audit note on `DESCRIPTION.md`
|
| 160 |
|
|
|
|
| 1 |
# `ligandome/` β sources, provenance and citations
|
| 2 |
|
| 3 |
+
Four reference sets used as *background* rather than as labelled training data: what a foreign
|
| 4 |
+
peptide looks like, what a novel viral ORF looks like, which self genes are tumour-restricted
|
| 5 |
+
enough to be targeted safely, and what a mouse presents outside the thymus.
|
| 6 |
|
| 7 |
Every citation below was resolved against **PubMed** and carries its PMID and DOI. Where a source
|
| 8 |
could not be resolved, that is stated as unresolved rather than filled in with a plausible guess.
|
|
|
|
| 145 |
|
| 146 |
---
|
| 147 |
|
| 148 |
+
## `tissue_self_mmu.tsv.gz`
|
| 149 |
+
|
| 150 |
+
Mouse **self** peptides eluted from 18 normal tissues β the non-thymic counterpart to
|
| 151 |
+
`thymus/thymus_immunopeptidome_mmu.tsv.gz`, and the first mouse self-ligandome in this compendium.
|
| 152 |
+
|
| 153 |
+
| | |
|
| 154 |
+
|---|---|
|
| 155 |
+
| rows | **46,334** (17,256 distinct peptides) |
|
| 156 |
+
| columns | `peptide`, `mhc_a`, `mhc_class`, `mhc_species`, `source_protein`, `species`, `tissue`, `dataset_origin` |
|
| 157 |
+
| class | MHC-I 13,139 distinct Β· MHC-II 4,348 distinct |
|
| 158 |
+
| host | MusMusculus, 100% (C57BL/6) |
|
| 159 |
+
| alleles | `H-2Kb`, `H-2Db` (MHC-I) Β· `I-Ab` (MHC-II) |
|
| 160 |
+
| tissues | 18 |
|
| 161 |
+
| provenance | **experimental** β MS-eluted ligands; identifications and the FDR cutoff **derived** |
|
| 162 |
+
|
| 163 |
+
**Origin.** PRIDE [PXD008733](https://www.ebi.ac.uk/pride/archive/projects/PXD008733), the deposit's
|
| 164 |
+
own Trans-Proteomic Pipeline PSM tables (`raw_first_batch.csv`, `raw_second_batch.csv`,
|
| 165 |
+
`raw_third_batch.csv`, `raw_orbi.csv`, `raw_lumos.csv` β 850,396 PSMs, 151 MB), not its raw spectra.
|
| 166 |
+
|
| 167 |
+
> Schuster H, Shao W, Weiss T, Pedrioli PGA, Roth P, Weller M, Campbell DS, Deutsch EW, Moritz RL,
|
| 168 |
+
> Planz O, Rammensee HG, Aebersold R, Caron E.
|
| 169 |
+
> **A tissue-based draft map of the murine MHC class I immunopeptidome.**
|
| 170 |
+
> *Sci Data* 2018;5:180157.
|
| 171 |
+
> PMID [30084848](https://pubmed.ncbi.nlm.nih.gov/30084848/) Β·
|
| 172 |
+
> doi:[10.1038/sdata.2018.157](https://doi.org/10.1038/sdata.2018.157)
|
| 173 |
+
|
| 174 |
+
**The FDR is recomputed here, not inherited.** The PSM tables carry `DECOY_`-prefixed entries, so
|
| 175 |
+
distinct peptides were ranked by best `probability_ip` (iProphet) and the largest set with
|
| 176 |
+
decoy/target β€ 0.01 kept: **`probability_ip` β₯ 0.974142 β 35,470 target peptides against 354 decoy
|
| 177 |
+
peptides, 0.0100 estimated peptide-level FDR**. Requiring an `sp|` protein then drops the `iRT`
|
| 178 |
+
spike-ins, `CONT_*` and `LMP_*` entries, leaving 32,827 distinct peptides across all 19 tissues β
|
| 179 |
+
against the 28,448 the paper reports, so the cutoff is neither loose nor lossy.
