Ambient surface mass spectrometry encompasses a broad range of sampling and ionization techniques. To date, only a small subset of these, based on liquid microjunction extraction, have proven suitable for intact protein analysis from thin tissue sections. Liquid extraction surface analysis shows particular promise for this application. Recently, a range of ion mobility spectrometry approaches have been coupled with ambient mass spectrometry. Improvements in signal-to-noise ratios, decreased chemical noise and separation of molecular classes have been described for the analysis of various biological substrates. Similar benefits have been described for ambient mass spectrometry imaging studies. In this review, we discuss the application of ambient mass spectrometry and ion mobility spectrometry to the analysis of intact proteins, and discuss opportunities and challenges for the field.