A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies.
Camille Lombard-BanekKerstin I PohlEdward J KweeJohn T ElliottJohn E SchielPublished in: Journal of proteome research (2022)
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).
Keyphrases
- mass spectrometry
- electronic health record
- single cell
- cell therapy
- liquid chromatography
- big data
- ms ms
- endothelial cells
- induced apoptosis
- multiple sclerosis
- high resolution
- stem cells
- gene expression
- dna methylation
- signaling pathway
- machine learning
- gas chromatography
- cell death
- transcription factor
- endoplasmic reticulum stress
- tandem mass spectrometry
- simultaneous determination