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Great Lakes Bioenergy Research Center

EMSL Project ID


The researchers of the GLBRC will utilize state of the art proteomics facilities resident at the Pacific Northwest National Laboratory that allow for rapid global determination of protein expression patterns of cells or organelles. While enabling the qualitative survey of proteins expressed in the cell, the main strength of the approach is the qualtitative determination of relative protein expression changes in a statistically rigorous manner. The PNNL proteomics process consists of two steps where the first step creates a peptide database for use in the high through put experiments in the second stage. The first stage relies on tandem mass spectrometry (MS/MS) interfaced with liquid chromatography (LC) to produce peptide identifications through fragmentation spectra. These identifications are stored along with mass and elution time information in the peptide database. While the limited dynamic range of the MS/MS instruments require extensive fractionation of the samples (soluble versus insoluble fractions and ion exchange fractions of peptide mixtures), these analyses are only needed a single time since the data is stored in the peptide database.

The second stage utilizes the Fourier transform ion cyclotron resonance instruments for validation and quantiation of the peptides in any mixture. The extensive dynamic range and sensitivity of these instruments eliminates the need for up front fractionation and whole cell lysates can be analyzed in a single experiment and this throughput enables statistically rigorous quantitation.

Project Details

Start Date
End Date


Principal Investigator

Mary Lipton
Environmental Molecular Sciences Laboratory

Team Members

Amy Boaro
Pacific Northwest National Laboratory

Li Cao
Pacific Northwest National Laboratory

Thomas Taverner
Pacific Northwest National Laboratory

Related Publications

Aylward FO, KE Burnum, JJ Scott, G Suen, SG Tringe, SM Adams, KW Barry, CD Nicora, PD Piehowski, SO Purvine, GJ Starrett, LA Goodwin, RD Smith, MS Lipton, and CR Currie. 2012. "Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens." The ISME Journal. doi:10.1038/ismej.2012.10 (Epub ahead of print)
Chundawat SP, MS Lipton, SO Purvine, N Uppugundla, D Gao, V Balan, and BE Dale. 2011. "Proteomics based compositional analysis of complex cellulase-hemicellulase mixtures." Journal of Proteome Research 10(10):4365-4372. doi:10.1021/pr101234z