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

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 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 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.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): T Cell

SUBMITTER: Camille Lombard-Banek

LAB HEAD: John E. Schiel

PROVIDER: PXD029780 | Pride | 2022-04-11

REPOSITORIES: Pride

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			Action	DRS
	20200313_CL03_IDA_1ug_K562_1.wiff	Wiff
	20200313_CL03_IDA_1ug_K562_1.wiff.scan	Wiff
	20200313_CL03_IDA_1ug_K562_2.wiff	Wiff
	20200313_CL03_IDA_1ug_K562_2.wiff.scan	Wiff
	20200313_CL03_IDA_1ug_K562_3.wiff	Wiff

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