mzML—a Community Standard for Mass Spectrometry Data

Abstract

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.

Analysis of protein–RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry

“…The steps for data analysis are based on our previously published work [25]; OpenMS software is used, with OMSSA as search engine. To apply this workflow with subsequent database search on the raw data that is generated by the manufacturer's instrument software, the raw files are converted into .mzML format [48] by using msconvert of ProteoWizard software [49]. The first step in the workflow is a conventional database search to identify residual non-cross-linked peptides and also non-cross-linked oligonucleotides.…”

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

“…3). OpenMS provides implementations for over 30 file formats, including the current and upcoming open standards defined by the Proteomics Standards Initiative of the Human Proteome Organization (HUPO-PSI) such as mzML, TraML, mzIdentML, mzQuantML, mzTab and qcML [2,3,4,5,17,18] (see Supplementary Note 1). In addition, OpenMS includes standard algorithms related to biomolecular properties (such as mass calculation, isotopic composition, protein digestion etc.)…”

“…Past efforts to mitigate these issues have led to the development of standardized data exchange formats [2,3,4,5] , which have recently been adopted by several software projects [6,7,8,9,10] . These standard formats enable the integration of tools from different sources, simplify the analysis of MS data from multiple vendors, and render published results more readily accessible.…”

Exploring the potential of public proteomics data

“…This ongoing endeavor, led by the HUPO‐PSI (Human Proteome Organization−Proteomics Standards Initiative−http://www.psidev.info), has resulted in key data standards for the field, including mzML (for MS data), mzIdentML (for peptide/protein identification data), mzTab (for peptide/protein identification and quantification data), mzQuantML (for peptide/protein quantification data), and TraML (for transition lists in targeted proteomics approaches) 18, 19, 20, 21, 22. Importantly, support for these standards is provided through software libraries or tools such as ProteoWizard 23, PRIDE Converter 24, 25, mzidLibrary 26, and PRIDE Inspector 27.…”