Online database to accelerate protein analysis

1st April 2013

AB SCIEX and scientists at the Swiss Federal Institute of Technology (ETH Zurich), in collaboration with the Institute for Systems Biology in Seattle, WA, USA, used next-generation QTRAP mass spectrometry technology to create assays for approximately 20,000 human proteins, generating the world’s first human Multiple Reaction Monitoring (MRM) Atlas, an online database that will be made publicly available. 

Scientists around the world can use this atlas to significantly advance biomarker research, protein-based drug development and fundamental biological and biomedical research. 

The MRMAtlas provides simple, validated assays expanding into never-before-seen areas of the proteome. This project involved ETH scientists led by Dr Ruedi Aebersold, PhD of a technical presentation about the MRMAtlas.   
The MRMAtlas is a new database that provides mass spectrometry-based assays to a large proportion of the human proteome, enabling researchers to minimise the tedious and time-consuming task of assay development.  Many scientists see MRM assays as an improvement over current immunoassays, such as Western Blotting and ELISA, which use antibodies.  Immunoassays can be very costly and time-consuming to develop and can have issues with specificity. 

The new database of MRM assays is similar to a large library of ready-to-go antibodies to specific proteins, but the difference is that hundreds of proteins and peptides can be detected and quantified in a simple mass spectrometry assay and without the issues of cross reactivity. 
The development of the MRMAtlas was dependent on QTRAP technology, which uniquely combines in a single analysis the quantitative MRM capabilities of normal triple quadrupole systems, with advanced linear ion trap capabilities for protein identification and confirmation. This gives researchers a clearer picture of each assay and eliminates ambiguity, meeting the requirements of the scientists at ETH Zurich.  The industry-leading sensitivity of the AB SCIEX QTRAP systems also means the scientists were able to develop assays to low abundant proteins in the proteome. Using synthetic peptides for the QTRAP technology to analyze, the scientists at ETH developed this comprehensive library of MRM assays with unprecedented speed of 100 peptides per hour. 
Ruedi Aebersold, PhD, Professor, Institute of Biotechnology at the Swiss Federal Institute of Technology (ETH): “MRM assays are set to change the world of proteomics. The MRMAtlas is a tool for advancing protein analysis.  This accomplishment by a dedicated group of scientists is an important milestone and will improve our understanding of the analysis of the human proteome. We could not have developed the MRMAtlas as quickly and productively without QTRAP technology.”
Andy Boorn, Chief Operating Officer, AB SCIEX, said: “The adoption of AB SCIEX QTRAP systems to help create the MRMAtlas will unlock the real power of mass spectrometry for proteomics analysis. Scientists will now be able to analyze huge numbers of proteins in the human body all at the same time, which has significant ramifications for biomarker research and ultimately personalized medicine. The QTRAP systems are essentially the best triple quadrupoles available but with additional, unique capabilities.  They continue to help deliver significant scientific results, such as this landmark MRMAtlas project.”
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