Newbie question, I am wanting to get a sample report output from my msqrob2 analysis, one which has protein IDs and raw abundances for example. Are there any tutorials describing what code to use to enable such a report?

The DE tutorial on msqrob2 is great, but it does not go into enough detail, is there anywhere else that one can get tutorials for using this analysis approach?

If you use msqrob2, you data is probably stored as a QFeatures object. Assuming it is called qf and the assay with the protein data you want is called "prot", you can get the quantitative data with assay(qf[["prot"]]). You can then write it to a csv file with write.csv(assay(qf[["prot"]]), file = "prots.csv").