Abstract
Single-cell proteomics (SCP) aims to characterize the proteome of
individual cells, providing insights into complex biological systems. It
reveals subtle differences in distinct cellular populations that bulk
proteome analysis might overlook, which is essential for understanding
disease mechanisms and developing targeted therapies. Mass spectrometry
(MS) methods in SCP allow the identification and quantification of
thousands of proteins from individual cells and this review highlights
the role of data-independent acquisition MS (DIA-MS) in SCP. One major
hurdle in SCP is the limited material in single-cell samples, but
DIA-based techniques offer multiple potential solutions for their
analysis. Utilizing wide precursor isolation windows to fragment
multiple peptides simultaneously, DIA-based methods improve sensitivity,
quantitative accuracy, and reproducibility at a cost in data analysis
complexity. DIA methods can also be combined with sample multiplexing
methods to increase the sample throughput, currently a key limitation in
SCP. Challenges remain for interpreting sample multiplexed data from
DIA-based SCP experiments, particularly with regards to isobaric tagging
methods. Even still, we believe that DIA-based SCP approaches will play
a major role in our understanding of systems biology.