Improving qualitative and quantitative performance for MSE-based label-free proteomics
(2013) Journal of Proteome Research — Vol. 12, n° 6, p. 2340-2353 (2013)
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- Abstract
- Label-free quantitation by data independent methods (for instance MS E) is growing in popularity due to the high technical reproducibility of mass spectrometry analysis. The recent introduction of Synapt hybrid instruments capable of incorporating ion mobility separation within mass spectrometry analysis now allows acquisition of high definition MSE data (HDMSE). HDMSE enables deeper proteome coverage and more confident peptide identifications when compared to MSE, while the latter offers a higher dynamic range for quantitation. We have developed synapter as, a versatile tool to better evaluate the results of data independent acquisitions on Waters instruments. We demonstrate that synapter can be used to combine HDMSE and MSE data to achieve deeper proteome coverage delivered by HDMSE and more accurate quantitation for high intensity peptides, delivered by MSE. For users who prefer to run samples exclusively in one mode, synapter allows other useful functionality like false discovery rate estimation, filtering on peptide match type and mass error, and filling missing values. Our software integrates with existing tools, thus permitting us to easily combine peptide quantitation information into protein quantitation by a range of different approaches.
- Affiliations
University of Cambridge
Citations
Bond, N. J., Shliaha, P. V., Lilley, K. S., & Gatto, L. (2013). Improving qualitative and quantitative performance for MSE-based label-free proteomics. Journal of Proteome Research, 12(6), 2340-2353. https://doi.org/10.1021/pr300776t (Original work published 2013)