here is the file showing the results from the experiment..
http://littledomain.com/james/files/breakdown.pdf
to answer your questions:
1. I just injecting something to get the run started from the autosampler. Too lazy to change configuration to remove the autosamper. After started, I just wait for the signal to come to the baseline before changing the parameter of interest on the tune page. In the example above, was doing full scan acquisition to see how the spectrum changed as a function of the cone (skimmer) voltage.
2. I think I was doing a scan of about 10 to 475 for this particular compound every 0.3 seconds. Could just observe on tune page, but I wanted to automatically export the peaks from the chromatgram function to Excel. By making separated post column injections manually, I get distinct peaks to remind me when I changed the parameter of the value. Like to use area, better precision than height..
3. I knew at what % solvent A and solvent B my component eluted, so I dissolved it in this solvent mix and used the same solvent mix through the column. Could just do the chromatoraphy each time, but would take forever to obtain the data. I often do the injections in duplicate or triplicate and average results to get better data. I think in this case I was injecting 5 ul of 1.5 ppm solution post column. Just use the column to minimize pump pulsation. I just make sure the concentration I inject isn's so large the response is starting to saturate..