On chip: multiplexed low input TMT-labelled quantitative proteomics with digital microfluidics.

Digital microfluidics (DMF) technology facilitates miniaturised, automated, multiplexed liquid handling in multiple bioanalytical applications. However, in LC-MS-based proteomics its use has been limited to qualitative analysis, where the compatibility with sample preparation of detergents used to facilitate droplet flow is not an issue.

Seeking to extend the use of DMF into tandem mass tag (TMT)-labelled, quantitative LC-MS, Leipert et al. here test different commercially available detergents. They identify the non-ionic detergent DDOPM (3-dodecyloxypropyl-1-β-D- maltopyranoside) as fully compatible with both reproducible on-chip droplet movement and sample preparation for LC-MS, with TMT-labelling efficiency comparable to conventional protocols.

Using LC-MS on Thermo Fisher Q Exactive instrumentation, the new protocol was successfully employed to identify 39 differentially abundant proteins in low cell number derived proteomes – evaluated first with a protein standard digest spiked into cells in tube and on chip, then with multiplexed samples on DMF chip, where IonOpticks Aurora Series columns were chosen to perform the sensitive LC separation of peptides from TMT samples.

In combination with larger chip arrays and optimized hardware, the confirmation of this detergent as a compatible reagent represents an important step toward automated and reliable sample preparation for multiplexed quantitative proteomics. This will be crucial in the emerging field of high throughput low cell number and other ultrasensitive proteomics workflows (potentially also multiomics) and be useful for other technological applications of DMF.

Read the full paper
Isobaric Peptide Labelling on Digital Microfluidics for Quantitative Low Cell Number Proteomics.
Analytical Chem. 2021 93 (15), 6278-6286, April 6, 2021. doi: https://doi.org/10.1021/acs.analchem.1c01205

Jan Leipert, Max K. Steinbach, and Andreas Tholey

Commentary by Jarrod Sandow, PhD.

About the author
Jarrod has a background in biotechnology and completed his PhD at the Institute of Medical and Veterinary Science in Adelaide. He is a co-inventor of IonOpticks’ core technology and is driven towards developing innovative solutions for the global proteomics research community that will enable scientists and clinicians to discover more from their samples to accelerate advances in biological and medical research.