Pioneer and its companion tool, Altimeter, are together an open-source and performant solution for analysis of protein MS data acquired by data-independent acquisition (DIA). Poineer includes routines for searching DIA experments from Thermo and Sciex instruments and for building spectral libraries using the Koina interface. Given a spectral library of precursor fragment ion intensities and retention time estimates, Pioneer identifies and quantifies peptides and protein groups from the library in the data.
- Open-Source: Pioneer is completely open source.
- Cross-Platform: Pioneer and the .raw file conversion tool run on Linux, MacOS, and Windows
- High-Performance: Pioneer achieves high sensitivity, FDR control, and both quantitative precision and accuracy on benhcmark datat-sets
- Scalability: Memory consumption and speed should remain constant as the number of raw files in an analysis grows. Pioneer should scale to very large experiments with hundreds to thousands of raw files (experimental)
- Fast: Pioneer searches data several times faster than it can be aquired and faster than state-of-the-art search tools.
See documentation for full installation and usage instructions.
Download the installer for your operating system from the releases page. The installer adds a pioneer command to your PATH.
pioneer --helpLists subcommands such as predict, params-predict, search, params-search, convert-raw, and convert-mzml.
On the first run macOS performs a Gatekeeper security check.
A minimal end-to-end workflow is:
pioneer params-predict lib_dir lib_name fasta_dir --params-path=predict_params.json
pioneer predict predict_params.json
pioneer convert-raw raw_dir
pioneer params-search library.poin ms_data_dir results_dir --params-path=search_params.json
pioneer search search_params.jsonparams-predict and params-search write template JSON files. Review and edit these configurations before running predict or search. See the
Parameter Configuration
guide for available options.
Pioneer can also be run from a Docker container:
docker pull dennisgoldfarb/pioneer:latestRun Pioneer inside the container, mounting a host directory to access your data:
docker run --rm -it -v /path/on/host:/work dennisgoldfarb/pioneer:latest pioneer --helpReplace /path/on/host with the directory containing your data and pioneer --help with any Pioneer subcommand. The repository includes a Dockerfile for building the image locally:
docker build -t pioneer .We welcome contributions! Please see our Contributing Guide for details on our Git Flow workflow and development process.
Pioneer is developed in the Goldfarb Lab: https://goldfarblab.wustl.edu
