Abstract:
Background & Summary
T-cells are the central regulators of adaptive immunity and among the most diverse cellular compartment in
human physiology1
. While advanced transcriptomics, including single cell transcriptomics, is commonly applied
to investigate T-cell subsets to infer T-cell function, post-translational modifcations (PTMs), splice variants and
other downstream modifcations regularly occur and must not be overlooked. Accordingly, quantitative T-cell
proteomics is an essential tool in understanding the workings of T-cells in health and disease1–3
. Nanoscale liquid
chromatography-coupled tandem mass spectrometry (LC-MS/MS) has become a standard technique for quanti tative proteomic studies in human biology and disease, by which traditional data dependent acquisition (DDA)
mass spectrometry (MS) proteomics has added signifcant understanding to the immunological process4–6
.
Te stochastic selection of precursor ions has led to large proportion of missing data, which impacts down stream statistical analyses in proteomics annotation, functional interpretation and therapeutic development7,8
.
To overcome these limitations, data-independent acquisition (DIA-MS) was performed to acquire all ions by
dividing ion space. Te introduction of the sequential window acquisition of all theoretical fragment ion spectra
(SWATH-MS) which is a combination of tandem mass spectrometry performed by quadrupole time-of-fight
(QTof) instruments, DIA-MS and a peptide-centric data query method, facilitated the reproducible quantif cation of proteomes to perform high-throughput analysis of immunological samples9
. Tis technique is now
standardized to obtain highly reproducible data in international laboratories1
