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

J Proteome Res. 2022 May 6;21(5):1229-1239. doi: 10.1021/acs.jproteome.1c00887. Epub 2022 Apr 11.


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).

Keywords: SWATH acquisition; biopharmaceutical; bottom-up proteomics; cell therapies; data-independent acquisition; mass spectrometry; performance qualification (PQ); quality control (QC).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Data Accuracy
  • Humans
  • Mass Spectrometry / methods
  • Proteome* / analysis
  • Proteomics* / methods
  • Reproducibility of Results


  • Proteome