title: Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level.
abstract: Proteomics studies typically analyze proteins at a population level, using extracts prepared from tens of thousands to millions of cells. The resulting measurements correspond to average values across the cell population and can mask considerable variation in protein expression and function between individual cells or organisms. Here, we report the development of micro-proteomics for the analysis of Caenorhabditis elegans, a eukaryote composed of 959 somatic cells and ∼1500 germ cells, measuring the worm proteome at a single organism level to a depth of ∼3000 proteins. This includes detection of proteins across a wide dynamic range of expression levels (>6 orders of magnitude), including many chromatin-associated factors involved in chromosome structure and gene regulation. We apply the micro-proteomics workflow to measure the global proteome response to heat-shock in individual nematodes. This shows variation between individual animals in the magnitude of proteome response following heat-shock, including variable induction of heat-shock proteins. The micro-proteomics pipeline thus facilitates the investigation of stochastic variation in protein expression between individuals within an isogenic population of C. elegans. All data described in this study are available online via the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd), an open access, searchable database resource.
authors.affiliation: Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom.
authors.forename: Dalila
authors.initials: D
authors.lastname: Bensaddek
authors.affiliation: Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom.|Department of Biochemistry and Biophysics, Genentech Hall, University of California, San Francisco, CA, USA.
authors.forename: Vikram
authors.initials: V
authors.lastname: Narayan
authors.affiliation: Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom.
authors.forename: Armel
authors.initials: A
authors.lastname: Nicolas
authors.affiliation: Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom.
authors.forename: Alejandro Brenes
authors.initials: AB
authors.lastname: Murillo
authors.affiliation: Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom.
authors.forename: Anton
authors.initials: A
authors.lastname: Gartner
authors.affiliation: Department of Biochemistry and Biophysics, Genentech Hall, University of California, San Francisco, CA, USA.
authors.forename: Cynthia J
authors.initials: CJ
authors.lastname: Kenyon
authors.affiliation: Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom.
authors.forename: Angus I
authors.initials: AI
authors.lastname: Lamond
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism*; D056148:Chromatography, Reverse-Phase; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006360:Heat-Shock Proteins / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D013058:Mass Spectrometry; D020543:Proteome / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods* / Q000706:statistics & numerical data
chemical_list: D029742:Caenorhabditis elegans Proteins; D002843:Chromatin; D006360:Heat-Shock Proteins; D020543:Proteome
keywords: Caenorhabditis elegans; Heat-shock; Micro-proteomics; Nematode; Single worm proteomics; Technology