RT Journal Article
SR Electronic
T1 A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 600130
DO 10.1101/600130
A1 Brian H. Lee
A1 Geoffrey Kelly
A1 Shermineh Bradford
A1 Melanie Davila
A1 Xinzheng V. Guo
A1 El-ad David Amir
A1 Emily M. Thrash
A1 Michael D. Solga
A1 Joanne Lannigan
A1 Brian Sellers
A1 Julian Candia
A1 John Tsang
A1 Ruth R. Montgomery
A1 Stanley J. Tamaki
A1 Tara K. Sigdel
A1 Minnie M. Sarwal
A1 Lewis L. Lanier
A1 Yuan Tian
A1 Cheryl Kim
A1 Denise Hinz
A1 Bjoern Peters
A1 Alessandro Sette
A1 Adeeb H. Rahman
YR 2019
UL http://biorxiv.org/content/early/2019/04/05/600130.abstract
AB Mass cytometry is a powerful tool for high dimensional single cell characterization. Since the introduction of the first commercial CyTOF mass cytometer by DVS Sciences in 2009, mass cytometry technology has matured and become more widely utilized, with sequential platform upgrades designed to address specific limitations and to expand the capabilities of the platform. Fluidigm’s 3rd-generation Helios mass cytometer introduced a number of upgrades over the previous CyTOF2. One of these new features is a modified narrow bore sample injector that generates smaller ion clouds, which is expected to improve sensitivity and throughput. However, following rigorous testing we find that the narrow-bore sample injector may have unintended negative consequences on data quality and result in lower median signal intensities and higher coefficients of variation in antibody expression. We describe an alternative Helios acquisition protocol using a wider bore injector, which largely mitigates these data quality issues. We directly compare these two protocols in a multi-site study of 10 Helios instruments across 7 institutions and show that the modified protocol improves data quality and reduces inter-instrument variability. These findings highlight and address an important source of technical variability in mass cytometry experiments that is of particular relevance in the setting of multi-center studies.