ArticleMolecular & cellular proteomics : MCP2014
Numerical compression schemes for proteomics mass spectrometry data.
Article in Molecular & cellular proteomics : MCP, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Perspectives in computational mass spectrometry: recent developments and key challenges.Bioinformatics advances · 2025Article
- Interaction of Bartonella henselae with Fibronectin Represents the Molecular Basis for Adhesion to Host Cells.Microbiology spectrum · 2022Article
- 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
- ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis.Scientific data · 2021Article
- BtuB-Dependent Infection of the T5-likeViruses · 2021Article
- Streptococcus pyogenes Forms Serotype- and Local Environment-Dependent Interspecies Protein Complexes.mSystems · 2021Article
- Bacteriophages fEV-1 and fD1 InfectViruses · 2021Article
- Cerebrospinal fluid proteome maps detect pathogen-specific host response patterns in meningitis.eLife · 2021Article
- Multinodal Acoustic Trapping Enables High Capacity and High Throughput Enrichment of Extracellular Vesicles and Microparticles in miRNA and MS Proteomics Studies.Analytical chemistry · 2021Article
- CHICKN: extraction of peptide chromatographic elution profiles from large scale mass spectrometry data by means of Wasserstein compressive hierarchical cluster analysis.BMC bioinformatics · 2021Article
- 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
- MassComp, a lossless compressor for mass spectrometry data.BMC bioinformatics · 2019Article
- A quantitative Streptococcus pyogenes-human protein-protein interaction map reveals localization of opsonizing antibodies.Nature communications · 2019Article
- Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.Journal of proteome research · 2017Article
- The arc of Mass Spectrometry Exchange Formats is long, but it bends toward HDF5.Mass spectrometry reviews · 2017Review
- Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry.Scientific reports · 2017Article
- Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival.Scientific reports · 2017Article
- BatMass: a Java Software Platform for LC-MS Data Visualization in Proteomics and Metabolomics.Journal of proteome research · 2016Article
- Dinosaur: A Refined Open-Source Peptide MS Feature Detector.Journal of proteome research · 2016Article
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Authors and funding
11 authors.
Funding
Abstract
The open XML format mzML, used for representation of MS data, is pivotal for the development of platform-independent MS analysis software. Although conversion from vendor formats to mzML must take place on a platform on which the vendor libraries are available (i.e. Windows), once mzML files have been generated, they can be used on any platform. However, the mzML format has turned out to be less efficient than vendor formats. In many cases, the naïve mzML representation is fourfold or even up to 18-fold larger compared with the original vendor file. In disk I/O limited setups, a larger data file also leads to longer processing times, which is a problem given the data production rates of modern mass spectrometers. In an attempt to reduce this problem, we here present a family of numerical compression algorithms called MS-Numpress, intended for efficient compression of MS data. To facilitate ease of adoption, the algorithms target the binary data in the mzML standard, and support in main proteomics tools is already available. Using a test set of 10 representative MS data files we demonstrate typical file size decreases of 90% when combined with traditional compression, as well as read time decreases of up to 50%. It is envisaged that these improvements will be beneficial for data handling within the MS community.
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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.