Pioneer and Altimeter: Fast Analysis of DIA Proteomics Data Optimized for Narrow Isolation Windows

2026 · doi:10.64898/2026.02.16.706201
preprint OA: closed
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The paper studied how to enable faster, more accurate data-independent acquisition (DIA) proteomics analysis as experiments become larger and increasingly use narrow isolation windows that distort MS2 spectra via fragment isotope effects, leading to systematic deviations from spectral libraries. The authors developed open-source tools, Pioneer and Altimeter, which explicitly model isolation-window effects by predicting deisotoped fragment intensities and by re-isotoping predicted spectra per scan, using an intensity-aware fragment index, spectral deconvolution, and dual-window quantification. Across instruments, experimental designs, and sample inputs, the methods achieved high-confidence identification and precise quantification at scale while completing analyses 2–6x faster and maintaining conservative false-discovery rate control. This paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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Abstract

Advances in mass spectrometry have enabled increasingly fast data-independent acquisition (DIA) experiments, producing datasets whose scale and complexity challenge existing analysis tools. Those same advances have also led to the use of narrow isolation windows, which alter MS2 spectra via fragment isotope effects and give rise to systematic deviations from spectral libraries. Here we introduce Pioneer and Altimeter, open-source tools for fast DIA analysis with explicit modeling of isolation-window effects. Altimeter predicts deisotoped fragment intensity as a continuous function of collision energy, allowing a single spectral library to be reused across datasets. Pioneer re-isotopes predicted spectra per scan and combines an intensity-aware fragment index, spectral deconvolution, and dual-window quantification for fast, spectrum-centric DIA analysis. Across instruments, experimental designs, and sample inputs, Pioneer enables high-confidence identification and precise quantification at scale, completing analyses 2–6x faster and maintaining conservative false-discovery rate control.
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Abstract Advances in mass spectrometry have enabled increasingly fast data-independent acquisition (DIA) experiments, producing datasets whose scale and complexity challenge existing analysis tools. Those same advances have also led to the use of narrow isolation windows, which alter MS2 spectra via fragment isotope effects and give rise to systematic deviations from spectral libraries. Here we introduce Pioneer and Altimeter, open-source tools for fast DIA analysis with explicit modeling of isolation-window effects. Altimeter predicts deisotoped fragment intensity as a continuous function of collision energy, allowing a single spectral library to be reused across datasets. Pioneer re-isotopes predicted spectra per scan and combines an intensity-aware fragment index, spectral deconvolution, and dual-window quantification for fast, spectrum-centric DIA analysis. Across instruments, experimental designs, and sample inputs, Pioneer enables high-confidence identification and precise quantification at scale, completing analyses 2–6x faster and maintaining conservative false-discovery rate control. Competing Interest Statement The authors have declared no competing interest. Footnotes Author "Michael Major" was changed to "Michael B. Major"

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