|
| 180 |
+
|
| 181 |
+
**`mhc_a` is the immunoprecipitating antibody, as reported β not a prediction.** The `spectrum`
|
| 182 |
+
field names the run and the run name names the antibody: **Y3 β H-2Kb**, **B22 β H-2Db**,
|
| 183 |
+
**M5 / M15 / M15classII β I-Ab** (C57BL/6 is I-Ab only; *Ea* is deleted in the b haplotype). The
|
| 184 |
+
mapping is checked rather than assumed β on 9-mers it yields H-2Kb P5 = F 48%, P9 = L 49% and
|
| 185 |
+
H-2Db P5 = N 77%, P9 = L/I/V 48/22/10%, the canonical Kb and Db anchor motifs.
|
| 186 |
+
|
| 187 |
+
**Why it matters here.** `mimicry`'s `self` channel is a *proteome* β being encoded is not being
|
| 188 |
+
presented. This is the first mouse set that says which self peptides are actually presented, and by
|
| 189 |
+
which allele, in tissue a T cell can reach. Paired with the thymic deposit it separates two
|
| 190 |
+
different tolerance arguments: met during negative selection (thymus) versus reachable in the
|
| 191 |
+
periphery (here).
|
| 192 |
+
|
| 193 |
+
**Caveats.**
|
| 194 |
+
- Cell lines in the source atlas (EL4, B16F10, GL261, LLC/LLC1/LLC2) are **excluded** β tumour
|
| 195 |
+
lines, not normal tissue.
|
| 196 |
+
- Coverage is very uneven, and it is sampling depth, not biology: small_intestine carries 5,635
|
| 197 |
+
MHC-I peptides and spinal_cord 239. Do not read a tissue's peptide count as presentation breadth.
|
| 198 |
+
- MHC-II coverage is incidental β only a few runs used an anti-I-A/I-E antibody, so 15 of 18 tissues
|
| 199 |
+
have under 200 MHC-II peptides and five have fewer than 10.
|
| 200 |
+
- `source_protein` is **re-derived** by exact lookup against `proteome/mouse.fasta.gz`, not taken
|
| 201 |
+
from the deposit. I and L are not collapsed: MS cannot distinguish them, so an I/L-collapsed match
|
| 202 |
+
would assert an identification the data does not carry. 3 rows map to no mouse protein.
|
| 203 |
+
- 28,833 rows were dropped by the length filter (MHC-I 8β11, MHC-II 11β25, matching
|
| 204 |
+
`mhcmatch.mimics._LEN`) because every consumer drops them silently anyway.
|
| 205 |
+
|
| 206 |
+
---
|
| 207 |
+
|
| 208 |
## Re-fetch / regenerate
|
| 209 |
|
| 210 |
None of these three are regenerated by this repository β they are deposited as fetched.
|
|
|
|
| 215 |
# https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE272406
|
| 216 |
# cancer_targets_tsarina:
|
| 217 |
# pip install tsarina # https://github.com/pirl-unc/tsarina (CTA table export)
|
| 218 |
+
# tissue_self_mmu: regenerated, unlike the three above.
|
| 219 |
+
# cd ~/vcs/projects/2026-mouse-thymus
|
| 220 |
+
# aria2c -i src/urls_results.txt -d ~/hf/pmhc_data/raw/thymus_mouse -x4 -j3 --continue
|
| 221 |
+
# ./src/ingest_pxd008733.py && ./src/build_tissue_mmu.py
|
| 222 |
|
| 223 |
## Audit note on `DESCRIPTION.md`
|
| 224 |
|
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:7559895435b9f0f8c37e56137b13be88e4a1a8edc10c879fb780861ad3b32076
|
| 3 |
+
size 691877
|
|
@@ -1,8 +1,12 @@
|
|
| 1 |
# `thymus/` β sources
|
| 2 |
|
| 3 |
The central-tolerance reference: what a developing T-cell repertoire was negatively selected
|
| 4 |
-
against.
|
| 5 |
-
harmonisation into this schema is computed.
