ArticleMolecular & cellular proteomics : MCP2012
mz5: space- and time-efficient storage of mass spectrometry data sets.
Article in Molecular & cellular proteomics : MCP, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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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.
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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.
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Who cites it
30 citing papers in PubMed.
- Dear-OMG: An Omics-General Compression Method for Genomics, Proteomics and Metabolomics Data.Interdisciplinary sciences, computational life sciences · 2026Article
- Storing Mass-Spectrometry Data in Simple Databases Enables Flexible and Intuitive Exploration without Time or Space Penalties.Journal of proteome research · 2025Article
- Top-down proteomics.Nature reviews. Methods primers · 2024Article
- arcMS: transformation of multi-dimensional high-resolution mass spectrometry data to columnar format for compact storage and fast access.Bioinformatics advances · 2024Article
- 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
- Aird: a computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time.BMC bioinformatics · 2022Article
- Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics.Journal of the American Society for Mass Spectrometry · 2021Review
- mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements.Journal of proteome research · 2021Article
- AlphaTims: Indexing Trapped Ion Mobility Spectrometry-TOF Data for Fast and Easy Accession and Visualization.Molecular & cellular proteomics : MCP · 2021Article
- BD5: An open HDF5-based data format to represent quantitative biological dynamics data.PloS one · 2020Article
- Expanding the Use of Spectral Libraries in Proteomics.Journal of proteome research · 2018Review
- BASIS: High-performance bioinformatics platform for processing of large-scale mass spectrometry imaging data in chemically augmented histology.Scientific reports · 2018Article
- JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals.BMC bioinformatics · 2017Article
- The arc of Mass Spectrometry Exchange Formats is long, but it bends toward HDF5.Mass spectrometry reviews · 2017Review
- A Simple Method for Improving the Spatial Resolution in Infrared Laser Ablation Mass Spectrometry Imaging.Journal of the American Society for Mass Spectrometry · 2017Article
- Fast, axis-agnostic, dynamically summarized storage and retrieval for mass spectrometry data.PloS one · 2017Article
- Data standards can boost metabolomics research, and if there is a will, there is a way.Metabolomics : Official journal of the Metabolomic Society · 2016Review
- Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry.Nature protocols · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Across a host of MS-driven-omics fields, researchers witness the acquisition of ever increasing amounts of high throughput MS data and face the need for their compact yet efficiently accessible storage. Addressing the need for an open data exchange format, the Proteomics Standards Initiative and the Seattle Proteome Center at the Institute for Systems Biology independently developed the mzData and mzXML formats, respectively. In a subsequent joint effort, they defined an ontology and associated controlled vocabulary that specifies the contents of MS data files, implemented as the newer mzML format. All three formats are based on XML and are thus not particularly efficient in either storage space requirements or read/write speed. This contribution introduces mz5, a complete reimplementation of the mzML ontology that is based on the efficient, industrial strength storage backend HDF5. Compared with the current mzML standard, this strategy yields an average file size reduction to ∼54% and increases linear read and write speeds ∼3-4-fold. The format is implemented as part of the ProteoWizard project and is available under a permissive Apache license. Additional information and download links are available from http://software.steenlab.org/mz5.
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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.