MS-based sequencing is carried out on nano-flow liquid chromatography systems (UltiMate 3000, Dionex) coupled to a linear ion trap with ICR analyzer (LTQ-FT, Thermo) in a thoroughly optimized setup. Even for membrane proteins, analysis is usually more sensitive than standard ECL+-developed western blots (lower femtomole range or less). Sequence coverage of isolated proteins is often higher than 50%, a prerequisite for studying protein processing and expression of splice variations. Very good run-to-run reproducibility and high mass accuracy allow for reliable relative quantification of proteins over a broad dynamic range.