|
|
|
|
|
|
|
|
|
|
|
|
|
| 6 |
|
| 7 |
## `thymus_immunopeptidome.tsv.gz` β 53,878 rows
|
| 8 |
|
|
@@ -14,7 +18,8 @@ Thymus-eluted self peptides, **HLA Ligand Atlas** (`dataset_origin = hla_ligand_
|
|
| 14 |
| MHCI | 25,891 |
|
| 15 |
|
| 16 |
Schema: `peptide`, `mhc_a`, `mhc_class`, `mhc_species`, `source_protein`, `species`,
|
| 17 |
-
`dataset_origin`. Human only.
|
|
|
|
| 18 |
|
| 19 |
**A hit here is a tolerance argument and an autoimmunity flag, and those are the same fact read two
|
| 20 |
ways**: a neoantigen resembling a thymically presented peptide had its reactive clones plausibly
|
|
@@ -22,6 +27,92 @@ deleted (lower expected immunogenicity), and a vaccine built on it risks cross-r
|
|
| 22 |
`mhcmatch.mimics` keeps it as its own category for exactly that reason and never sums it with the
|
| 23 |
foreign ones β see `mhcmatch.mimics.KINDS`.
|
| 24 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 25 |
## `thymus_expression.tsv.gz` β 10,493 rows
|
| 26 |
|
| 27 |
Thymically expressed self, by gene. Schema: `gene`, `species`, `evidence`, `value`.
|
|
@@ -33,11 +124,45 @@ Thymically expressed self, by gene. Schema: `gene`, `species`, `evidence`, `valu
|
|
| 33 |
|
| 34 |
The two lines of evidence are kept in a column rather than pooled: one is "a peptide from this
|
| 35 |
protein was eluted from thymus", the other is "this gene is thymus-enriched by expression". They
|
| 36 |
-
support each other; they are not interchangeable.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 37 |
|
| 38 |
## Not here
|
| 39 |
|
| 40 |
-
**No mouse thymus
|
| 41 |
-
proteome (PXD007288) is a 12 GB MaxQuant archive
|
| 42 |
-
|
| 43 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
# `thymus/` β sources
|
| 2 |
|
| 3 |
The central-tolerance reference: what a developing T-cell repertoire was negatively selected
|
| 4 |
+
against. All three files are **experimental** (mass spectrometry / antibody-based expression); the
|
| 5 |
+
harmonisation into this schema, and every FDR cutoff, is computed.
|
| 6 |
+
|
| 7 |
+
Human and mouse are separate files rather than one two-species table, matching the `_mmu` / `_hsa`
|
| 8 |
+
convention in `neoantigens/`. Every consumer already filters on `mhc_species`, and the human deposit
|
| 9 |
+
is an LFS object all of them read.
|
| 10 |
|
| 11 |
## `thymus_immunopeptidome.tsv.gz` β 53,878 rows
|
| 12 |
|
|
|
|
| 18 |
| MHCI | 25,891 |
|
| 19 |
|
| 20 |
Schema: `peptide`, `mhc_a`, `mhc_class`, `mhc_species`, `source_protein`, `species`,
|
| 21 |
+
`dataset_origin`. Human only. `mhc_a` is empty throughout β the atlas gives donor-level candidate
|
| 22 |
+
alleles, not a per-peptide deconvolution.
|
| 23 |
|
| 24 |
**A hit here is a tolerance argument and an autoimmunity flag, and those are the same fact read two
|
| 25 |
ways**: a neoantigen resembling a thymically presented peptide had its reactive clones plausibly
|
|
|
|
| 27 |
`mhcmatch.mimics` keeps it as its own category for exactly that reason and never sums it with the
|
| 28 |
foreign ones β see `mhcmatch.mimics.KINDS`.
|
| 29 |
|
| 30 |
+
## `thymus_immunopeptidome_mmu.tsv.gz` β the mouse counterpart
|
| 31 |
+
|
| 32 |
+
Same schema, column for column. `mhc_species = species = MusMusculus` throughout. Added 2026-08-21;
|
| 33 |
+
this file is what the `## Not here` block of this document used to say was impossible.
