ArticleAnalytical chemistry2024
The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.
Article in Analytical chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Computational metabolomics at scale: from open data to insight.Current opinion in biotechnology · 2026Review
- Proteomics in Antitumor Drug Target Discovery, Toxicity, Resistance, and Precision Oncology.Drug design, development and therapy · 2026Review
- Koina: Democratizing machine learning for proteomics research.Nature communications · 2025Article
- Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics.Nature communications · 2025Article
- A Universal Spectrum Annotator for Complex Peptidoforms in Mass Spectrometry-Based Proteomics.Analytical chemistry · 2025Article
- Carafe enables high qualitybioRxiv : the preprint server for biology · 2025Article
- Quetzal: Comprehensive Peptide Fragmentation Annotation and Visualization.Journal of proteome research · 2025Article
- A multi-species benchmark for training and validating mass spectrometry proteomics machine learning models.Scientific data · 2024Article
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Authors and funding
26 authors.
Funding
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.
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