The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF

Published

August 5, 2024

Author(s)

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

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 non-peptidic analytes.

Citation

Analytical Chemistry

Pub Type

Journals

Keywords

Proteomics Standards Initiative, mass spectrometry, spectral libraries, spectral archives, file formats, data standards, fragment ion annotations

Citation

Klein, J. , Lam, H. , Mak, T. , Bittremieux, W. , Perez-Riverol, Y. , Gabriels, R. , Shofstahl, J. , Hecht, H. , Binz, P. , Kawano, S. , Van Den Bossche, T. , Carver, J. , Neely, B. , Mendoza, L. , Suomi, T. , Claeys, T. , Payne, T. , Schulte, D. , Sun, Z. , Hoffmann, N. , Zhu, Y. , Neumann, S. , Jones, A. , Bandeira, N. , Vizcaino, J. and Deutsch, E. (2024), The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF, Analytical Chemistry (Accessed September 26, 2024)