pirl-unc / hitlist / 24108904093
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coverage: 33.52%. Remained the same
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Curate top human + non-human studies, flag non-MS data (49 PMIDs) (#10)

* Curate top 10 uncurated human immunopeptidome studies (44 total PMIDs)

Critical findings:
- PMID 32903714 (Wendorff 2020): NOT immunopeptidome data — peptide
  binding microarray. Flagged with exclude_from_ms: true.
- PMID 33968037: IEDB tissue "Lymphoid" is WRONG (MDA-MB-231 is breast)
- PMID 32157095: "healthy skin" is WRONG (melanoma cell lines);
  matched normal lung is adjacent, not healthy
- PMID 32938616: "Lymph Node" is WRONG (melanoma cell lines, not tissue)

Perturbation studies added:
- 33968037: IFN-gamma 50 IU/mL 48h on TNBC
- 29242379: IFN-gamma 100 IU/mL 24h on B-LCLs + ovarian CA
- 32938616: IFN-gamma on melanoma cell lines
- 33592498: CIITA transduction forcing HLA-II on GBM

Also added:
- 34357683: C1R HLA-II haplodome (71K class II peptides)
- 32350084: HLA-DP allelic variants (EBV-LCLs + K562)
- 30315122: mono-allelic spliced peptide study (17 alleles)
- 32387766: THP-1 deep immunopeptidome (42K peptides)

* Curate top 10 human + 5 non-human studies, flag 3 non-MS datasets (49 PMIDs)

New human studies (top 10 by uncurated peptide count):
- 33968037: TNBC ± IFNg (tissue mislabeled as "Lymphoid")
- 29242379: Mixed B-LCLs/ovarian/meningioma/TILs ± IFNg
- 34357683: C1R HLA-II haplodome (71K class II)
- 32938616: Melanoma spliced peptides ± IFNg (cell lines, not "Lymph Node")
- 32350084: HLA-DP allelic variants (EBV-LCLs + K562)
- 32157095: Melanoma + lung (adjacent normal mislabeled as "healthy")
- 33592498: GBM CIITA-transduced (forced HLA-II expression)
- 30315122: Mono-allelic spliced peptides (17 alleles)
- 32387766: THP-1 deep immunopeptidome (42K peptides)

Non-human species:
- 33460454: Tasmanian devil DFTD (26K peptides, DFT1 ± IFNg, DFT2, fibroblasts)
- 26811146: Rhesus Mamu-B*08 vs HLA-B*27 (elite controller alleles)
- 34428180: Mouse transplant tolerance (42K peptides, AAV, Tap1 KO, skin grafts)

Flagged as NOT immunopeptidome data (exclude_from_ms:... (continued)

478 of 1426 relevant lines covered (33.52%)

0.34 hits per line

Jobs
ID Job ID Ran Files Coverage
1 24108904093.1 15
33.52
 GitHub Action Run
Source Files on build 24108904093