1. A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies
- Author
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Camille Lombard-Banek, Kerstin I. Pohl, Edward J. Kwee, John T. Elliott, and John E. Schiel
- Subjects
Proteomics ,Proteome ,Humans ,Reproducibility of Results ,General Chemistry ,Biochemistry ,Mass Spectrometry ,Data Accuracy - Abstract
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 qualifications (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 multiattribute method (MAM) principles to characterize the proteome of cell therapies. Here, we describe the development of a DIA method for the sensitive identification and quantification of proteins on a Q-TOF instrument. Using the improved acquisition parameters, we defined a control strategy and highlighted some 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. Raw and processed data were deposited in PRIDE (PXD029780).
- Published
- 2022
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