|
| 34 |
+
|
| 35 |
+
**4,969 rows / 3,835 distinct peptides** as deposited here.
|
| 36 |
+
|
| 37 |
+
| `dataset_origin` | `mhc_class` | `mhc_a` | rows | peptides |
|
| 38 |
+
|---|---|---|--:|--:|
|
| 39 |
+
| `pride_pxd008733_thymus` | MHCI | `H-2Db` | 1,574 | 1,574 |
|
| 40 |
+
| `pride_pxd008733_thymus` | MHCI | `H-2Kb` | 1,089 | 1,089 |
|
| 41 |
+
| `pride_pxd008733_thymus` | MHCII | `I-Ab` | 2 | 2 |
|
| 42 |
+
| `pride_pxd042241_tec` | MHCI | *(empty)* | 2,304 | 2,304 |
|
| 43 |
+
|
| 44 |
+
MHC-I lengths run 8β11 with a median of 9. The two MHC-II rows are all that survive the 11β25 window
|
| 45 |
+
from PXD008733's 16 thymic anti-I-A/I-E PSMs β that immunoprecipitation returned mostly 9β10mers,
|
| 46 |
+
which is the class-I-length contamination the Nanaware paper is about. 121 rows carry an empty
|
| 47 |
+
`source_protein`; they are PXD042241 peptides from non-canonical ORFs that are not in UP000000589.
|
| 48 |
+
|
| 49 |
+
Unlike the human file, `mhc_a` is populated where the deposit records an immunoprecipitating
|
| 50 |
+
antibody, in the `pmhc/`+`ligandome/` spelling `H-2Kb` / `H-2Db` / `I-Ab` β **not** the `H2-Kb` form
|
| 51 |
+
found in the contaminated CEDAR rows of `neoantigens/neoag_tested.tsv.gz`. It is as-reported
|
| 52 |
+
attribution; nothing is predicted, and it is empty where the immunoprecipitation was pan-H-2.
|
| 53 |
+
|
| 54 |
+
### `pride_pxd008733_thymus` β whole thymus, H-2Kb and H-2Db
|
| 55 |
+
|
| 56 |
+
The thymus slice of the murine MHC-I tissue atlas; the other 18 tissues are in
|
| 57 |
+
`ligandome/tissue_self_mmu.tsv.gz`, which carries the full provenance and the FDR derivation.
|
| 58 |
+
|
| 59 |
+
> Schuster H, Shao W, Weiss T, Pedrioli PGA, Roth P, Weller M, Campbell DS, Deutsch EW, Moritz RL,
|
| 60 |
+
> Planz O, Rammensee HG, Aebersold R, Caron E.
|
| 61 |
+
> **A tissue-based draft map of the murine MHC class I immunopeptidome.**
|
| 62 |
+
> *Sci Data* 2018;5:180157.
|
| 63 |
+
> PMID [30084848](https://pubmed.ncbi.nlm.nih.gov/30084848/) Β·
|
| 64 |
+
> doi:[10.1038/sdata.2018.157](https://doi.org/10.1038/sdata.2018.157)
|
| 65 |
+
|
| 66 |
+
Taken from the deposit's own Trans-Proteomic Pipeline PSM tables, not its raw spectra. Peptide-level
|
| 67 |
+
FDR recomputed from the deposit's `DECOY_` entries at 1%: `probability_ip` β₯ 0.974142, 35,470 target
|
| 68 |
+
against 354 decoy peptides.
|
| 69 |
+
|
| 70 |
+
### `pride_pxd042241_tec` β sorted cortical and medullary thymic epithelial cells
|
| 71 |
+
|
| 72 |
+
The cells that actually induce central tolerance, which whole thymus dilutes.
|
| 73 |
+
|
| 74 |
+
> Larouche JD, Laumont CM, Trofimov A, Vincent K, Hesnard L, Brochu S, CΓ΄tΓ© C, Humeau JF,
|
| 75 |
+
> Bonneil Γ, Lanoix J, Durette C, Gendron P, Laverdure JP, Richie ER, Lemieux S, Thibault P,
|
| 76 |
+
> Perreault C.
