A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies

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).