I've been meaning to put together something like this for a while. This is just a start. Please refer me to other good resources if you have them!
Nature Focus Articles on Proteomics - This is a nice compilation of relatively recent reviews on the topic. Definitely a nice starting point (here.)
Fundamentals of peptide and protein mass spectrometry (from the Broad Institute, circa 2013!)
Quantitative proteomics from the Broad (video from 2012)
Older -- but really thorough description of proteomics from the NIAAA. I like this because it starts from the perspective of someone who knows genomics/transcriptomics and goes forward.
This is nice!
The theory behind all mass analyzers by the ChromAcademy!
I'll add more later!