A common open representation of mass spectrometry data and its application to proteomics research

By Patrick G. A. Pedrioli, Jimmy K. Eng, Robert M. Hubley, M. Vogelzang, Eric W. Deutsch, B. Raught, Brian S. Pratt, Erik J. Nilsson, R. Angeletti, Rolf Apweiler and 15 more. Nature Biotechnology, 2004

782 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/19fc13f1fa9f5df98090a675a1a0b21878125c7c

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Citations in the corpus

Comet: An open‐source MS/MS sequence database search tool (2013, methodology): “com/p/mstoolkit/) to support the mzXML [8], mzML [9], and ms2 [10] input formats.”
A Guided Tour of the Trans-Proteomic Pipeline (2010, methodology): “Raw mass spectrometer output files are first converted to an open format such as mzXML [8] or mzML [9].”
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics (2009, positive): “These files were transformed into the open XML format mzXM”
The Skyline Ecosystem: Informatics for Quantitative Mass Spectrometry Proteomics (2017, positive): “Skyline derives information from the native, vendor-specific file formats or from portable files like mzXML (Pedrioli et al. 2004) or mzML and caches the information into a single, high-performance data file.”
Applying mass spectrometry-based proteomics to genetics, genomics and network biology (2009, background): “Several initiatives have led to standardized machine-readable formats for the description of MS experiments using controlled vocabularies and the exchange of MS dat”
Mass spectrometry-based metabolomics. (2007, background): “Currently, a universal mzXML format (Pedrioli et al., 2004) is becoming more widely accepted, however it is not design to contain biological descriptive information.”
MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data (2006, methodology): “MZmine supports import of the NetCDF as well as mzXML (Pedrioli et al., 2004) raw data formats.”
A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language (2011, background): “It imports spectra in *.mzXML [44] or peak lists in the *.dta/*.csv format.”
MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics (2006, neutral): “[15,18,44] as well as MeMo) share a crude structure that enables the storage of both experimental data and associated metadata.”
iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates* (2011, methodology): “MS/MS Database Search and PeptideProphet Analysis—All raw MS data were converted to the mzXML file format (24) searched with six search engines (see below), then processed with PeptideProphet, iProphet: Improved Analysis of Shotgun Proteomic Data”