|
| 77 |
+
> **Transposable elements regulate thymus development and function.**
|
| 78 |
+
> *eLife* 2024;12:e91037.
|
| 79 |
+
> PMID [38635416](https://pubmed.ncbi.nlm.nih.gov/38635416/) Β·
|
| 80 |
+
> doi:[10.7554/eLife.91037](https://doi.org/10.7554/eLife.91037)
|
| 81 |
+
|
| 82 |
+
`mhc_a` is empty: the deposit does not name the immunoprecipitating antibody.
|
| 83 |
+
|
| 84 |
+
**Its FDR is not recomputable, and the cutoff is a stated convention.** The mzid declares
|
| 85 |
+
`no threshold` at protocol level and carries no decoy entries, and its `passThreshold` attribute is
|
| 86 |
+
not a quality filter β it passes PSMs down to β10lgP = 5.00 while rejecting others up to 35.62.
|
| 87 |
+
The retained set is rank-1 PSMs at **PEAKS β10lgP β₯ 20**. That cutoff is doing real work: 8β11mers
|
| 88 |
+
rise from 67.2% to 82.0% of distinct peptides and 9-mers from 28.0% to 38.1%. It is **not** a
|
| 89 |
+
measured 1% FDR and must not be described as one.
|
| 90 |
+
|
| 91 |
+
Source proteins in this deposit are Ensembl and transposable-element identifiers from a personalized
|
| 92 |
+
mTEC/cTEC database, so peptides derived from non-canonical ORFs carry an empty `source_protein`
|
| 93 |
+
after re-mapping.
|
| 94 |
+
|
| 95 |
+
### `massive_msv000087031_thymus` β I-Ab, the MHC class II arm β **pending, not in this revision**
|
| 96 |
+
|
| 97 |
+
The only source of mouse **class II** thymic ligands. No identifications were deposited, so this arm
|
| 98 |
+
is a re-search of the raw spectra with nf-core/mhcquant 3.2.0, which is still running on aldan3 at
|
| 99 |
+
the time of this commit. **No `massive_msv000087031_thymus` rows are present in the file yet** β the
|
| 100 |
+
two `dataset_origin` values it currently carries are `pride_pxd008733_thymus` and
|
| 101 |
+
`pride_pxd042241_tec`. This section documents the arm so the provenance is written down once; the
|
| 102 |
+
counts land with it.
|
| 103 |
+
|
| 104 |
+
> Nanaware PP, Jurewicz MM, Clement CC, Lu L, Santambrogio L, Stern LJ.
|
| 105 |
+
> **Distinguishing Signal From Noise in Immunopeptidome Studies of Limiting-Abundance Biological
|
| 106 |
+
> Samples: Peptides Presented by I-A^b in C57BL/6 Mouse Thymus.**
|
| 107 |
+
> *Front Immunol* 2021;12:658601.
|
| 108 |
+
> PMID [33995376](https://pubmed.ncbi.nlm.nih.gov/33995376/) Β·
|
| 109 |
+
> doi:[10.3389/fimmu.2021.658601](https://doi.org/10.3389/fimmu.2021.658601)
|
| 110 |
+
|
| 111 |
+
Twelve of the deposit's 37 runs β the four thymus samples (`120116WTII`, `020617WT_MHCII`,
|
| 112 |
+
`061417MHCII_WT1`, `061417MHCII_WT2`) in three technical replicates each. The splenic B-cell and
|
| 113 |
+
dendritic-cell arms and the human LCL runs are deliberately **not** included: this is a thymic
|
| 114 |
+
reference, and pooling peripheral APCs into it would destroy the distinction the file exists to make.
|
| 115 |
+
|
| 116 |
## `thymus_expression.tsv.gz` β 10,493 rows
|
| 117 |
|
| 118 |
Thymically expressed self, by gene. Schema: `gene`, `species`, `evidence`, `value`.
