Evaluation of the Compact High-Field Orbitrap for Top-Down Proteomics of Human Cells

Mass spectrometry based proteomics generally seeks to
identify
and fully characterize protein species with high accuracy and throughput.
Recent improvements in protein separation have greatly expanded the
capacity of top-down proteomics (TDP) to identify a large number of
intact proteins. To date, TDP has been most tightly associated with
Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry.
Here, we couple the improved separations to a Fourier-transform instrument
based not on ICR but using the Orbitrap Elite mass analyzer. Application
of this platform to H1299 human lung cancer cells resulted in the
unambiguous identification of 690 unique proteins and over 2000 proteoforms
identified from proteins with intact masses <50 kDa. This is an
early demonstration of high throughput TDP (>500 identifications)
in an Orbitrap mass spectrometer and exemplifies an accessible platform
for whole protein mass spectrometry.