ArticleJournal of proteome research2021
mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements.
Article in Journal of proteome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed.
- Dear-OMG: An Omics-General Compression Method for Genomics, Proteomics and Metabolomics Data.Interdisciplinary sciences, computational life sciences · 2026Article
- Review
- The data substrate of exposome intelligence: an interoperability profile for untargeted metabolomics.Frontiers in artificial intelligence · 2026Article
- Storing Mass-Spectrometry Data in Simple Databases Enables Flexible and Intuitive Exploration without Time or Space Penalties.Journal of proteome research · 2025Article
- mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format.Journal of proteome research · 2025Review
- arcMS: transformation of multi-dimensional high-resolution mass spectrometry data to columnar format for compact storage and fast access.Bioinformatics advances · 2024Article
- Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future.Proteomics · 2023Article
- Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.Journal of proteome research · 2023Review
- MZA: A Data Conversion Tool to Facilitate Software Development and Artificial Intelligence Research in Multidimensional Mass Spectrometry.Journal of proteome research · 2023Article
- StackZDPD: a novel encoding scheme for mass spectrometry data optimized for speed and compression ratio.Scientific reports · 2022Article
- Review
- Article
- Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics.Journal of the American Society for Mass Spectrometry · 2021Review
- AlphaTims: Indexing Trapped Ion Mobility Spectrometry-TOF Data for Fast and Easy Accession and Visualization.Molecular & cellular proteomics : MCP · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
With ever-increasing amounts of data produced by mass spectrometry (MS) proteomics and metabolomics, and the sheer volume of samples now analyzed, the need for a common open format possessing both file size efficiency and faster read/write speeds has become paramount to drive the next generation of data analysis pipelines. The Proteomics Standards Initiative (PSI) has established a clear and precise extensible markup language (XML) representation for data interchange, mzML, receiving substantial uptake; nevertheless, storage and file access efficiency has not been the main focus. We propose an HDF5 file format "mzMLb" that is optimized for both read/write speed and storage of the raw mass spectrometry data. We provide an extensive validation of the write speed, random read speed, and storage size, demonstrating a flexible format that with or without compression is faster than all existing approaches in virtually all cases, while with compression is comparable in size to proprietary vendor file formats. Since our approach uniquely preserves the XML encoding of the metadata, the format implicitly supports future versions of mzML and is straightforward to implement: mzMLb's design adheres to both HDF5 and NetCDF4 standard implementations, which allows it to be easily utilized by third parties due to their widespread programming language support. A reference implementation within the established ProteoWizard toolkit is provided.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.