mzML—a Community Standard for Mass Spectrometry Data

By Lennart Martens, Matthew Chambers, Marc Sturm, Darren Kessner, F. Levander, J. Shofstahl, Wilfred H Tang, A. Römpp, Steffen Neumann, Angel D. Pizarro and 8 more. Molecular & Cellular Proteomics, 2010

644 citations recorded by the source corpus.

Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With the rapid advances in mass spectrometry technology and methods, it has become imperative to provide a standard output format for mass spectrometry data that will facilitate data sharing and analysis. Initially, the efforts to develop a standard format for mass spectrometry data resulted in multiple formats, each designed with a different underlying philosophy. To resolve the issues associated with having multiple formats, vendors, researchers, and software developers convened under the banner of the HUPO PSI to develop a single standard. The new data format incorporated many of the desirable technical attributes from the previous data formats, while adding a number of improvements, including features such as a controlled vocabulary with validation tools to ensure consistent usage of the format, improved support for selected reaction monitoring data, and immediately available implementations to facilitate rapid adoption by the community. The resulting standard data format, mzML, is a well tested open-source format for mass spectrometer output files that can be readily utilized by the community and easily adapted for incremental advances in mass spectrometry technology.

Subfields: Information Systems and Management, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/6cade22a0fe2fd35b243d3afa995c6891664cdb6

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Citations in the corpus

2016 update of the PRIDE database and its related tools (2015, methodology): “The pipeline makes use of different open source libraries that have been developed in the last years to support the PSI open standard data formats, most notably jmzIdentML (25) (for mzIdentML files), jmzML (26) (for mzML files, the PSI standard for mass spectra data (27)), jmzTab (28) (for mzTab dat”
OpenMS: a flexible open-source software platform for mass spectrometry data analysis (2016, background): “Past efforts to mitigate these issues led to the development of standardized data-exchange formats 2–5 , which have recently been adopted by several software projects 6–10 .”
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences (2021, background): “as mzTab (5), mzIdentML (6) and mzML (7) to store, process and visualize the proteomics data deposited.”
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.”
MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data (2012, methodology): “Currently, we accept all data formats for ‘raw’ instrumental data, converted open source ﬁle formats and any processed data, but we strongly recommend that processed data should be made available in open formats, such as mzML (23) for MS data.”
The ProteomeXchange consortium at 10 years: 2023 update (2022, neutral): “PX resources fully support the main open PSI data standards for MS, namely mzML (for MS data) (17), mzIdentML (18) and mzTab (tab-delimited file for peptide and protein identification and quantification) (19).”
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition (2016, methodology): “The PRIDE team also actively develops a stand-alone visualization and data analysis tool called PRIDE Inspector (18,19), that supports the PSI data standards mzIdentML, mzTab and mzML (13), PRIDE XML and other open data formats.”
jPOSTrepo: an international standard data repository for proteomes (2016, background): “mzML (18) and Mascot Generic Format (MGF; http://www.”
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics (2015, methodology): “The mscon-verttoolwithinthefreeandopen-sourceProteoWizard[13,14] toolkit remains the standard for converting each of the vendor formats into the Proteomics Standards Initiative (PSI; [15]) mzML format [16].”
iProX: an integrated proteome resource (2018, background): “…Standards Initiative (HUPO-PSI) (9) has developed and published co-ordinated standards for proteomics data representation, including the mzML (10) standard representing MS raw data, the mzIdentML (11) standard designed to report peptide and protein identification data, the mzQuantML (12)…”