|
|
|
|
| 124 |
|
| 125 |
The two lines of evidence are kept in a column rather than pooled: one is "a peptide from this
|
| 126 |
protein was eluted from thymus", the other is "this gene is thymus-enriched by expression". They
|
| 127 |
+
support each other; they are not interchangeable. Human only β there is no mouse counterpart yet.
|
| 128 |
+
|
| 129 |
+
## Caveats on the mouse file
|
| 130 |
+
|
| 131 |
+
- **It is not the human file's equal in size, and cannot be.** The human deposit is one large
|
| 132 |
+
multi-donor atlas; the mouse side is assembled from three smaller studies with different
|
| 133 |
+
antibodies, instruments and search pipelines. Read the `dataset_origin` column before pooling.
|
| 134 |
+
- **Three different FDR regimes are present**, one per `dataset_origin` β a recomputed 1%
|
| 135 |
+
peptide-level FDR (PXD008733), a stated PEAKS score convention (PXD042241), and mhcquant's 1%
|
| 136 |
+
peptide-level FDR (MSV000087031). They are not interchangeable; the column is the handle.
|
| 137 |
+
- `source_protein` is **re-derived** by exact lookup against `proteome/mouse.fasta.gz`, not taken
|
| 138 |
+
from the deposits, because the three name their proteins in three incompatible ways. I and L are
|
| 139 |
+
not collapsed β MS cannot distinguish them, so an I/L-collapsed match would assert an
|
| 140 |
+
identification the data does not carry.
|
| 141 |
+
- Lengths are clipped to `mhcmatch.mimics._LEN` (MHC-I 8β11, MHC-II 11β25) because every consumer
|
| 142 |
+
drops the rest silently.
|
| 143 |
|
| 144 |
## Not here
|
| 145 |
|
| 146 |
+
**No mouse thymus *expression* table.** The mTEC-TRA gene list (Sansom, GSE53111) is
|
| 147 |
+
journal-supplement-only, and the mouse thymus proteome (PXD007288) is a 12 GB MaxQuant archive.
|
| 148 |
+
`thymus_expression.tsv.gz` stays human-only until one of those is processed β **absent, not
|
| 149 |
+
overlooked**.
|
| 150 |
+
|
| 151 |
+
**PXD031966 is not here, and that is a labelling problem rather than a data problem.** The NOD-mouse
|
| 152 |
+
MHC-I deposit covers thymus *and* pancreas, but its experiment labels (`ICR1`, `ICR6`, `NOD2_3`,
|
| 153 |
+
`NOD4`, `NOD5`) name neither, PMID 36210013 is closed-access with no PMC copy, and its deposited
|
| 154 |
+
tables give 30β50 peptides per run β too few for the pancreatic acinar signature
|
| 155 |
+
(Cela/Prss/Cpa/Ctrb/Pnlip) to separate the two. Its peptides will not be labelled `thymus` on a
|
| 156 |
+
guess. See `~/vcs/projects/2026-mouse-thymus/SOURCES.md`.
|
| 157 |
+
|
| 158 |
+
## Re-fetch / regenerate
|
| 159 |
+
|
| 160 |
+
cd ~/vcs/projects/2026-mouse-thymus
|
| 161 |
+
# results-only deposits (671 MB); verify every file against PRIDE's SHA-1 `checksum` field
|
| 162 |
+
aria2c -i src/urls_results.txt -d ~/hf/pmhc_data/raw/thymus_mouse -x4 -j3 --continue
|
| 163 |
+
./src/ingest_pxd008733.py
|
| 164 |
+
./src/ingest_pxd042241.py
|
| 165 |
+
# MSV000087031 raw spectra + re-search, on aldan3
|
| 166 |
+
aldan3 slurm submit src/fetch_raw.sbatch -- <srcdir> <destdir>
|
| 167 |
+
aldan3 slurm submit src/mhcquant.sbatch -- mhc2 /projects/hla_epitope/mouse_thymus
|
| 168 |
+
./src/build_thymus_mmu.py
|
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:29fcc416692d12f9d7836f09cdacf17ede3e1c9323bc04149cae524f944bca97
|
| 3 |
+
size 77778
|