A – This will of course depend on which triple quadrupole or QTRAP® system you are comparing to SWATH acquisition. We did some work to compare the top end QTRAP 6500 system with SWATH acquisition on the TripleTOF® system to understand how they compare for quantitative profiling. With SWATH acquisition, you can quantify very large numbers of peptides and proteins in a single acquisition and achieve quantitative reproducibility that approaches that of MRM analysis. On the QTRAP 6500 system, the numbers of MRMs that can be time scheduled for analysis are far fewer than that of SWATH acquisition, but due to the higher sensitivity of the QTRAP 6500 system and the specificity of MRM, we were able to get better quantitative data on the very low abundant peptides in the samples (see technical note). The key point is also that it is very straightforward to transition from SWATH acquisition to MRM on these platforms as they use the similar ion source and collision cell technology, therefore all of the peptide information from SWATH can directly transfer to an MRM method.