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

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

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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.

Original languageEnglish
Pages (from-to)18491-18501
Number of pages11
JournalAnalytical Chemistry
Volume96
Issue number46
Early online date8 Nov 2024
DOIs
Publication statusPublished - 19 Nov 2024

Bibliographical note

Publisher Copyright:
© 2024 The Authors. Published by American Chemical Society.

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