Open AccessTMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples
Author(s) -
Jiaming Li,
Jonathan G. Van Vranken,
Laura Pontano Vaites,
Devin K. Schweppe,
Edward L Huttlin,
Chris Etienne,
Premchendar Nandhikonda,
Rosa Viner,
Aaron M. Robitaille,
Andrew Thompson,
Karsten Kuhn,
Ian Pike,
Ryan Bomgarden,
John C. Rogers,
Steven P. Gygi,
João A. Paulo
Publication year - 2020
Publication title -
nature methods
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 19.469
H-Index - 318
eISSN - 1548-7105
pISSN - 1548-7091
DOI - 10.1038/s41592-020-0781-4
Subject(s) - proteome , isobaric labeling , isobaric process , tandem mass tag , quantitative proteomics , reagent , staurosporine , tandem mass spectrometry , computational biology , chemistry , proteomics , mass spectrometry , biology , chromatography , biochemistry , protein mass spectrometry , kinase , gene , physics , thermodynamics , protein kinase c
Isobaric labeling empowers proteome-wide expression measurements simultaneously across multiple samples. Here an expanded set of 16 isobaric reagents based on an isobutyl-proline immonium ion reporter structure (TMTpro) is presented. These reagents have similar characteristics to existing tandem mass tag reagents but with increased fragmentation efficiency and signal. In a proteome-scale example dataset, we compared eight common cell lines with and without Torin1 treatment with three replicates, quantifying more than 8,800 proteins (mean of 7.5 peptides per protein) per replicate with an analysis time of only 1.1 h per proteome. Finally, we modified the thermal stability assay to examine proteome-wide melting shifts after treatment with DMSO, 1 or 20 µM staurosporine with five replicates. This assay identified and dose-stratified staurosporine binding to 228 cellular kinases in just one, 18-h experiment. TMTpro reagents allow complex experimental designs-all with essentially no missing values across the 16 samples and no loss in quantitative integrity.