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

2020 ◽  
Author(s):  
Wout Bittremieux ◽  
Christopher Chen ◽  
Pieter C. Dorrestein ◽  
Emma L. Schymanski ◽  
Tobias Schulze ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Web Service ◽  
Tandem Mass ◽  
Spectral Library ◽  
Data Repositories ◽  
Data Formats ◽  
Universal Spectrum ◽  
Machine Readable ◽  
Online Web

AbstractThe 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 Initiative’s 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.

Authentication of Closely Related Fish and Derived Fish Products Using Tandem Mass Spectrometry and Spectral Library Matching

2016 ◽  
Vol 64 (18) ◽  
pp. 3669-3677 ◽  
Author(s):  
Merel A. Nessen ◽  
Dennis J. van der Zwaan ◽  
Sander Grevers ◽  
Hans Dalebout ◽  
Martijn Staats ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Spectral Library ◽  
Fish Products

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics

2008 ◽  
Vol 33 (1) ◽  
pp. 18-25 ◽  
Author(s):  
Eric W. Deutsch ◽  
Henry Lam ◽  
Ruedi Aebersold
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Open Source Software ◽  
Software Tools ◽  
Tandem Mass ◽  
Critical Component ◽  
Data Repositories ◽  
The Past ◽  
Proteomics Experiment ◽  
Proteomics Research

Data processing is a central and critical component of a successful proteomics experiment, and is often the most time-consuming step. There have been considerable advances in the field of proteomics informatics in the past 5 years, spurred mainly by free and open-source software tools. Along with the gains afforded by new software, the benefits of making raw data and processed results freely available to the community in data repositories are finally in evidence. In this review, we provide an overview of the general analysis approaches, software tools, and repositories that are enabling successful proteomics research via tandem mass spectrometry.

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