Houston Methodist. Leading Medicine.
Houston Methodist. Leading Medicine

Research Brief: Top Down Proteomics Nature Report

Research Brief: Top Down Proteomics Nature Report

HOUSTON (November 4, 2011)Dr. Adaikkalam Vellaichamy, TMHRI Assistant Member in the Department of Nanomedicine and Co-Director of the Proteomics Programmatic Core, coauthored a report in Nature in late October on top down proteomics. This paper demonstrates proof-of-concept for a new method of protein analysis that makes it possible for proteomics researchers to discern lots of information from hundreds of whole (intact) proteins in a proteome -- including multiple variants of a single gene product. The paper will appear in a future print edition of the journal.

Vellaichamy, who collaborated on the project while he was an Institute for Genomic Biology Fellow at the University of Illinois Urbana-Champaign, joined The Methodist Hospital Research Institute as an assistant member late last year.

"Mapping intact protein isoforms in discovery mode using top-down proteomics" describes the method developed by Vellaichamy, lead author John Tran, principal investigator Neil Kelleher (currently at North Western), and other coauthors. In top down proteomics, the output of two-dimensional liquid electrophoresis (solution isoelectric focusing and gel-eluted liquid fraction entrapment electrophoresis), is subjected to two other dimensions of online separation and analysis: nanocapillary liquid chromatography and mass spectrometry (LC-MS).

The commonly followed bottom-up proteomics methods uses enzymatic cleavage of proteins into peptides, identification of peptide sequence by mass spectrometry, and then working back to from the smaller peptide sequences to identify the full proteins sequences. Although the technology is robust, there are two major problems with this approach. First, this approach has a high number of protein mis-identifications. Second, bottom-up analysis often misses important information such as post-translational modifications and alternative splicing.

The four-dimensional top-down approach taken by the Nature publication authors allowed them to identify 1,043 gene products, and more than 3,000 modified protein species based on those products. In addition to using collision induced dissociation, the authors have also used source induced dissociation for sequencing of intact proteins with a whole range of molecular weights of up to 105 kilodaltons. Dr. Vellaichamy was the lead author of the referenced paper that reported the application of source induced dissociation for large size proteins which was published earlier in Analytical Chemistry in 2010 (v. 82, p. 1234). Neil Kelleher of UIUC was the PI on that project as well.

Their research was funded by the National Institute on Drug Abuse, the National Institute of General Medical Sciences, and the National Science Foundation.To speak with a representative of TMHRI, please contact David Bricker, The Methodist Hospital, at 832-667-5811 or dmbricker@houstonmethodist.org.  For more information on The Methodist Hospital Research Institute, visit our website. Follow Methodist on Facebook and Twitter.