PepLocus

Map mass-spectrometry peptides directly to eukaryotic genome assemblies, including splice-junction peptides. PepLocus searches all six reading frames, always treats I/L as equivalent, and can use GTF/GFF annotations or RNA-seq BAM evidence.

Install

Requires Python 3.9 or newer. Linux and macOS are recommended.

python -m pip install "git+https://github.com/qussai96/PepLocus.git"

Once published on PyPI:

python -m pip install peplocus

Dependencies are installed automatically; no external aligner is needed.

Run

Map a peptide list to an assembly:

peplocus -a assembly.fa -p peptides.tsv --out results

Add annotation and/or RNA-seq evidence to find splice-junction placements:

peplocus -a assembly.fa -p peptides.tsv -g models.gtf -b rnaseq.bam --out results_spliced

-g accepts GTF or GFF. Either -g or -b can be used alone. A BAM index is not required.

Optional one-edit rescue searches peptides with no exact match for one amino-acid substitution, insertion or deletion:

peplocus -a assembly.fa -p peptides.tsv -g models.gtf --rescue-one-edit --out results_rescue

The default is 8 workers (--threads). Rescue uses a minimum query length of 9 aa; short candidates can be highly ambiguous. Use --min-rescue-length 12 for a more conservative search. --discover-junctions optionally searches for bounded canonical single-intron matches without supplied evidence.

Peptides can be a plain list, FASTA, CSV or TSV; FragPipe's Peptide Sequence column is recognised automatically. Assembly FASTA may be plain or gzip-compressed. Use a fresh output directory for each run.

peplocus -h

Results

BED files use standard BED12 coordinates, with peptide names in biological N-to-C orientation on both strands. Rescue candidates are kept separately in rescue/, with their own all/tryptic BED files and detailed TSV. A reusable junctions.tsv is also saved when splice evidence is supplied.

Contiguous matching is exhaustive for the chosen translation table. Splice mapping depends on available junctions and search limits. Placements show sequence compatibility; one-edit candidates are not confirmed variants, and tryptic compatibility alone does not establish biological origin.

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