Microplate Sonicator Validated in Peer-Reviewed Proteomics Study

Hielscher Ultrasonics announces that its UIP400MTP ultrasonic microplate sonicator has been successfully validated in a peer-reviewed comparative proteomics study published in Proteomics (2024). The study demonstrates that ultrasonic microplate-based sample preparation delivers reproducible, high-quality protein extracts fully compatible with advanced shotgun proteomics and terminomics workflows.

The publication, “TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data”, introduces a new bioinformatics framework for the analysis of endogenous proteolysis directly from standard mass spectrometry datasets. As part of the method validation, the authors compared three commonly used tissue homogenization techniques: bead beating (Precellys), bath sonication (Bioruptor), and ultrasonic microplate sonication using the UIP400MTP.

Comparable Proteome Coverage Without Artificial Proteolysis

A central objective of the comparative study was to assess whether different extraction methods influence the identification and quantification of semi-specific peptides, which are critical for studying endogenous proteolytic processing. The results show that UIP400MTP-based ultrasonic extraction achieves proteome coverage comparable to established mechanical disruption methods, while maintaining consistent proportions of fully specific and semi-specific peptides.
Importantly, the data demonstrate that high-power ultrasonic microplate sonication does not introduce artificial protein cleavage, addressing a common concern in terminomics and semi-specific peptide analysis. This confirms that the UIP400MTP provides efficient sample disruption while preserving biologically meaningful proteolytic signatures.

Quantitative reproducibility of semi-specific peptides across extraction methods –
Pearson correlation heatmaps of log2-transformed intensities of semi-specific peptides comparing different protein extraction methods for wild-type (WT, left) and knock-out (KO, right) samples. High correlation coefficients (typically ≥0.95) are observed between UIP400MTP ultrasonic microplate sonication, bead beating (Precellys®), and bath sonication (Bioruptor®), demonstrating excellent quantitative agreement. These results confirm that microplate-based ultrasonication preserves relative peptide abundances and is fully compatible with quantitative proteomics and terminomics analyses.
Study and graphics: ©Cosenza-Contreras et al. 2024

High Reproducibility in Quantitative Proteomics

The study further reports high quantitative reproducibility across extraction methods. Pearson correlation analyses of peptide intensities revealed strong agreement between UIP400MTP-processed samples and those prepared using bead beating or bath sonication, with correlation coefficients typically exceeding 0.95.
These findings confirm that ultrasonic microplate sonication preserves relative peptide abundances, making it well suited for differential proteomics, TMT-based multiplexing, and disease-focused studies requiring precise quantitative comparisons.

Number of identified peptide precursors by specificity and extraction method
Comparison of the number of identified peptide precursors classified by enzymatic specificity (fully specific, C-terminal semi-specific, and N-terminal semi-specific) across three protein extraction methods: bead beating (Precellys®), bath sonication (Bioruptor®), and ultrasonic microplate sonication using the UIP400MTP. Data are shown for biological replicates from wild-type (WT) and knock-out (KO) mouse kidney samples. The results demonstrate comparable proteome coverage and similar distributions of peptide specificities across all extraction methods, indicating that UIP400MTP-based microplate sonication provides efficient protein extraction without increasing non-specific proteolytic cleavage.
Study and graphics: ©Cosenza-Contreras et al. 2024


Enabling High-Throughput and Standardized Proteomics Workflows

By combining non-contact ultrasonic energy delivery with parallel processing of entire 96-well plates, the UIP400MTP supports high-throughput, standardized, and automation-compatible sample preparation. In the published study, the system was successfully integrated into a DIA-enabled, TMT-labeled proteomics workflow applied to a mouse model of polycystic kidney disease.
The authors conclude that microplate ultrasonication is fully compatible with modern shotgun proteomics and enables the analysis of endogenous proteolysis without the need for labor-intensive biochemical enrichment steps.

Commitment to Scientifically Validated Solutions

“The inclusion of the UIP400MTP in a rigorous, peer-reviewed comparative study underscores Hielscher Ultrasonics’ commitment to providing scientifically validated sample preparation technologies,” said a company representative. “Independent validation in demanding proteomics workflows is essential for laboratories seeking robust, reproducible, and scalable solutions.”
The full study is available as an open-access publication in Proteomics (DOI: 10.1002/pmic.202300491).

Find information about the multi-well plate sonicator UIP400MTP here!