TY - JOUR T1 - Precise label-free quantitative proteomes in high-throughput by microLC and data-independent SWATH acquisition JF - bioRxiv DO - 10.1101/073478 SP - 073478 AU - Jakob Vowinckel AU - Aleksej Zelezniak AU - Artur Kibler AU - Roland Bruderer AU - Michael Muelleder AU - Lukas Reiter AU - Markus Ralser Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/09/05/073478.abstract N2 - 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. ER -