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TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples

by Pike, Ian , Kuhn, Karsten , Bomgarden, Ryan D. , Schweppe, Devin K. , Etienne, Chris , Viner, Rosa , Gygi, Steven P. , Rogers, John C. , Van Vranken, Jonathan G. , Li, Jiaming , Huttlin, Edward L. , Pontano Vaites, Laura , Paulo, Joao A. , Nandhikonda, Premchendar , Robitaille, Aaron M. , Thompson, Andrew H.

in 631/1647/2067 / 631/1647/296 / 631/45/475 / Affinity labeling / Bioinformatics / Biological Microscopy / Biological Techniques / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Cell Line / Cell lines / Humans / Isotope Labeling / Kinases / Labeling / Life Sciences / Methods / Peptides / Peptides - chemistry / Proline / Proteins / Proteome - chemistry / Proteomes / Proteomics / Proteomics - methods / Reagents / Staurosporine / Tandem Mass Spectrometry - methods / Thermal stability

2020

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TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples

2020

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TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples

2020

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Journal Article

TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples

Pike, Ian,

Kuhn, Karsten,

Bomgarden, Ryan D.,

Schweppe, Devin K.,

Etienne, Chris,

Viner, Rosa,

Gygi, Steven P.,

Rogers, John C.,

Van Vranken, Jonathan G.,

Li, Jiaming,

Huttlin, Edward L.,

Pontano Vaites, Laura,

Paulo, Joao A.,

Nandhikonda, Premchendar,

Robitaille, Aaron M.,

Thompson, Andrew H.

2020

Overview

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. A set of isobaric labeling reagents called TMTpro enables deep quantitative comparisons of proteome measurements across 16 samples.

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Publisher

Nature Publishing Group US,Nature Publishing Group

Subject

/ Biological Microscopy

/ Biological Techniques