The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF Article Swipe
Joshua Klein
,
Henry Lam
,
Tytus D. Mak
,
Wout Bittremieux
,
Yasset Pérez‐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 Hoffmann
,
Yunping Zhu
,
Steffen Neumann
,
Andrew R. Jones
,
Nuno Bandeira
,
Juan Antonio Vizcaíno
,
Eric W. Deutsch
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1021/acs.analchem.4c04091
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1021/acs.analchem.4c04091
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.
Related Topics
Concepts
Standardization
Identifier
Serialization
Chemistry
Proteogenomics
Metadata
Human proteome project
Computer science
Fragment (logic)
Vocabulary
Computational biology
Information retrieval
Proteomics
World Wide Web
Programming language
Genome
Genomics
Operating system
Gene
Biology
Biochemistry
Philosophy
Linguistics
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1021/acs.analchem.4c04091
- OA Status
- hybrid
- Cited By
- 7
- References
- 42
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4404176855
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4404176855Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1021/acs.analchem.4c04091Digital Object Identifier
- Title
-
The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAFWork title
- Type
-
articleOpenAlex work type
- Language
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enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-11-08Full publication date if available
- Authors
-
Joshua Klein, Henry Lam, Tytus D. Mak, Wout Bittremieux, Yasset Pérez‐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 Hoffmann, Yunping Zhu, Steffen Neumann, Andrew R. Jones, Nuno Bandeira, Juan Antonio Vizcaíno, Eric W. DeutschList of authors in order
- Landing page
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https://doi.org/10.1021/acs.analchem.4c04091Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
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https://doi.org/10.1021/acs.analchem.4c04091Direct OA link when available
- Concepts
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Standardization, Identifier, Serialization, Chemistry, Proteogenomics, Metadata, Human proteome project, Computer science, Fragment (logic), Vocabulary, Computational biology, Information retrieval, Proteomics, World Wide Web, Programming language, Genome, Genomics, Operating system, Gene, Biology, Biochemistry, Philosophy, LinguisticsTop concepts (fields/topics) attached by OpenAlex
- Cited by
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7Total citation count in OpenAlex
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2025: 6, 2024: 1Per-year citation counts (last 5 years)
- References (count)
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42Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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