Absolute protein quantitation of the mouse macrophage Toll-like receptor and chemotaxis pathways

Manes, Nathan P.; Calzola, Jessica M.; Kaplan, Paul M.; Fraser, Iain D. C.; Germain, Ronald N.; Meier‐Schellersheim, Martin; Nita‐Lazar, Aleksandra

doi:10.1038/s41597-022-01612-y

Cited by 3 publications

(2 citation statements)

References 57 publications

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“…For protein copy number estimations, we assumed total protein mass of 230 pg/cell for BMDMs, 78 25 pg/cell for non-stimulated and 75 pg/cell for stimulated T cells. 28 …”

Section: Methodsmentioning

confidence: 99%

Proteomics of immune cells from liver tumors reveals immunotherapy targets

et al. 2023

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“…For protein copy number estimations, we assumed total protein mass of 230 pg/cell for BMDMs, 78 25 pg/cell for non-stimulated and 75 pg/cell for stimulated T cells. 28 …”

Section: Methodsmentioning

confidence: 99%

Proteomics of immune cells from liver tumors reveals immunotherapy targets

et al. 2023

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“…A focus is understanding the array of responses elicited by host cells to prevent the spread of an infection, including immune signaling. In this vein, the use of targeted proteomics defined the absolute numbers of protein molecules per cell in the mouse macrophage pathogen recognition receptor and chemotaxis pathways, providing the means for pathway modeling and simulation . Combinatorial phosphorylation, protein interaction, and microscopy studies have demonstrated that the immune factor IFI16, upon recognition and binding to viral DNA, undergoes phosphorylation-controlled liquid–liquid phase separation that regulates innate immune signaling .…”

Section: Biology and Disease-driven Hppmentioning

confidence: 99%

The 2023 Report on the Proteome from the HUPO Human Proteome Project

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et al. 2024

J. Proteome Res.

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Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1–4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.

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Absolute protein quantitation of the mouse macrophage Toll-like receptor and chemotaxis pathways

et al. 2022

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The Toll-like receptor (TLR) and chemotaxis pathways are key components of the innate immune system. Subtle variation in the concentration, timing, and molecular structure of the ligands are known to affect downstream signaling and the resulting immune response. Computational modeling and simulation at the molecular interaction level can be used to study complex biological pathways, but such simulations require protein concentration values as model parameters. Here we report the development and application of targeted mass spectrometry assays to measure the absolute abundance of proteins of the mouse macrophage Toll-like receptor 4 (TLR4) and chemotaxis pathways. Two peptides per protein were quantified, if possible. The protein abundance values ranged from 1,332 to 227,000,000 copies per cell. They moderately correlated with transcript abundance values from a previously published mouse macrophage RNA-seq dataset, and these two datasets were combined to make proteome-wide abundance estimates. The datasets produced during this investigation can be used for pathway modeling and simulation, as well as for other studies of the TLR and chemotaxis pathways.

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Absolute protein quantitation of the mouse macrophage Toll-like receptor and chemotaxis pathways

Cited by 3 publications

References 57 publications

Proteomics of immune cells from liver tumors reveals immunotherapy targets

Proteomics of immune cells from liver tumors reveals immunotherapy targets

The 2023 Report on the Proteome from the HUPO Human Proteome Project

Absolute protein quantitation of the mouse macrophage Toll-like receptor and chemotaxis pathways

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