General Terms

Proteomics is the large-scale study of proteins. The term proteomics was coined in 1997 in analogy with genomics, the study of the genome. The word proteome is a portmanteau of protein and genome, and was coined by Marc Wilkins in 1994. The proteome is the entire set of proteins, produced or modified by an organism or system.

Tandem mass spectrometry, also known as MS/MS or MS2, involves multiple steps of mass spectrometry selection, with some form of fragmentation occurring in between the stages. In a tandem mass spectrometer, ions are formed in the ion source and separated by mass-to-charge ratio in the first stage of mass spectrometry (MS1). Ions of a particular mass-to-charge ratio (precursor ions) are selected and fragment ions (product ions) are created by collision-induced dissociation, ion-molecule reaction, photodissociation, or other process. The resulting ions are then separated and detected in a second stage of mass spectrometry (MS2).

Shotgun proteomics refers to the use of bottom-up proteomics techniques in identifying proteins in complex mixtures using a combination of high performance liquid chromatography combined with mass spectrometry. The name is derived from shotgun sequencing of DNA which is itself named after the rapidly expanding, quasi-random firing pattern of a shotgun. The most common method of shotgun proteomics starts with the proteins in the mixture being digested and the resulting peptides are separated by liquid chromatography. Tandem mass spectrometry is then used to identify the peptides.

Global Profiling

Isobaric labeling is a mass spectrometry strategy used in quantitative proteomics. Peptides or proteins are labeled with various chemical groups that are (at least nominally) isobaric, or the same in mass, but which fragment during tandem mass spectrometry to yield reporter ions of different mass. In a typical bottom-up proteomics workflow, proteins are enzymatically digested by a protease to produce peptides, which are then labeled with different isobaric tags such as TMT-10plex kit. The samples are mixed in equal ratios. During a liquid chromatography-mass spectrometry analysis, the peptides are fragmented to produce sequence-specific product ions, which help to determine the peptide sequence, as well as the reporter tags, whose abundances reflect the relative ratio of the peptide in the samples that were combined. There are two types of isobaric tags commercially available: tandem mass tags (TMT) and isobaric tags for relative and absolute quantitation (iTRAQ). TMT is available in duplex, 6-plex and 10plex forms, while iTRAQ is available in 4-plex and 8-plex forms.

Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) is a metabolic labeling technique for mass spectrometric (MS)-based quantitative proteomics. It was developed in the Center for Experimental Bioinformatics (CEBI) at the University of Southern Denmark (Ong SE, et al, MCP, 2002). In SILAC, differentially labeled samples are mixed early in the experimental process, and analyzed together by LC-MS/MS. Since the labeling does not affect the chemical properties of the molecules, they co-elute from the LC column and analyzed together in the mass spectrometer. The peptide peaks of the differentially labeled samples can be very accurately quantified relative to each other to determine the peptide and protein ratios.