Signal enhanced proteomics: a biological perspective on dissecting the functional organisation of cell proteomes

Dalila Bensaddek, Armel Nicolas, Angus I. Lamond (Lead / Corresponding author)

Research output: Contribution to journalReview article

Abstract

Proteomes are highly dynamic and can respond rapidly to environmental and cellular signals. Within cells, proteins often form distinct pools with different functions and properties. However, in quantitative proteomics studies it is common to measure averaged values for proteins that do not reflect variations that may occur between different protein isoforms, different subcellular compartments, or in cells at different cell cycle stages and so on. Here we review experimental approaches that can be used to enhance the signal from specific pools of protein that may otherwise be obscured through averaging across protein populations. This signal enhancement can help to reveal functions associated with specific protein pools, providing insight into the regulation of cellular processes. We review different strategies for proteomic signal enhancement, with a focus on the analysis of protein pools in different subcellular locations. We describe how MS-based proteome analyses can be combined with a general physico-chemical cell fractionation procedure that can be applied to many cultured cell lines.

Original languageEnglish
Pages (from-to)114-122
Number of pages9
JournalCurrent Opinion in Chemical Biology
Volume48
Early online date11 Dec 2018
DOIs
Publication statusPublished - Feb 2019

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Proteome
Proteomics
Proteins
Chemical Fractionation
Cells
Cell Fractionation
Fractionation
Cultured Cells
Cell Cycle
Protein Isoforms
Cell Line
Population

Cite this

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title = "Signal enhanced proteomics: a biological perspective on dissecting the functional organisation of cell proteomes",
abstract = "Proteomes are highly dynamic and can respond rapidly to environmental and cellular signals. Within cells, proteins often form distinct pools with different functions and properties. However, in quantitative proteomics studies it is common to measure averaged values for proteins that do not reflect variations that may occur between different protein isoforms, different subcellular compartments, or in cells at different cell cycle stages and so on. Here we review experimental approaches that can be used to enhance the signal from specific pools of protein that may otherwise be obscured through averaging across protein populations. This signal enhancement can help to reveal functions associated with specific protein pools, providing insight into the regulation of cellular processes. We review different strategies for proteomic signal enhancement, with a focus on the analysis of protein pools in different subcellular locations. We describe how MS-based proteome analyses can be combined with a general physico-chemical cell fractionation procedure that can be applied to many cultured cell lines.",
author = "Dalila Bensaddek and Armel Nicolas and Lamond, {Angus I.}",
note = "This work was funded by awards from the Wellcome Trust 073980/Z/03/BR and 098503/Z/12/Z and a BBSRC sLoLa grant BB/K003801/1. Imaging and image analysis was supported by two Wellcome Trust Strategic Awards (097945/B/11/Z and 095931/Z/11/Z) and an MRC Next generation Optical Microscopy Award (MR/K015869/1).",
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T2 - a biological perspective on dissecting the functional organisation of cell proteomes

AU - Bensaddek, Dalila

AU - Nicolas, Armel

AU - Lamond, Angus I.

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N2 - Proteomes are highly dynamic and can respond rapidly to environmental and cellular signals. Within cells, proteins often form distinct pools with different functions and properties. However, in quantitative proteomics studies it is common to measure averaged values for proteins that do not reflect variations that may occur between different protein isoforms, different subcellular compartments, or in cells at different cell cycle stages and so on. Here we review experimental approaches that can be used to enhance the signal from specific pools of protein that may otherwise be obscured through averaging across protein populations. This signal enhancement can help to reveal functions associated with specific protein pools, providing insight into the regulation of cellular processes. We review different strategies for proteomic signal enhancement, with a focus on the analysis of protein pools in different subcellular locations. We describe how MS-based proteome analyses can be combined with a general physico-chemical cell fractionation procedure that can be applied to many cultured cell lines.

AB - Proteomes are highly dynamic and can respond rapidly to environmental and cellular signals. Within cells, proteins often form distinct pools with different functions and properties. However, in quantitative proteomics studies it is common to measure averaged values for proteins that do not reflect variations that may occur between different protein isoforms, different subcellular compartments, or in cells at different cell cycle stages and so on. Here we review experimental approaches that can be used to enhance the signal from specific pools of protein that may otherwise be obscured through averaging across protein populations. This signal enhancement can help to reveal functions associated with specific protein pools, providing insight into the regulation of cellular processes. We review different strategies for proteomic signal enhancement, with a focus on the analysis of protein pools in different subcellular locations. We describe how MS-based proteome analyses can be combined with a general physico-chemical cell fractionation procedure that can be applied to many cultured cell lines.

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JO - Current Opinion in Chemical Biology

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