Hi Stoyan,
I needed a single term to apply to everything, and I chose "replicate". In Skyline parlance, "replicate" means a set of mass spec runs (often just one run) that was used to measure your targets once. In some cases, this may take many mass spec runs (also referred to as "injections") to cover your targets just once, as in the Targeted Method Refinement tutorial where around 50 runs are used to measure each target just once. Any such collection of runs or single run which measure your target once are referred to as a "replicate", and ten sets of these would be "ten replicates", regardless of their logical organization into concentrations, subjects, time points, etc. Or whether or not any of them are actually technical replicate measurements of the same sample. Logical groupings can be made using "replicate annotations", see the Existing and Quantitative Experiments tutorial for an example (pp 33-36).
https://skyline.gs.washington.edu/labkey/_webdav/home/software/Skyline/%40files/tutorials/ExistingQuant-1_4.pdf#page=33
Sorry for the confusion. It was hard to come up with a term for this. Hope I was able to clarify enough that you can continue.
--Brendan