The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF
: Klein, Joshua; Lam, Henry; Mak, Tytus D.; Bittremieux, Wout; Perez-Riverol, Yasset; Gabriels, Ralf; Shofstahl, Jim; Hecht, Helge; Binz, Pierre-Alain; Kawano, Shin; Van Den Bossche, Tim; Carver, Jeremy; Neely, Benjamin A.; Mendoza, Luis; Suomi, Tomi; Claeys, Tine; Payne, Thomas; Schulte, Douwe; Sun, Zhi; Hoffmann, Nils; Zhu, Yunping; Neumann, Steffen; Jones, Andrew R.; Bandeira, Nuno; Vizcaíno, Juan Antonio; Deutsch, Eric W.
Publisher: American Chemical Society (ACS)
: 2024
: Analytical Chemistry
: Analytical Chemistry
: 96
: 46
: 18491
: 18501
: 0003-2700
: 1520-6882
DOI: https://doi.org/10.1021/acs.analchem.4c04091
: https://doi.org/10.1021/acs.analchem.4c04091
: https://research.utu.fi/converis/portal/detail/Publication/459237890
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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The authors would like to acknowledge all other individuals whocontributed in various ways to the mzSpecLib and mzPAFspecifications. This work was funded in part by the NationalInstitutes of Health grants R01 GM087221 (EWD), R24GM148372 (NB,EWD), U19 AG023122 (RLM), U24DK133658 (NB), and by the National Science Foundationgrants DBI-2324882 (EWD) (DIAeXchange), DBI-1933311(EWD) (PTMeXchange), and IOS-1922871 (EWD) (Arabi-dopsis). JAV and YPR would like to acknowledge BBSRC grantBB/X001911/1 (DIAeXchange), APP9749, and the EPSRCgrant EP/Y035984/1. HH thanks the RECETOX ResearchInfrastructure (LM2023069) financed by the Ministry ofEducation, Youth and Sports, and the Operational ProgrammeResearch, Development and Education (the CETOCOENEXCELLENCE project No. CZ.02.1.01/0.0/0.0/17 043/0009632) for supportive background. This work was supportedfrom the European Union’s Horizon 2020 research andinnovation programme under grant agreement No 857560.This publication reflects only the author’s view and theEuropean Commission is not responsible for any use that maybe made of the information it contains. These opinions,recommendations, findings, and conclusions do not necessarilyreflect the views or policies of NIST or the United States Government. Identification of certain commercial equipment,instruments, software, or materials does not imply recommen-dation or endorsement by the National Institute of Standardsand Technology, nor does it imply that the products identifiedare necessarily the best available for the purpose.
