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bioRxiv · 10.1101/073478

Precise label-free quantitative proteomes in high-throughput by microLC and data-independent SWATH acquisition

Jakob Vowinckel·Aleksej Zelezniak·Artur Kibler·Roland Bruderer·Michael Muelleder·Lukas Reiter·Markus Ralser
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Abstract

While quantitative proteomics is a key technology in biological research, the routine industry and diagnostics application is so far still limited by a moderate throughput, data consistency and robustness. In part, the restrictions emerge in the proteomics dependency on nanolitre/minute flow rate chromatography that enables a high sensitivity, but is difficult to handle on large sample series, and on the stochastic nature in data-dependent acquisition strategies. We here establish and benchmark a label-free, quantitative proteomics platform that uses microlitre/minute flow rate chromatography in combination with data-independent SWATH acquisition. Being able to largely compensate for the loss of sensitivity by exploiting the analytical capacities of microflow chromatography, we show that microLC-SWATH-MS is able to precisely quantify up to 4000 proteins in an hour or less, enables the consistent processing of sample series in high-throughput, and gains quantification precisions comparable to targeted proteomic assays. MicroLC-SWATH-MS can hence routinely process hundreds to thousands of samples to systematically create precise, label free quantitative proteomes.

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Jakob Vowinckel, Aleksej Zelezniak, Artur Kibler, Roland Bruderer, Michael Muelleder, Lukas Reiter, Markus Ralser. 2016-09-05. Precise label-free quantitative proteomes in high-throughput by microLC and data-independent SWATH acquisition. https://doi.org/10.1101/073478

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