mzView : visualizing mass spectrometry data in the browser
- 1Department of Environmental Medicine, Icahn School of Medicine at Mount Sinai, 17E 102 Street, 3rd floor CAM Building, New York
Abstract
Routine inspection of raw mass spectrometry data is limited to installed desktop software which often needs high memory, security updates, compatible operating system, and hard-drive space. Existing web-based tools require uploading raw data files to a server. To address this, we introduce mzView, a zero-installation web application featuring client-side modules for visualizing mass spectrometry data files covering Data Dependent Acquisition (DDA), Data Independent Acquisition (DIA), Imaging, and Ion-mobility acquisitions. mzView supports mzML, imzML, MSP, Bruker (.d) file formats. It enables multi-target extraction ion chromatograms (EICs) with MS2-event overlays and isotope- and adduct-driven EIC visualization ; global filtering of DDA MS2 spectra by precursor and fragment ions; DIA fragment EICs by isolation window and fragment co-occurrence; and rapid in-browser MSP library parsing and filtering. Ion-mobility and imaging data are visualized using WebGL GPU based faster rendering. To assist in spectra annotation, mzView searches spectra against the IDSL spectral database of over 50,000 compounds curated from publicly available mass spectral databases, scored by spectral entropy and cosine similarity with interactive mirror plots. Accepted hits can be saved to a browser-local annotation library, edited, re-searched, and exported as MSP files. Demonstrated on publicly available DDA and DIA data files of NIST SRM 1950 plasma acquired on a SCIEX ZenoTOF 8600, and additional data collected using Bruker timsTOF Metabo and MALDI- Pro Ultra 2 instruments, mzView readily handles files up to 35 GB, with indexing, filtering, and EIC extraction completing in less than 60 seconds. mzView is freely available at https://mzview.org (License: CC-BY).
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BibTeX
@misc{nguyen2026mzview,
title = {{mzView : visualizing mass spectrometry data in the browser}},
author = {Tuan Nguyen and Sadjad Fakouri-Baygi and Dinesh Barupal},
howpublished = {ChemRxiv},
year = {2026},
month = oct,
doi = {10.26434/chemrxiv.15010847/v1},
url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010847/v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - mzView : visualizing mass spectrometry data in the browser
AU - Tuan Nguyen
AU - Sadjad Fakouri-Baygi
AU - Dinesh Barupal
PY - 2026
DA - 2026/10/22
PB - ChemRxiv
DO - 10.26434/chemrxiv.15010847/v1
UR - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010847/v1
AB - Routine inspection of raw mass spectrometry data is limited to installed desktop software which often needs high memory, security updates, compatible operating system, and hard-drive space. Existing web-based tools require uploading raw data files to a server. To address this, we introduce mzView, a zero-installation web application featuring client-side modules for visualizing mass spectrometry data files covering Data Dependent Acquisition (DDA), Data Independent Acquisition (DIA), Imaging, and Ion-mobility acquisitions. mzView supports mzML, imzML, MSP, Bruker (.d) file formats. It enables multi-target extraction ion chromatograms (EICs) with MS2-event overlays and isotope- and adduct-driven EIC visualization ; global filtering of DDA MS2 spectra by precursor and fragment ions; DIA fragment EICs by isolation window and fragment co-occurrence; and rapid in-browser MSP library parsing and filtering. Ion-mobility and imaging data are visualized using WebGL GPU based faster rendering. To assist in spectra annotation, mzView searches spectra against the IDSL spectral database of over 50,000 compounds curated from publicly available mass spectral databases, scored by spectral entropy and cosine similarity with interactive mirror plots. Accepted hits can be saved to a browser-local annotation library, edited, re-searched, and exported as MSP files. Demonstrated on publicly available DDA and DIA data files of NIST SRM 1950 plasma acquired on a SCIEX ZenoTOF 8600, and additional data collected using Bruker timsTOF Metabo and MALDI- Pro Ultra 2 instruments, mzView readily handles files up to 35 GB, with indexing, filtering, and EIC extraction completing in less than 60 seconds. mzView is freely available at https://mzview.org (License: CC-BY).
ER -