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Universal MS/MS Visualization and Retrieval with the Metabolomics Spectrum Resolver Web Service

Bittremieux, W.; Chen, C.; Dorrestein, P. C.; Schymanski, E. L.; Schulze, T.; Neumann, S.; Meier, R.; Rogers, S.; Wang, M.

2020-09-26 bioinformatics
10.1101/2020.05.09.086066 bioRxiv
Show abstract

The growth of online mass spectrometry metabolomics resources, including data repositories, spectral library databases, and online analysis platforms has created an environment of online/web accessibility. Here, we introduce the Metabolomics Spectrum Resolver (https://metabolomics-usi.ucsd.edu/), a tool that builds upon these exciting developments to allow for consistent data export (in human and machine-readable forms) and publication-ready visualisations of tandem mass spectrometry spectra. This tool supports the Human Proteome Organization - Proteomics Standards Initiatives Universal Spectrum Identifier (USI) specification, which has been extended to deal with the metabolomics use cases. To date, this resource already supports data formats from GNPS, MassBank, MS2LDA, MassIVE, MetaboLights, and Metabolomics Workbench and is integrated into several of these resources.

Matching journals

The top 1 journal accounts for 50% of the predicted probability mass.

1
Journal of Proteome Research
● 234 papers in training set
Top 0.1%
54.0%
Similar papers in this journal
50% of probability mass above
2
Analytical Chemistry
● 218 papers in training set
Top 0.4%
11.1%
Similar papers in this journal
3
Journal of the American Society for Mass Spectrometry
● 37 papers in training set
Top 0.1%
8.9%
Similar papers in this journal
4
Bioinformatics
◐ 1204 papers in training set
Top 4%
4.9%
Similar papers in this journal
5
PROTEOMICS
○ 43 papers in training set
Top 0.2%
3.2%
Similar papers in this journal
6
Scientific Data
○ 209 papers in training set
Top 1%
1.7%
7
Metabolites
○ 53 papers in training set
Top 0.5%
1.7%
8
Journal of Proteomics
○ 28 papers in training set
Top 0.3%
1.3%
9
BMC Bioinformatics
○ 457 papers in training set
Top 4%
1.3%
10
Nature Methods
○ 385 papers in training set
Top 6%
1.0%
11
Briefings in Bioinformatics
◐ 354 papers in training set
Top 7%
0.8%
12
Nature Protocols
○ 33 papers in training set
Top 0.5%
0.8%
13
PLOS ONE
● 5266 papers in training set
Top 58%
0.8%
14
Molecular & Cellular Proteomics
183 papers in training set
Top 2%
0.7%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.