Label-free proteomics with trace
clinical samples provides a wealth
of actionable insights for personalized medicine. Clinically acquired
primary cells, such as circulating tumor cells (CTCs), are usually
with low abundance that is prohibitive for conventional label-free
proteomics analysis. Here, we present a sickle-like inertial microfluidic
system for online rare cell separation and tandem label-free proteomics
(namely, Orcs-proteomics). Orcs-proteomics adopts a buffer system
with 0.1% N-dodecyl β-d-maltoside
(DDM), 1 mM Tris (2-carboxyethyl) phosphine (TCEP), and 2 mM 2-chloroacetamide
(CAA) for cell lysis and reductive alkylation. We demonstrate the
application of Orcs-proteomics with 293T cells and manage to identify
913, 1563, 2271, and 2770 protein groups with 4, 13, 68, and 119 cells,
respectively. We then spike MCF7 cells with white blood cells (WBCs)
to simulate the patient’s blood sample. Orcs-proteomics identifies
more than 2000 protein groups with an average of 61 MCF7 cells. We
further recruit two advanced breast cancer patients and collect 5
and 7 CTCs from each patient through minimally invasive blood drawing.
Orcs-proteomics manages to identify 973 and 1135 protein groups for
each patient. Therefore, Orcs-proteomics empowers rare cells simultaneously
to be separated and counted for proteomics and provides technical
support for personalized treatment decision making with rare primary
patient samples.