context-ms 0.1.1

Context-aware confidence estimation for targeted proteomics

Context: Confidence Estimation for Targeted Proteomics

Overview

Context produces PSM- and peptide-level q-values and PEPs for targeted mass-spec assays. Because the target panel is usually too small to train Percolator directly, Context trains Percolator on the non-target PSMs from the same run (a large, statistically well-behaved background) and transfers the learned linear discriminant to score the target panel. pyIsoPEP (q2pep) then computes FDR + q-values from TDC scores and fits an isotonic spline q -> PEP, separately at the PSM and peptide levels.

Context is distributed as both a container image (Podman-, Docker- and Apptainer-compatible) and a Python package exposing the same CLI.

---

Installation

PyPI

pip install context-ms

Context is a Python package with one external dependency: Percolator. For PyPI installations, either a local percolator executable on PATH or a container runtime (Podman or Docker) must be available. Context uses the local executable when present; otherwise, it runs ghcr.io/percolator/percolator:master through Podman or Docker (set with --container-cmd, default podman).

Container image

podman pull ghcr.io/shannon225/context:main
# or
apptainer build context.sif docker://ghcr.io/shannon225/context:main

---

Input & output

Input: two Percolator-compatible tsv files for non-target and target PSMs/peptides. They must share an identical header (same columns, same order).

Output: for context run --nontarget NT --target TG --prefix P --outdir results/ --seed K:

results/
  weights/P.seedK.weights.txt           # raw Percolator weights (3 CV-bin rows)
  P.seedK.rescored_features.tsv         # target features rescored with the seed weights
  P.seedK.psm.target.txt                # PSM-level target output
  P.seedK.peptide.target.txt            # peptide-level target output

---

Command-line reference

context run -h

flag	default	description
--nontarget FILE	required	nontarget (background) feature TSV used to train Percolator
--target FILE	required	target panel feature TSV
--prefix STR	required	output prefix for results files
--outdir DIR	results	where outputs land
--seed INT	1	Percolator seed
--container-cmd CMD	podman	container runtime for the Percolator / pyIsoPEP fallback paths (podman or docker)

---

Examples

PyPI

context run \
  --nontarget example/nontarget.tsv \
  --target    example/target.tsv \
  --prefix    run01 \
  --outdir    results

Container image

# Podman
podman run --rm -v "$PWD:/work" -w /work \
  ghcr.io/shannon225/context:main \
  run --nontarget example/nontarget.tsv --target example/target.tsv \
      --prefix run01 --outdir results

# Apptainer
apptainer run --bind "$PWD:/work" --pwd /work context.sif \
  run --nontarget example/nontarget.tsv --target example/target.tsv \
      --prefix run01 --outdir results

---

Links

• PyPI package: https://pypi.org/project/context-ms
• Container image: https://github.com/shannon225/Context/pkgs/container/context
• GitHub repository: https://github.com/shannon225/Context
• Percolator: http://percolator.ms
• pyIsoPEP: https://github.com/statisticalbiotechnology/smooth_q_to_pep