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Articles tagged: TMT
2D-TPP as easy as 1-2-3
Two-Dimensional Thermal Proteome Profiling (2DTPP) is a technique that profiles the thermal stability of a proteome as a function of ligand concentration as a way to detect ligand interaction. If the thermal stability changes with ligand concentration, there is an interaction between the ligand and that protein. The ligand can be a drug, metabolite or other small molecules. The analysis [...]
Mascot vs FragPipe: Uncovering endogenous proteolytic processing
Studying endogenous proteolytic processing, or N-terminomics, typically involves selective enrichment of protein N-termini. An alternative is to use the standard shotgun LC-MS/MS approach with the unenriched sample, which requires the database search to identify semi-specific peptides. Mascot Server 3.0 includes MS2PIP machine learning models for fragment intensity prediction, which can give a big boost to semi-specific identifications. Recent versions of [...]
Complementary reporter ion clusters in TMT/TMTpro labeling
We recently received a support request about complementary ions in TMTpro labeling. Complementary ions are formed during fragmentation, where the precursor loses the reporter ion and carbon monoxide, leaving behind the peptide and the balance region of the label. Complementary ion spacing is similar to reporter ions but the mass varies depending on peptide mass. The customer was concerned that [...]
MS3 reporter ion quantitation with Mascot Distiller
A common issue encountered when carrying out reporter ion quantitation methods, such as TMT and iTRAQ, is that of interfering ion signals in the reporter region. One commonly used strategy which can be taken to mitigate against this is to reisolate the most abundant ion in the MS/MS spectrum and refragment it. The resultant reporter ion signals in the MS3 [...]