Journal Article

Systematic analysis of protein turnover in primary cells

Franken, Holger, Steidel, Michael, Zinn, Nico, Sweetman, Gavain, Ratnu, Vikram S., Beck, Martin, Bantscheff, Marcus, Savitski, Mikhail M., Kosinski, Jan, Kurzawa, Nils, Schramm, Maike, Mathieson, Toby, Bergamini, Giovanna, Poeckel, Daniel, Becher, Isabelle, Noh, Kyung-Min

2018

Overview

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 unique protein identifications over the entire data set. We observed similar protein half-lives in B-cells, natural killer cells and monocytes, whereas hepatocytes and mouse embryonic neurons show substantial differences. Our data set extends and statistically validates the previous observation that subunits of protein complexes tend to have coherent turnover. Moreover, analysis of different proteasome and nuclear pore complex assemblies suggests that their turnover rate is architecture dependent. These results illustrate that our approach allows investigating protein turnover and its implications in various cell types. The proteome-wide characterization of proteostasis depends on robust approaches to determine protein half-lives. Here, the authors improve the accuracy and precision of mass spectrometry-based quantification, enabling reliable protein half-life determination in several non-dividing cell types.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 631/337/475 / 631/80 / 631/80/389/2029 / 631/80/474/2085 / 82/58 / Animals / Cells - chemistry / Cells - metabolism / Cells, Cultured / Embryos / Half-life / Hepatocytes / Humanities and Social Sciences / Humans / Lymphocytes B / Mass Spectrometry / Mice / Monocytes / multidisciplinary / Natural killer cells / Peptides - chemistry / Peptides - metabolism / Proteasome Endopeptidase Complex - chemistry / Proteasome Endopeptidase Complex - metabolism / Proteasomes / Protein turnover / Proteins / Proteins - chemistry / Proteins - metabolism / Proteomics / Science / Science (multidisciplinary) / Turnover rate