Biology subjects

Henneberg, L.

Publications and source records attributed to Henneberg, L..

5 recordsLinked to original sources

bioRxiv2026

In situ polymerized monolith tips for reproducible, format-flexible proteomic sample preparation applied to biofluids

Sample preparation increasingly sets the throughput and reproducibility of mass spectrometry (MS)-based proteomics. StageTips (stop-and-go extraction tips) and variants thereof have long been common implements to purify samples, and we recently extended the concept to solid-phase extraction capture (SPEC) tips, in which the entire digestion takes place in sub-microliter volumes. Here we replace the hand-packed bed with a strong anion-exchange (SAX) monolith photopolymerized directly inside the pipette tip from a defined recipe (pSPEC). A liquid-handling robot casts 384 tunable tips in minutes, at low cost and in any format, adding negligibly to the workflows variance. Across biofluids, pSPEC added [~]20% more identifications than in-solution plasma and reached 3,500 protein groups from a single injection of healthy urine and 4,800 from saliva at 100 samples per day, depths usually requiring depletion or fractionation. The same light-cast chemistry should extend to single cells, affinity capture, and population-scale studies.

biochemistry↗

bioRxiv2026

Scanning DIA on the ZenoTOF 8600 system enables ultra-sensitive and quantitative proteomics from single cells to post-translational modifications in a compact platform

Mass spectrometry-based proteomics increasingly demands platforms that combine quantitative rigor with the discovery capabilities of accurate mass systems. Here we present the ZenoTOF 8600 system, a compact mass spectrometry system that integrates enhanced ion capture and transmission optics with an optical detection system, Zeno trap-enhanced MS/MS, electron-activated dissociation, and scanning quadrupole data-independent acquisition (ZT Scan DIA). We show that ZT Scan DIA outperforms conventional variable-window DIA (Zeno SWATH DIA) in both identifications and quantitative reproducibility, and demonstrate the platforms versatility across proteomics applications: thousands of protein groups from bulk samples at up to 500 samples per day, single-cell proteomics yielding up to 4,700 proteins, accurate ratio recovery in mixed-species quantitative benchmarks, low-attomole targeted quantitation, and detection of disease-relevant phosphorylation in a Parkinsons disease cellular model using complementary CID and EAD fragmentation. The instruments compact footprint makes it attractive for settings where both analytical breadth and operational robustness are required.

biophysics↗

bioRxiv2025

A Solid-Phase Extraction Capture (SPEC) workflow in nanoliter volumes for fast, robust and ultrasensitive proteomics

Sample preparation remains a critical bottleneck in mass spectrometry (MS)-based proteomics, particularly for limited sample amounts where surface adsorption and dilution cause substantial losses. Here, we present Solid-Phase Extraction Capture (SPEC), a workflow that confines protein processing to nanoliter volumes within ion-exchange or C18 matrix inside a pipette tip. This achieves near-complete proteolysis within 5 minutes instead of hours and maintains full compatibility with strong detergents without cleanup steps, enabling effective lysis of challenging samples. From 200 ng FFPE tissue, SPEC achieves proteome depth and reproducibility exceeding conventional bulk protocols using 100 {micro}g, critical when sample is irreplaceable. The modular two-tip configuration enables on-tip chemical modifications for mTRAQ labeling and fractionation, while integration with enrichment workflows yields 2-fold improved glycopeptide identifications from plasma and 3-fold enhanced ubiquitin remnant identification at low amounts. SPEC enables nanoPhos for cell-type resolved tissue phosphoproteomics and provides a universal platform for proteomics sample preparation.

systems biology↗

bioRxiv2025

nanoPhos enables ultra-sensitive and cell-type resolved spatialphosphoproteomics

Mass spectrometry (MS)-based phosphoproteomics has transformed our understanding of cell signaling, yet current workflows face limitations in sensitivity and spatial resolution at sub-microgram inputs. Here, we present nanoPhos, a robust method that extends phosphoproteomics to nanogram scale, making it compatible with cell-type-resolved spatial analysis. It employs loss-less solid phase extraction capture (SPEC) for sample preparation, followed by automated phosphopeptide enrichment using Fe(III)-NTA cartridges. nanoPhos identifies over 57,000 unique phosphorylation sites from 1 {micro}g cell lysate and over 4,000 from only 10 ng, a hundred-fold improvement from recent protocols. Combined with Deep Visual Proteomics (DVP), it enables region- and cell-type resolved phosphoproteomics of mouse brain tissue with spatial fidelity and a depth of 13,000 phosphosites from only 1000 cell shapes. This establishes nanoPhos as a versatile and ultra-sensitive platform that extends DVP to post-translational modifications and opens up for cell-type-specific signaling analysis in intact tissue.

systems biology↗

bioRxiv2025

Gibberellin enhances germination of Nolana mollis and Heliotropium pycnophyllum seeds

Desert plants often exhibit seed dormancy, which enables seeds to wait out unfavorable conditions and germinate when there is enough water for the seedling to establish securely. Here, we tested several dormancy-breaking mechanisms for Nolana mollis and Heliotropium pycnophyllum, including storage temperature, scarification, hormones, germination temperature, and light cycles during germination. For both species, gibberellin enhanced germination significantly. All other treatments, or combinations of treatments, had no significant effect. Our results can be applied to restoration efforts in arid areas, or in urban areas in arid climates, where the use of native species reduces watering necessities.

plant biology↗