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Changes in protein expression and post-translational modifications are essential mechanisms of biological regulation and disease. Advancements in mass spectrometry (MS) instrumentation, bioinformatics and quantification methods, such as label-free quantification, metabolic labeling and chemical tagging, now enable researchers to identify and quantitatively analyze thousands of proteins in a given sample with a high degree of accuracy.1, 2Isobaric chemical tags are powerful tools that enable concurrent identification and quantitation of proteins in different samples using tandem mass spectrometry. They are small chemical molecules with identical structure that covalently attach to the free amino termini of lysine residues of peptides and proteins, thereby labeling various peptides in a given sample. During the MS/MS analysis, each isobaric tag produces a unique reporter ion signature that makes quantitation possible. In a typical MS analysis, the labeled peptides are indistinguishable from each other; however, in the tandem MS mode during which peptides are isolated and fragmented, each tag generates a unique reporter ion. Protein quantitation is then accomplished by comparing the intensities of the six reporter ions in the MS/MS spectra.Highlights:Enabling protein ID and quantitation from multiple samples of cells, tissues or biological fluids Consistent chemistry allowing efficient transition from method development to multiplex quantitation, enabling biomarker discovery research Efficient labeling of membrane and post-translationally modified proteins Expandable system allowing concurrent multiplexing of up to six different samples in a single experimentOptimized fragmentation and fully supported quantitation with Proteome Discoverer 1.0 for all Thermo Scientific LC MS/MS platforms, such as LTQ XL and LTQ Orbitrap XL SystemsEach TMT tag is based on the same chemical structure, eliminating the need to modify labeling conditions or HPLC separation conditions between experimentsThe tags consist of TMT0, the TMT2 two-plex set and the TMT6 six-plex setTMT0 tag allows testing and optimization of sample preparation, labeling, fractionation and MS fragmentation for peptide identification and reporter detection without using the more costly isotope-labeled compoundsTMT2 reagent set allows two-plex protein profiling for small studiesTMT6 reagent set allows six-plex protein profiling for multiple conditions, including time courses, dose responses, replicates or multiple sample comparisonsProtein expression profiling of normal vs. disease states or control vs. treatedQuantitative analysis of proteins for which no antibodies are availableIdentification and quantitation of membrane and post-translationally modified protei
