Figure 1
From: Proteomics with a pinch of salt: A cyanobacterial perspective
A general proteomic workflow. The main steps are, cell culture, protein extraction (liquid nitrogen freezing and cracking), sample fractionation (traditional 2DE and gel-free chromatography method), mass spectrometer analysis and protein quantitation and identification. Quantitation using 2DE is densitometry based and implemented with appropriate software (e.g. PD QUEST®, SameSpots®), but can also be undertaken on the mass spectrometer, relying on abundance of peptide peaks. Identification occurs with database search software (based on peptide mass fingerprint or sequence analysis). Proteins are commonly digested using trypsin. 
: indicate essential salt removal stages. RCDC® – protein quantitation assay kit, IEF- isoelectric focusing, HPLC- High Performance Liquid Chromatography, SCX- Strong Cation Exchange.