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Pre-print: High-throughput proteome profiling with low variation in a multi-center study using dia-PASEF

(A) Shows an overview of the study. Source: Kaspar-Schönefeld et al., 2024. “High-throughput proteome profiling with low variation in a multi-center study using dia-PASEF,” bioRxiv 2024.05.29.596405.

Mass spectrometry-based proteomics has the potential to provide invaluable insights into biological systems, but has historically lagged behind next-generation sequencing in terms of scale and depth. However, recent advancements in instrumentation, acquisition, and software have enabled proteomics to match and potentially surpass the data generation capabilities of NGS.

This study evaluates the performance of a dia-PASEF acquisition scheme on the timsTOF HT platform and IonOpticks Aurora Rapid 5×75 columns for high-throughput proteomics analysis using a 5-minute gradient.

The researchers optimized the method to achieve a cycle time of 0.73 seconds, resulting in an average peak coverage of 4 to 5 data points. In a multi-laboratory study involving 11 independent labs, they demonstrated excellent reproducibility and depth of coverage, identifying an average of 7,072 protein groups and 99,835 peptides across the sites.

This study highlights the potential of the timsTOF platform for large-scale, cross-laboratory proteomics studies, enabling access to larger sample cohorts.

The Aurora Rapid CSI 5×75 C18 UHPLC column’s ability to separate peptides quickly and effectively was essential for achieving high proteome coverage and reproducibility in this high-throughput workflow.


Publication
bioRxiv

Authors

Stephanie Kaspar-Schönefeld, Jonathan R. Krieger, Claudia Martelli, Ann-Christine König, Stefanie Hauck, Sebastian Johansson, Axel Karger, Uli Ohmayer, Matteo Pecoraro, Stefan Tenzer, Ute Distler, Sophie Braga-Lagache, Phillip Strohmidel, Lisa Abel, Raphael Schuster, Georg Kliewer, Tobias Kroniger, Laura Heikaus, Diego Assis, Torsten Mueller, Daniel Hornburg

Title

High-throughput proteome profiling with low variation in a multi-center study using dia-PASEF

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