title: Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development.
abstract: Regulation of protein abundance is a critical aspect of cellular function, organism development, and aging. Alternative splicing may give rise to multiple possible proteoforms of gene products where the abundance of each proteoform is independently regulated. Understanding how the abundances of these distinct gene products change is essential to understanding the underlying mechanisms of many biological processes. Bottom-up proteomics mass spectrometry techniques may be used to estimate protein abundance indirectly by sequencing and quantifying peptides that are later mapped to proteins based on sequence. However, quantifying the abundance of distinct gene products is routinely confounded by peptides that map to multiple possible proteoforms. In this work, we describe a technique that may be used to help mitigate the effects of confounding ambiguous peptides and multiple proteoforms when quantifying proteins. We have applied this technique to visualize the distribution of distinct gene products for the whole proteome across 11 developmental stages of the model organism Caenorhabditis elegans. The result is a large multidimensional dataset for which web-based tools were developed for visualizing how translated gene products change during development and identifying possible proteoforms. The underlying instrument raw files and tandem mass spectra may also be downloaded. The data resource is freely available on the web at http://www.yeastrc.org/wormpes/ . Graphical Abstract ᅟ.
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.|Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Riffle
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
authors.forename: Gennifer E
authors.initials: GE
authors.lastname: Merrihew
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Jaschob
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
authors.forename: Vagisha
authors.initials: V
authors.lastname: Sharma
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
authors.forename: Trisha N
authors.initials: TN
authors.lastname: Davis
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
authors.forename: William S
authors.initials: WS
authors.lastname: Noble
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA. maccoss@uw.edu.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: MacCoss
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000254:growth & development* / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D010446:Peptide Fragments / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D020543:Proteome / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics; D053719:Tandem Mass Spectrometry; D014584:User-Computer Interface
chemical_list: D029742:Caenorhabditis elegans Proteins; D010446:Peptide Fragments; D020543:Proteome
keywords: Caenorhabditis elegans; Database; Development; Protein separation; Proteoform; Proteomics; SDS-PAGE; Visualization