A dependency-free, streamable format and cross-language toolkit for scalable LC-MS feature detection: reading only what you need
- 1Murdoch University
Abstract
Mass spectrometry generates data faster than it can be read, and the exchange standard, mzML, is text-based and must be parsed in full before any spectrum is accessible. Binary alternatives are smaller but depend on storage engines such as HDF5, so access is dictated by the engine, not the file. We present Ionic (.ion), an open-source, compact, streamable binary format, and Quant{middle dot}ion, a processing toolkit built on the former. Ionic stores spectra, chromatograms and metadata as independently compressed, indexed blocks, so a reader retrieves only the bytes it needs, even inside a web browser, and converts losslessly to and from mzML. Ionic was smaller than compressed mzMLb on every acquisition type tested, and extracting one compound took under 40 ms, 35 to 90 times faster than an mzML reader. Quant{middle dot}ion exposes one core to R, Python, and JavaScript with identical results, and recovered 97% of true features on a ground-truth benchmark.
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BibTeX
@misc{mosquera2026dependencyfree,
title = {{A dependency-free, streamable format and cross-language toolkit for scalable LC-MS feature detection: reading only what you need}},
author = {J. Osorio Mosquera and N. G. Lawler and M. Cox and J. Osorio Mosquera and W. A. Moreno L and S. Sala and V. Nambiar and L. Whiley and J. K. Nicholson and E. Holmes and J. Wist},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.15.751169},
url = {https://www.biorxiv.org/content/10.64898/2026.09.15.751169v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - A dependency-free, streamable format and cross-language toolkit for scalable LC-MS feature detection: reading only what you need
AU - J. Osorio Mosquera
AU - N. G. Lawler
AU - M. Cox
AU - J. Osorio Mosquera
AU - W. A. Moreno L
AU - S. Sala
AU - V. Nambiar
AU - L. Whiley
AU - J. K. Nicholson
AU - E. Holmes
AU - J. Wist
PY - 2026
DA - 2026/09/15
PB - bioRxiv
DO - 10.64898/2026.09.15.751169
UR - https://www.biorxiv.org/content/10.64898/2026.09.15.751169v1
AB - Mass spectrometry generates data faster than it can be read, and the exchange standard, mzML, is text-based and must be parsed in full before any spectrum is accessible. Binary alternatives are smaller but depend on storage engines such as HDF5, so access is dictated by the engine, not the file. We present Ionic (.ion), an open-source, compact, streamable binary format, and Quant{middle dot}ion, a processing toolkit built on the former. Ionic stores spectra, chromatograms and metadata as independently compressed, indexed blocks, so a reader retrieves only the bytes it needs, even inside a web browser, and converts losslessly to and from mzML. Ionic was smaller than compressed mzMLb on every acquisition type tested, and extracting one compound took under 40 ms, 35 to 90 times faster than an mzML reader. Quant{middle dot}ion exposes one core to R, Python, and JavaScript with identical results, and recovered 97% of true features on a ground-truth benchmark.
ER -