3607178
doi
10.5281/zenodo.3607178
oai:zenodo.org:3607178
Bandeira, Nuno
University of California San Diego
Bittremieux, Wout
University of California San Diego
Carver, Jeremy J
University of California San Diego
Chambers, Matthew
University of Birmingham
Kawano, Shin
Toyama University of International Studies
Lam, Henry
Hong Kong University of Science and Technology
Mak, Tytus
National Institute of Standards and Technology
Perez-Riverol, Yasset
European Bioinformatics Institute
Pullman, Benjamin J
University of California San Diego
Sharma, Vagisha
University of Washington
Shofstahl, Jim
Thermo Fisher Scientific Inc
Van Den Bossche, Tim
VIB-UGent Center for Medical Biotechnology
Vizcaino, Juan Antonio
European Bioinformatics Institute
Zhu, Yunping
Beijing Institute of Life Omics
Deutsch, Eric W
Institute for Systems Biology
The HUPO-PSI standardized spectral library format
Gabriels, Ralf
VIB-UGent Center for Medical Biotechnology
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
HUPO-PSI
Proteomics
Standards
Spectral libraries
Mass Spectrometry
Computational Proteomics
Bioinformatics
Ontology
GitHub
PSI-MS
HDF
JSON
EuBIC
<p>More and more proteomics datasets are becoming available in public repositories. The knowledge embedded in these datasets can be used to improve peptide identification workflows. Spectral library searching provides a straightforward method to boost identification rates using previously identified spectra. Alternatively, machine learning methods can learn from these spectra to accurately predict the behavior of peptides in a liquid chromatography-mass spectrometry system.<br>
<br>
At the basis of both approaches are spectral libraries: Unified collections of previously identified spectra. Organizations and projects such as the National Institute of Standards and Technology (NIST), the Global Proteome Machine, PeptideAtlas, PRIDE Archive and MassIVE have all compiled spectral libraries for a multitude of species and experimental setups. A large obstacle, however, is that each organization provides libraries in a different file format. At the software level the problem propagates (if not expands), as different software tools require different file formats.<br>
<br>
The solution is a standardized spectral library format that is sufficiently flexible to meet all users' demands, but that is also standardized enough to be usable across environments and software packages. This balance is achieved by setting up a standardized framework and a controlled vocabulary with metadata terms, and allow the format to be represented in different forms, such as plain text, JSON and HDF.<br>
<br>
So far, the required (and optional) meta data has been compiled and added to the PSI-MS ontology, and versions of the text and JSON representations have been drafted. The tabular and HDF representations of the format are in development, as well as converters and validators in various programming languages.</p>
Zenodo
2020-01-13
info:eu-repo/semantics/conferencePoster
3607177
1.0.0
1579540723.165398
168634
md5:216e71dcee8bf44d25d3e058fc703439
https://zenodo.org/records/3607178/files/2020-01 EuBIC Dev Meeting - SpecLibFormat.pdf
public
10.5281/zenodo.3607177
isVersionOf
doi