The SCIEX Triple TOF 5600 is coupled to a capillary flow (1-10µL/min) liquid chromatography (Cap-LC) system (Eksigent LC425). Cap-LC became increasingly widespread over the past decade in favor of nano-LC due to its robustness and stability, which provides the quantitative accuracy and therefore statistical power needed for solid biological results. This is of particular importance when running SWATH runs (Data Independent Acquisition). Herein, a library of peptide identifications is first generated on all the samples in the experiment using conventional DDA (Data Dependent Acquisition). Next, these same samples are acquired by sequential fragmentation of small m/z windows to generate quantitative information on the transitions found in the library. It is, in essence, a post-acquisition MRM-like data-extraction approach providing the user with a permanent record of everything. This implies that future hypotheses can be pursued in a targeted analysis long after the samples were acquired using SWATH.

No need to say that the intrinsic sensitivity and speed of this instrument equally allow for high quality DDA, while the high resolution can be applied for intact protein analysis.