Reliable Identification of Cardiac Maturation Markers Using Robust and Flexible Label-Free Proteomic Quantitation by Spectral Counting on Relatively Abundant Proteins

The identification of biomarkers has been one of the
major applications
in proteomics research. The high specificity and sensitivity of a
good biomarker can be evaluated only in population studies, which
is costly and a limited number of candidate proteins can be evaluated.
However, high throughput proteomics usually identifies thousands of
proteins from a biological sample and yields tens to hundreds of candidate
biomarkers. We demonstrate the use of robust and flexible spectral
counting, a label-free semiquantitative method, on relatively abundant
proteins to integrate proteomic results from different samples obtained
from different laboratories for reliable biological insights and high-quality
biomarkers. Furthermore, this strategy can be easily tuned for one
or a few biomarkers on demand. We illustrate the use of this strategy
to reveal the biological differences between terminally differentiated
myocardium and rapidly proliferating HEK293T cells, as well as the
successful selection of both positive and negative maturation markers
for cardiomyocytes differentiated from human induced pluripotent stem
cells (hiPSCs). The advantage of this strategy is the capacity to
utilize the exponentially growing number of proteomic results deposited
in the public repository for candidate biomarker selection and to
derive biological insights.