Proteomics

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Systematic analysis of protein turnover in primary cells - Part V

ABSTRACT: To better understand proteostasis in health and disease, determination of protein half-lives is essential. We improved the precision and accuracy of peptide-ion intensity based quantification in order to enable accurate determination of protein turnover in non-dividing cells using dynamic-SILAC. This enabled precise and accurate protein half-life determination ranging from 10 to more than 1000 hours. We achieve good proteomic coverage ranging from four to six thousand proteins in several types of non-dividing cells, corresponding to a total of 9699 unique proteins over the entire dataset. Good agreement was observed in half-lives between B-cells, natural killer cells and monocytes, while hepatocytes and mouse embryonic neurons showed substantial differences. Our comprehensive dataset enabled extension and statistical validation of the previous observation that subunits of protein complexes tend to have coherent turnover. Furthermore, we observed complex architecture dependent turnover within complexes of the proteasome and the nuclear pore complex. Our method is broadly applicable and might be used to investigate protein turnover in various cell types.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain, Neuron

SUBMITTER: Maria Faelth Savitski  

LAB HEAD: Marcus Bantscheff

PROVIDER: PXD008514 | Pride | 2018-06-08

REPOSITORIES: Pride

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01920_F1_R1_P0166140B02_SILAC3.raw.gz Raw
01920_F1_R1_P0166140B03_SILAC3.raw.gz Raw
01920_F1_R1_P0166140B04_SILAC3.raw.gz Raw
01920_F1_R1_P0166140B05_SILAC3.raw.gz Raw
01920_F1_R1_P0166140B06_SILAC3.raw.gz Raw
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Publications

A better understanding of proteostasis in health and disease requires robust methods to determine protein half-lives. Here we improve the precision and accuracy of peptide ion intensity-based quantification, enabling more accurate protein turnover determination in non-dividing cells by dynamic SILAC-based proteomics. This approach allows exact determination of protein half-lives ranging from 10 to >1000 h. We identified 4000-6000 proteins in several non-dividing cell types, corresponding to 9699  ...[more]

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