The quantitative proteome of a human cell line

By Martin Beck, A. Schmidt, Manfred Claassen, A. Ori, Anna Szymborska, Franz Herzog, Oliver Rinner, Jan Ellenberg, R. Aebersold. Molecular Systems Biology, 2011

786 citations recorded by the source corpus.

The generation of mathematical models of biological processes, the simulation of these processes under different conditions, and the comparison and integration of multiple data sets are explicit goals of systems biology that require the knowledge of the absolute quantity of the system's components. To date, systematic estimates of cellular protein concentrations have been exceptionally scarce. Here, we provide a quantitative description of the proteome of a commonly used human cell line in two functional states, interphase and mitosis. We show that these human cultured cells express at least ∼10 000 proteins and that the quantified proteins span a concentration range of seven orders of magnitude up to 20 000 000 copies per cell. We discuss how protein abundance is linked to function and evolution.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/ef68a702c9d4b9ee880c00eb4b6bdded2e176778

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Citations in the corpus

The in silico human surfaceome (2018, background): “The comparison of abundance of surfaceome proteins from the quantitative proteome of Beck et al. (65) with gene expression data from Klijn et al. (49) showed only a low correlation ( SI Appendix , Fig.”
The Size of the Human Proteome: The Width and Depth (2016, background): “Blood plasma is a complex mixture with a dynamic range of protein concentrations varying by >10 orders of magnitude [20], while the protein concentration range of tissue or cell lines is within seven orders of magnitude [21].”
Phosphorylation of the FUS low‐complexity domain disrupts phase separation, aggregation, and toxicity (2017, neutral): “FUS is highly abundant (Beck et al , 2011; Uhlen et al , 2015) and involved in RNA processing, splicing, and transport (Sama et al , 2014).”
A subcellular map of the human proteome (2017, result): “However, the TPM-based number corresponds more accurately to the number of proteins actually detected in this and other proteomic studies (30, 31).”
Deep Proteomics of the Xenopus laevis Egg using an mRNA-derived Reference Database (2014, neutral): “Recent advancements in mass spectrometry-based proteomics now enable global identification and quantification for up to ~10K proteins in a single experiment, along with associated post-translational modifications [1-3].”
Ultrasensitive proteome analysis using paramagnetic bead technology (2014, neutral): “…through generation of conditions favorable for proteolytic digestion and sample recovery (Leo´n et al , 2013; Tanca et al , 2013) and have led to charting of the near-complete proteomes of various mammalian cell lines (Beck et al , 2011; Moghaddas Gholami et al , 2013; Branca et al , 2014).”
Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins (2012, background): “Significantly higher numbers of identified proteins were so far only achieved by combining multiple diverse cell lines or tissues in one analysis (11), or by investing weeks of measurement for single samples (12, 13).”
Formation and Maturation of Phase Separated Liquid Droplets by RNA Binding Proteins (2015, methodology): “We observed that in the presence of crowding agents, hnRNPA1IDR underwent LLPS at 150mMNaCl and at a concentration of 1 mM (Figure S1B), which is below the concentration of hnRNPA1 in cells (1.17 3 107 molecules per cell or approximately 5–10 mM; Beck et al., 2011).”
The endoplasmic reticulum: structure, function and response to cellular signaling (2015, background): “Through various techniques and in various cell types Climp63 was shown to be a highly abundant protein [88–90] that localizes to perinuclear ER and is absent from the nuclear envelope [91, 92].”
Proteomic Analyses Provide Novel Insights into Plant Growth and Ginsenoside Biosynthesis in Forest Cultivated Panax ginseng (F. Ginseng) (2016, background): “The proteins with high and intermediate abundance with central importance in cells may reflect the genetic relationships between different species to some extent (Beck et al., 2011; Zhong et al., 2012).”