12.2018 | THE SCIENTIST 47Fasmatech Omnitrap
10X Genomics Chromium Immune
Repertoire Profiling Solution
With the Chromium Immune Repertoire
Profiling Solution, researchers can study
the body’s adaptive immune response to
different types of infections and identify
the specific cell types that respond to
immune system activation, whether it’s
triggered by bacteria, viruses, or even can-
cer. Released commercially in March, the
10X Genomics technology builds on the
power of single-cell sequencing by allow-
ing researchers to distinguish each and
every T and B cell in a sample, along with
the genetic sequence of the Y-shape recep-
tors on each cell.
“I don’t think people realize that they
can get all of that information from this
product,” says Giovanna Prout, the direc-
tor of strategic marketing for single cell
genomics at 10X. “And, with some of the
new products recently released, research-
ers can get even more.”
With DNA barcoding technology, the tool
can now determine which type of T or B cell
responds to a particular antigen. “Now you
can look at clonal expansion of these cells in
response to a certain virus or disease,” Prout
explains. The barcoding technology also
improves the analysis of cell phenotypes by
combining gene expression with cell-surface
protein expression data, because antibodies
are connected to barcodes, rather than to the
fluorescent tags used in flow cytometry.
Because the barcodes are diverse, researchers
can detect many more cell-surface markers
simultaneously, providing an unprecedented
look at the immune systems of both humans
and mice. Each sample costs $1,500 to screen.
In Chris Klebanoff’s lab at Memorial
Sloan Kettering Cancer Center, he and his
colleagues are looking for novel T cells as a
treatment for solid malignancies. “The 10x
platform is unique in its ability to combineT-cell-receptor data with gene expression at
the single-cell level in a user friendly man-
ner,” says Smita Chandran, a senior research
scientist in the lab. “I am most excited about
its translational application to identify and
zero in on unique T cells that are capable of
mediating a tumor response.”VAN VLIET:“PProfiling the receptor
sequencing among T cells and B cells with this
approach provides an informative data set that
can aid understanding of the initial starting
population prior to any sorting or transduction
strategies, and can help contribute to definitions
of biological cell attributes of such cells.”For protein scientists looking to analyze
large molecules with tandem mass spec-
trometry, the Omnitrap device offers fresh
capabilities. The platform is a radio fre-
quency ion trap that processes proteins
even at high molecular weights—a limi-
tation of older trapping technologies—to
gain information on protein sequences,
structures, and molecular interactions.
“The Omnitrap allows one to obtain
unique information that was impossible,
or nearly impossible, to obtain by other
means,” says Roman Zubarev, a chemist at
the Karolinska Institute who was the first
Omnitrap customer.
Zubarev is leading a team to use the
device as part of a project to perform so-
called top-down sequencing of antibodies.
Top-down analyses keep large protein
structures intact, rather than digesting
them as other analytical methods require,
and Zubarev says the Omnitrap
will be critical to the endeavor.
One of the product’s major
advantages, according to Dimitris
Papanastasiou, the founder and
chief scientific officer of Athens-
based Fasmatech, is the ability
to fragment proteins in multiple
ways. This allows users to look at
a protein’s characteristics under
different circumstances—and do
so using one device. “It’s really
unique,” he says.
Omnitrap is an add-on to
Thermo Scientific’s Q Exactive Mass
Spectrometer and costs €250,000
($288,000 USD).ZHANG:“Improvements in protein
mass spectrometry will be transfor-
mative for biological research.”