The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF

Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding spectral libraries, but none have undergone a standardization process to ensure broad applicability to many applications. As part of the Human Proteome Organization Proteomics Standards Initiative (PSI), we have developed a standardized format for encoding spectral libraries, called mzSpecLib (https://psidev.info/mzSpecLib). It is primarily a data model that flexibly encodes metadata about the library entries using the extensible PSI-MS controlled vocabulary and can be encoded in and converted between different serialization formats. We have also developed a standardized data model and serialization for fragment ion peak annotations, called mzPAF (https://psidev.info/mzPAF). It is defined as a separate standard, since it may be used for other applications besides spectral libraries. The mzSpecLib and mzPAF standards are compatible with existing PSI standards such as ProForma 2.0 and the Universal Spectrum Identifier. The mzSpecLib and mzPAF standards have been primarily defined for peptides in proteomics applications with basic small molecule support. They could be extended in the future to other fields that need to encode spectral libraries for nonpeptidic analytes.

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Publication Details

Journal
Analytical Chemistry
Published
2024-11-08
DOI
https://doi.org/10.1021/acs.analchem.4c04091
Citations
9
Primary Topic
Advanced Proteomics Techniques and Applications
Type
article
Field-Weighted Citation Impact
2.17

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article

The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF

Henry Lam, Thomas Payne, Jeremy Carver, Joshua Klein et al.
9 citations
Analytical Chemistry
Advanced Proteomics Techniques and Applications
2.17
article

The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF

Henry Lam, Thomas Payne, Jeremy Carver, Joshua Klein, Benjamin A. Neely, Jim Shofstahl, Douwe Schulte, Steffen Neumann, Shin Kawano, Juan Antonio Vizcaíno, Tytus D. Mak, Ralf Gabriels, Wout Bittremieux, Yasset Pérez‐Riverol, Helge Hecht, Tine Claeys, Eric W. Deutsch, Andrew R. Jones, Pierre‐Alain Binz, Luis Mendoza, Zhi Sun, Tomi Suomi, Tim Van Den Bossche, Nuno Bandeira, Nils Hoffmann, Yunping Zhu
article en
9 citations

Abstract

Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding spectral libraries, but none have undergone a standardization process to ensure broad applicability to many applications. As part of the Human Proteome Organization Proteomics Standards Initiative (PSI), we have developed a standardized format for encoding spectral libraries, called mzSpecLib (https://psidev.info/mzSpecLib). It is primarily a data model that flexibly encodes metadata about the library entries using the extensible PSI-MS controlled vocabulary and can be encoded in and converted between different serialization formats. We have also developed a standardized data model and serialization for fragment ion peak annotations, called mzPAF (https://psidev.info/mzPAF). It is defined as a separate standard, since it may be used for other applications besides spectral libraries. The mzSpecLib and mzPAF standards are compatible with existing PSI standards such as ProForma 2.0 and the Universal Spectrum Identifier. The mzSpecLib and mzPAF standards have been primarily defined for peptides in proteomics applications with basic small molecule support. They could be extended in the future to other fields that need to encode spectral libraries for nonpeptidic analytes.

Analytical ChemistryVol. 96(46)
Boston University (US), Åbo Akademi University (FI), European Bioinformatics Institute (GB), National Institute of Standards and Technology (US), University of Liverpool (GB), University of Antwerp (BE), University of Turku (FI), Forschungszentrum Jülich (DE), Turku Centre for Computer Science (FI), Utrecht University (NL), Hong Kong University of Science and Technology (HK), Masaryk University (CZ), German Centre for Integrative Biodiversity Research (DE), Institute for Systems Biology (US), Ghent University (BE), University of California San Diego (US), Leibniz Institute of Plant Biochemistry (DE), Thermo Fisher Scientific (United States) (US), VIB-UGent Center for Medical Biotechnology (BE), Research Organization of Information and Systems (JP), Kitasato University (JP), Wellcome Trust (GB), University of Hong Kong (HK), University of Lausanne (CH)
Ministerstvo Školství, Mládeže a Tělovýchovy, Horizon 2020 Framework Programme, Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council, National Institute on Aging, National Institute of General Medical Sciences, National Institute of Diabetes and Digestive and Kidney Diseases, Division of Biological Infrastructure, Division of Integrative Organismal Systems
Quality Education
Openalex Percentile: Top 12%
Advanced Proteomics Techniques and Applications
2.17
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