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A Sensitive and Controlled SWATH Acquisition Method for Proteomic Analysis of Cell Therapies



Camille Lombard-Banek, Kerstin Pohl, Edward Kwee, John T. Elliott, John E. Schiel


Mass Spectrometry (MS)-based proteomic measurements are uniquely poised to impact the development of cell and gene therapies. With the adoption of rigorous instrumental performance controls (PQs), large-scale proteomics can move from a research to a manufacturing control tool. Especially suited, data-independent acquisition (DIA) approaches have distinctive qualities to extend multi-attribute method (MAM) principles to characterize the proteome of cell therapies. Here we describe the development of a DIA method by SWATH Acquisition for the sensitive identification and quantification of proteins on a Q-TOF instrument. Using the improved acquisition parameters, we defined some control metrics to improve the reproducibility of SWATH Acquisition-based proteomic measurements. Finally, we applied the method to analyze the proteome of Jurkat cells that here serves as a model for human T-cells.
ACS Journal of Proteome Research


CAR-T, SWATH Acquisition


Lombard-Banek, C. , Pohl, K. , Kwee, E. , Elliott, J. and Schiel, J. (2022), A Sensitive and Controlled SWATH Acquisition Method for Proteomic Analysis of Cell Therapies, ACS Journal of Proteome Research, [online],, (Accessed June 16, 2024)


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Created April 11, 2022, Updated November 29, 2022