Digital microfluidics (DMF) is a technology suitable for bioanalytical applications requiring miniaturized, automated, and multiplexed liquid handling. Its use in LC-MS-based proteomics, however, has so far been limited to qualitative proteome analyses. This is mainly due to the need for detergents that enable facile, reproducible droplet movement, which are compatible with organic solvents commonly used in targeted chemical modifications of peptides. Aiming to implement isobaric peptide labeling, a widely applied technique allowing multiplexed quantitative proteome studies, on DMF devices, we tested different commercially available detergents. We identified the maltoside-based detergent 3-dodecyloxypropyl-1-β-d-maltopyranoside (DDOPM) to enable facile droplet movement and show micelle formation even in the presence of organic solvent, which is necessary for isobaric tandem mass tag (TMT) labeling. The detergent is fully compatible with reversed phase LC-MS, not interfering with peptide identification. Tryptic digestion in the presence of DDOPM was more efficient than without detergent, resulting in more protein identifications. Using this detergent, we report the first on-DMF chip isobaric labeling strategy, with TMT-labeling efficiency comparable to conventional protocols. The newly developed labeling protocol was evaluated in the multiplexed analyses of a protein standard digest spiked into 25 cells. Finally, using only 75 cells per biological replicate, we were able to identify 39 proteins being differentially abundant after treatment of Jurkat T cells with the anticancer drug doxorubicin. In summary, we demonstrate an important step toward multiplexed quantitative proteomics on DMF, which, in combination with larger chip arrays and optimized hardware, could enable high throughput low cell number proteomics.

Miniaturization of sample preparation, including omissible manual sample handling steps, is key for reproducible nanoproteomics, as material is often restricted to only hundreds of cells or single model organisms. Here, we demonstrate a highly sensitive digital microfluidics (DMF)-based sample preparation workflow making use of single-pot solid-phase enhanced sample preparation (SP3) in combination with high-field asymmetric-waveform ion mobility spectrometry (FAIMS), and fast and sensitive ion trap detection on an Orbitrap tribrid MS system. Compared to a manual in-tube SP3-supported sample preparation, the numbers of identified peptides and proteins were markedly increased, while lower standard deviations between replicates were observed. We repeatedly identified up to 5000 proteins from single nematodes. Moreover, label-free quantification of protein changes in single Caenorhabditis elegans treated with a heat stimulus yielded 45 differentially abundant proteins when compared to the untreated control, highlighting the potential of this technology for low-input proteomics studies. LC-MS data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD033143.

While most nanoproteomics approaches for the analysis of low‐input samples are based on bottom‐up proteomics workflows, top‐down approaches enabling proteoform characterization are still underrepresented. Using mammalian cell proteomes, we established a facile one‐pot sample preparation protocol based on protein aggregation on magnetic beads and intact proteoform elution using 40 % formic acid. Performed on a digital microfluidics device, the workflow enabled sensitive analyses of single Caenorhabditis elegans nematodes, thereby increasing the number of proteoform identifications compared to in‐tube sample preparation by 46 %. Label‐free quantification of single nematodes grown under different conditions allowed to identify changes in the abundance of proteoforms not distinguishable by bottom‐up proteomics. The presented workflow will facilitate proteoform‐directed analysis on samples of limited availability.

Während die meisten Ansätze zur Analyse von geringen Probemengen durch Nanoproteomik auf der bottom-up-Strategie basieren, sind top-down-Ansätze zur Charakterisierung von Proteoformen nach wie vor unterrepräsentiert. An Proteomen von Säugerzellen haben wir eine einfache Probenvorbereitungsmethode etabliert, welche auf Proteinaggregation an magnetischen Partikeln und anschließender Elution intakter Proteoformen durch 40 %ige Ameisensäure basiert. Die Implementierung der Methode auf einer Plattform für digitale Mikrofluidik ermöglichte die sensitive Analyse von einzelnen Individuen des Nematoden Caenorhabditis elegans. Die Anzahl identifizierter Proteoformen konnte dabei im Vergleich zu herkömmlicher Probenvorbereitung in einem Reaktionsgefäß um 46 % erhöht werden. Ferner erlaubte die markierungsfreie (labelfree) Quantifizierung von Proteomen einzelner Nematoden, welche unter verschiedenen Bedingungen kultiviert wurden, Änderungen der Abundanz von Proteoformen zu erkennen, welche in bottom-up-Experimenten nicht festgestellt wurden. Die hier präsentierte Methode wird die Proteoform-zentrische Analytik in Proben mit limitierter Verfügbarkeit vereinfachen.