mTMT: An Alternative, Nonisobaric, Tandem Mass Tag Allowing for Precursor-Based Quantification

Stable isotope labeling
of peptides is the basis for numerous mass-spectrometry-based
quantification strategies. Isobaric tagging and metabolic labeling,
namely, tandem mass tagging (TMT) and SILAC, are among the most widely
used techniques for relative protein quantification. Here we report
an alternative, precursor-based quantification method using nonisobaric
TMT variants: TMTzero (TMT0) and superheavy TMT (shTMT). We term this
strategy mass difference tandem mass tagging (mTMT). These TMT
variants differ by 11 mass units; however, peptides labeled with these
reagents coelute, analogous to SILAC-labeled peptide pairs. As a proof-of-concept,
we profiled the proteomes of two cell lines that are frequently used
in neuroscience studies, SH-SY5Y and SVGp12, using mTMT and standard
SILAC-labeling approaches. We show similar quantified proteins and
peptides for each method, with highly correlated fold-changes between
workflows. We conclude that mTMT is a suitable alternative for precursor-based
protein quantification.