Waters instruments have the capability to optimally organize MRMs into overlapping time windows using Quanpedia, available with MassLynx Software. The user also gains the added benefit of automatically creating a data analysis method in the TargetLynx processing software.

Learn more about Quanpedia here; select the Application Notes tab to dig deeper into demonstrations of how it's used.

http://www.waters.com/waters/nav.htm?cid=10148049

For AB-Sciex and Thermo, the terms are "Scheduled MRM" and "Timed MRM" respectively.

The idea is basically the same for all of them.

I think that an explanation is quicker and simpler than a reference, in this case.

As you know, the main problem with an MRM assay is time. In conventional MRM you search for your target analyte during the whole run. In scheduled MRM, you tell the instrument to search  for a particular analyte around the time (time window) it is expected to elute from the column.

By doing this, you can acquire an higher number of data point per compound, even if you prepare a 50+ compounds MRM assay. You just need to know WHEN they need to be analysed by your QqQ.

By the way, a good reference is the following

Selected reaction monitoring for quantitative proteomics: a tutorial, Lange, V. et all, Mol Syst Biol. 2008; 4: 222.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583086/

Well, it depends on how many compounds you are measuring in your method, and also depends on how good is your column (for LC).

If you have a lot of samples, then scheduled MRM is pretty helpful for a higher sensitivity. However, if your LC column is not very consistent in terms of retention times and causes shifts in the peaks observed from a week to another or month to another, then you better avoid scheduled MRM and stick to the conventional one.

You can report either because the m/z is the same but check whichever has higher sensitivity

https://www.agilent.com/cs/library/applications/5990-5092en_lo%20CMS.pdf