pirl-unc / hitlist / 24674298138
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coverage: 44.962% (+0.5%) from 44.456%
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v1.11.1: Add peptide-level bulk proteomics (Bekker-Jensen 2017, #67) (#84)

Adds load_bulk_peptides() — peptide-level shotgun MS detections per
cell line, for building intra-protein MS detectability models.
Complements load_bulk_proteomics() (protein-level abundance) added in
v1.11.0.

Both live in hitlist.bulk_proteomics and are explicitly marked as bulk
shotgun / NOT MHC-ligand data in the module docstring and function
docstrings. No risk of conflation with observations.parquet.

Source: Bekker-Jensen et al. 2017 "An Optimized Shotgun Strategy for
the Rapid Generation of Comprehensive Human Proteomes", Cell Systems
(PMID 28591648, PXD004452). 46-fraction peptide-level MaxQuant output,
parsed from the deposit's SearchResults.zip (ZIP64; peptides.txt was
extracted via range-request without downloading the full 21 GB zip).

5 cell lines, ~1.03M peptide-level detections:

| cell_line | peptides |
|-----------|---------:|
| HEK293    | 243,052  |
| HCT116    | 238,386  |
| A549      | 215,492  |
| MCF7      | 206,809  |
| HeLa      | 128,264  |

HeLa and HEK293 are new — neither is in the CCLE panel (v1.11.0 CCLE
protein-level covers A549, HCT116, Jurkat, K562, MCF7, MDA-MB-231,
THP-1). Peptide and protein indices together now cover 9 cell lines
with substantial hitlist MHC MS overlap.

Schema (hitlist/data/bulk_proteomics/bekker_jensen_2017_peptides.csv.gz,
22 MB):
  peptide, cell_line, uniprot_acc, gene_symbol, length,
  start_position, end_position, source, reference.

start_position/end_position give position within the parent protein —
required for the user's stated goal of modeling intra-protein MS
detectability bias (take top-k proteins by abundance, look at which
tryptic peptides within each are observed vs not).

API additions:
  load_bulk_peptides(cell_line=, gene_name=, uniprot_acc=) -> DataFrame
  available_protein_cell_lines() -> list[str]
  available_peptide_cell_lines() -> list[str]
  available_cell_lines() -> list[str]  # now returns union

1285 of 2858 relevant lines covered (44.96%)

0.45 hits per line

Jobs
ID Job ID Ran Files Coverage
1 24674298138.1 21
44.96
 GitHub Action Run
Source Files on build 24674298138