mikessh Claude Opus 5 commited on
Commit
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1 Parent(s): f437d55

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 CHANGED
@@ -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`; `mhc_a` is null β€” the HLA Ligand Atlas gives
43
- donor-level candidate alleles, not a per-peptide deconvolution, and the seqtree self-similarity
44
- use is peptide-level). Thymus data is **human only**: the mouse thymic immunopeptidome (Schuster
45
- PXD008733) is deposited as raw MS with the processed peptides on the now-defunct SysteMHC atlas,
46
- the mouse thymus proteome (PXD007288) is a 12 GB MaxQuant archive, and the mTEC-TRA gene list
47
- (Sansom GSE53111) is journal-supplement-only β€” a mouse pass would require reprocessing raw spectra.
 
 
 
 
 
 
 
 
 
 
 
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 βˆ’10lgP 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)
ligandome/SOURCES.md CHANGED
@@ -1,8 +1,8 @@
1
  # `ligandome/` β€” sources, provenance and citations
2
 
3
- Three 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, and which self genes are tumour-restricted
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 ≀ 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 8–11, MHC-II 11–25, 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
 
ligandome/tissue_self_mmu.tsv.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:7559895435b9f0f8c37e56137b13be88e4a1a8edc10c879fb780861ad3b32076
3
+ size 691877
thymus/SOURCES.md CHANGED
@@ -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. Both files are **experimental** (mass spectrometry / antibody-based expression); the
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 reference.** The candidate deposits do not survive contact: the mouse thymus
41
- proteome (PXD007288) is a 12 GB MaxQuant archive and the mTEC-TRA gene list (Sansom, GSE53111) is
42
- journal-supplement-only, so a mouse pass means reprocessing raw spectra. Recorded in
43
- `DESCRIPTION.md` and open in the benchmark repo's TODO β€” **absent, not overlooked**.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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 8–11 with a median of 9. The two MHC-II rows are all that survive the 11–25 window
45
+ from PXD008733's 16 thymic anti-I-A/I-E PSMs β€” that immunoprecipitation returned mostly 9–10mers,
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 βˆ’10lgP = 5.00 while rejecting others up to 35.62.
87
+ The retained set is rank-1 PSMs at **PEAKS βˆ’10lgP β‰₯ 20**. That cutoff is doing real work: 8–11mers
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 8–11, MHC-II 11–25) 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 30–50 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
thymus/thymus_immunopeptidome_mmu.tsv.gz ADDED
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