Enhancing quantitative proteomics through the accurate prediction of retention time of peptides labeled with tandem mass tags

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The combination of liquid chromatography and mass spectrometry (LC-MS) for the analysis of proteins and peptides has become an indispensible component of analytical science applied to human health, agriculture, energy, and environmental studies. The mass-spectrometry component of this technique has been the primary focus of instrument development. At the same time, the LC component of the system can provide very valuable information, given the ability to predict the retention properties of analyzed molecules. Overall this will make LC-MS a "double-edged sword", where the outcomes from both methods can be used to improve the analysis output. My laboratory has been the leader in the peptide retention time prediction field for more than a decade. Our Sequence-Specific Retention Calculator (SSRCalc) model has become a benchmark tool in the field, attracting attention both from the proteomic/chromatographic community and from major vendors of proteomics equipment and software. In this proposal we aim to join our expertise with the leading provider of LC-MS proteomic systems, Thermo Fisher Scientific (TFS).**One of the key applications developed by TFS targets protein quantitation through peptide labeling with tandem-mass tag (TMT) reagents, followed by LC-MS analysis. Chromatographic properties of the labeled peptides are significantly different from their non-labeled counterparts, thus limiting application of current retention prediction algorithms, including SSRCalc. Another improvement introduced by TFS is the use of ultra small chromatographic particles and higher separation temperature to reduce column backpressure. This alters the accuracy prediction models, too. The focus of this Collaborative Research and Development Grant is to extend the SSRCalc prediction methodology into peptides labeled with TMT and separations using various temperatures. This will result in the new generation of our model - Universal Sequence-Specific Retention Calculator (USSRCalc) - as it will cover wider range of chromatographic conditions with unmatched performance, and will lead to development of simplified quantitation protocols for clinical proteomics.**