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Posted by Richard Jacob (December 18, 2024)

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 [...]

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Posted by Richard Jacob (October 14, 2022)

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 [...]

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Posted by Patrick Emery (February 12, 2018)

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 [...]

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