Data from shotgun-MS, which consists of chromatograms attached to mass spectra, are analyzed by complex computational algorithms to reconstruct the protein sequences based in the masses of all peptides measured and fragmented. This process is known as “bottom-up proteomics.” MS-based proteomics have rapidly developed in the past 10 years. Nowadays, a single LC-MS experiment is able to reveal 3000 to 7000 proteins in an hour, which would only be doable—if at all—by combining 2DE-MS over some

weeks of work. For proteome quantitation, there are Inhibitors,research,lifescience,medical several alternatives that can be taken into consideration13 for a given LC-MS experiment, such as stable AZD6244 nmr isotope labeling in vitro (ie, isotope-coded affinity tags [ICAT]14 and isobaric tags for relative and absolute quantitation [iTRAQ]15) or even in vivo (ie, stable Inhibitors,research,lifescience,medical isotope labeling by/with amino acids in cell culture [SILAC]16 or stable isotope labeling in mammals [SILAM]),

as well as diverse label-free approaches.17 Shotgun-MS still presents difficulty in representing hydrophobic and low abundant proteins depending Inhibitors,research,lifescience,medical on the type of sample preparation and MS acquisition. Moreover, information of intact proteins is lost by conventional bottom-up proteomics, which can be represented by 2DE, as well as the characterization of certain protein post-translational modifications. Proteome findings in patients with depression Brain tissue and cerebrospinal fluid Surprisingly, and unlike other psychiatric disorders such as schizophrenia,18,19 only one research group focused their efforts on the large-scale proteome investigation of postmortem Inhibitors,research,lifescience,medical human brains from depressed patients, through two articles. Samples from the dorsolateral prefrontal cortex (DLPFC) of 24 patients with MDD were compared with 12 controls using a shotgun label-free approach. Some of the protein candidates were further

validated by selected reaction monitoring (SRM). Inhibitors,research,lifescience,medical Several biological functions were associated with MDD, such as energy metabolism, cellular transport, and cell communication and signaling.20 Energy metabolism has already been described for a long time as a pattern for psychiatric disorders in general, via several different Bumetanide techniques.21-23 However, it has been possible to delineate exactly which energy metabolism pathways are more involved in each disorder, by using proteomics. Glycolysis is the main affected pathway in schizophrenia brains,24 whereas in MDD, oxidative phosphorylation is the most affected. Not only have several subunits of oxidative phosphorylation complexes been shown to be expressed differentially, but adenosine triphosphate (ATP) levels were also determined to be lower in MDD.20 Additionally, a proteomic study of a preclinical model for anxiety has shown both pathways to be differentially regulated.