Using protein chemistry to solve biochemical mysteries in the environment

Proteins are the biochemical machines of the cell and can provide a seasoned chemist with a wide range of information on the status or plans of a cell.  We use state-of-the-art tandem mass spectrometry technology and bioinformatic tools in order to analyze and decipher protein expression from a variety of samples from the environment.  Our specialty is in the marine world.  Be it particles floating in the ocean, sediments on the ocean floor, phytoplankton adapting to climate change, or bacteria surviving on hydrothermal vent plumes or in Arctic ice channels, we are interested and excited to tackle the project.  

WE ARE CURRENTLY SEEKING NEW COLLABORATIONS
ALL DATA IS PUBLICLY AVAILABLE on PRIDE for DOWNLOAD
MetaGOmics is ready to use!
This tool will allow you to examine functional and taxonomic expression between metaproteomic samples while taking into account homologous peptides and proteins that are inherent to meta-omic analyses.  
The first tool of its kind!!
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"Fear the awesome power of metaproteo-oceanographiomics(TM pending)"-Michael Riffle
Christina Le and Hana Abay (2 high school students) did a fabulous job at the Washington State Science and Engineering Fair in Bremerton WA in March of 2018.  They won several awards (see below).
  • WSSEF finalists (top 15 out of over 300 projects!)
  • 1st in senior division & 1st in category
  • Best in category
  • Wolfram Alpha Mathematical Software Special Award
  • Ohio University Scholarship Special Award

Our latest work

July 2017:  Emma's paper is published in ISME Journal!! Great work team!
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Critical decisions in metaproteomics: Achieving high confidence protein annotations in a sea of unknowns
Emma Timmins-Schiffman*, Damon H. May, Molly Mikan, Michael Riffle, Chris Frazar, 
H. Rodger Harvey, William S. Noble, Brook L. Nunn*
Damon May's paper is released on the JPR website and his fabulous tool, SIXGILL, is on GalaxyP!
Great job DAMON!
An alignment-free ‘metapeptide’ strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing

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Teaching environmental proteomics to local area high school students.

Brook Nunn runs the environmental division of the MacCoss Lab

Brook Nunn joined the lab group of Michael MacCoss in the Department of Genome Sciences where she is a Research Assistant Professor in 2015.  Historically, the Nunn lab has focused our efforts on proteomic profiling.  Proteomic profiling allows the investigator to catalog all the proteins expressed at the time of harvest in an unbiased manner and is a very thorough hypothesis-generating method.  This method allows us to figure out how the organism is adapting to a unique environment by globally assaying the organism's response or to find out which protein functional groups are common in preserved organic matter.  Since joining the MacCoss lab group, the focus of the lab has shifted.  We now include more targeted and quantitative methods.  It is an exciting time to be in the proteomics field!
This lab is a division of the MacCoss lab of Biological Mass Spectrometry at the University of Washington Department of Genome Sciences.  It is currently funded independently by Dr. Brook Nunn through the generous grants provided by the National Science Foundation.
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University of Washington
Seattle, WA USA