Figure 2: (A) Schematic of a full proteomics experiment. The protein sample is separated/fractionated under non-denaturing (1) and denaturing (2) conditions, digested (3) and analyzed by LC-MS/MS (4) (bottom-up proteiomics).. Database search and data analysis (5) led to identification of proteins, post-translational modifications (PTMs) in proteins and protein-protein interactions (PPIs), that were verified and then validated by Western blotting (6), and then monitored by single reaction monitoring (SRM), multiple reaction monitoring (MRM) and/or cross-validation. The original protein samples can also be analyzed by MALDI-MS (8) that leads to identification od specific protein/peptide patterns whose data analysis (10) leads to identification of proteins, PTMs and PPIs. The fractionated samples in (2) can also be investigated without using electrophoretic denaturing conditions (2A) in a process called in solution digestion, or analyzed without any digestion (2B) in a process called top down proteomics. In a third alternative, the fractionated dsampled from (2) are analyzed without digestion directly by MALDI-MS (2C).