Improved mass spectrometry-based multiplexing strategies for quantitative proteomics
Inventors: Hanno Steen, Dominic Winter, Marc Kirchner, Judith Jebanathirajah
Invention Types: Information Technology/Software, Research Tool
Keywords: Proteomics, SoftwareFor More Information Contact: Caron, Connie
Researchers at Boston Children's have created novel and improved methods for the multiplexed quantification of peptides and proteins using mass spectrometry. The current method uses proteins that are digested to peptides and analyzed by mass spectrometry. The shortcoming of current quantitative proteomics methods is that isotope clusters of the different peptide isotopologues have to be fully resolved. Methods have been developed to overcome this hurdle. However, researchers in Dr. Hanno Steen's lab have developed a better method. They have created an algorithm to computationally unmix/deconvolve overlapping isotope patterns of the differentially labeled peptide species. Specifically, this novel strategy allows researchers to increase the multiplexity of the well-established SILAC (Stable Isotope Labeling by Amino acids in Cell culture) strategy from a 2- or 3-plex to a 5-plex version using commercially available stable isotope labeled L-arginine and L-lysine isotopologues. Using these amino acids results in overlapping isotope peaks, which can be unmixed using our novel algorithm.
This novel broadly applicable computer algorithm can also be applied to other labeling strategies, including extension of known enzymatic and chemical strategies for duplex labeling--up to five labels. Similarly, by combining the different strategies, the lab has developed a 15-plex labeling strategy.
• Software to improve mass spectrometry multiplexing for quantitative proteomic research
• Extends existing labeling techniques to true multiplexing
• Price reduction of up to 90%
• Stable reagents leads to an unlimited shelf-life
• Easy labeling conditions