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!
Really truly beginning? Maybe start with this -- The fastest, character number limited-est overview of mass spectrometry I've ever seen. Courtesy of @BioTweeps.
New! (9/14/2020) A beginner's guide to mass spectrometry-based proteomics by Ankit Sinha & some other guy.
Do you learn well through video based lectures? Matt Padula has been putting up great video lectures on YouTube for Years!
Do you want to know more about stats? Nikolai Slavov has another very active YouTube channel with a lot of intro material into -omics based data analysis principles
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.
Proteomics Data Analysis. This 2017 review chapter is a great place to start.
A Gentle Introduction to Proteomics False Discovery Rates -- You won't get very far at all before you run into this topic. This may be the best review you'll find that will clarify the topic (September 2018)
Phil Wilmarth's GitHub has great tutorials on FDR and Parsimony, as well as other primary concepts in proteomics data processing.
This is nice!
The theory behind all mass analyzers by the ChromAcademy!
For Mass Spectrometry Fundamentals, check out this page that is put together by ASMS. There are some great talks here!
I'll add more later!