Pioneer identifies and quantifies precursors and proteins from data-independent
acquisition (DIA) experiments. Pioneer runs through both a graphical and a command-line interface,
and it scales to thousands of runs on standard desktop hardware.
Released November 9, 2026 for macOS, Windows, and Linux.
Bruker timsTOF Ultra AIP, 120 SPD
170 runs of oral squamous cell carcinoma tissue from
Klingeberg et al., Mol. Cell. Proteomics 2026
(PXD069877), searched against an in silico library of the human proteome.
To test scaling, the 340- and 680-run searches include each of the 170 files
two and four times. Pioneer analyses were carried out on one 16-core, 64 GB node.
Protein groups from a human, yeast, and E. coli mixture. Dashed lines mark the expected
ratios. Data from this work (PXD074310).
Thermo Orbitrap Astral, 180 SPD, yeast knockouts
312 runs (104 yeast knockout strains in triplicate, 8 minutes per run) from
Guzman et al., Nat. Biotechnol. 2024
(PXD046386). The 1,248-, 4,992- and 9,984-run searches include each file 4, 16 and 32
times. Search time on one 16-core, 64 GB node.
Searches files many times faster than data acquisition with whole-proteome in silico libraries, even on the latest fast-scanning TOF instruments.
Scalable
Processes experiments with hundreds to thousands of runs on standard desktop hardware (32–64 GB of RAM).
Deep Proteome Coverage
Delivers high sensitivity, quantitative precision, and accuracy on diverse benchmark datasets.
Regression Testing and FDR Control
Maintains a public suite of regression tests across diverse instruments and acquisition schemes. Each tagged release triggers searches on the benchmark datasets, which include entrapment false discovery rate and false transfer rate analyses. Browse the benchmarks.
Non-Commercial License
If seeking a commercial license, please contact Washington University's Office of
Technology Management:
otm@wustl.edu.
Read the license.
Citing Pioneer
Wamsley, N. T., Wilkerson, E. M., Major, M., Goldfarb, D. "Pioneer and Altimeter: Fast Analysis of DIA Proteomics Data Optimized for Narrow Isolation Windows." bioRxiv (2026).
doi:10.64898/2026.02.16.706201