The ability to sequence and identify proteins, map their sites of post-translational modification (PTM), and assess their abundances is central to modern biology. Mass spectrometry (MS) is the gold standard technology by which this information is obtained. Serving as the centerpiece, tandem MS (MS/MS) is a principal component. Electron transfer dissociation (ETD), a relatively new MS/MS dissociation method, has generated significant excitement for its compatibility with previously intractable peptide/protein classes. Five years ago m/z range, mass accuracy, and mass resolution considerably restricted the application of ETD. Our initial RO1 proposal successfully eliminated this limitation by coupling ETD to the orbitrap mass analyzer. The resulting system routinely analyzes peptides and proteins, with and without labile PTMs, with a high-fidelity readout (orbitrap). As a result, it realized many of our anticipated outcomes and created numerous unforeseen opportunities. Just in the PI's laboratory, the latter set includes data-dependent selection of dissociation method (i.e., Decision Tree), discovery of the unique chemical compositions of z-type ions, internal spectral calibration using ETD reagents, activated-ion ETD, and several biological applications. By 2008, the commercial implementation of our technology began to reach researchers across the globe-nearly 300 to date-enabling access to numerous previously intractable problems such as mapping Arg methylation sites, increasing coverage of low molecular weight proteins, providing unambiguous PTM site assignment, and screening glycopeptide libraries, among many others. We detail two new aims that build upon the high impact results of our initial funding period.
Aim 1, how do we broaden the utility of ETD for biomedical research? Aim 2, what is the role of gas- phase purification in quantitative proteomics? We continue with a balance of instrumentation, method, informatic, and applied projects constructed upon the widely used ETD-orbitrap platform we described 3.5 years ago.

Public Health Relevance

Cutting edge MS based technology, Electron transfer dissociation (ETD), continues to be developed. This new MS/MS dissociation method enables previously intractable peptide/protein classes to be sequenced and identified, have their sites of post-translational modification (PTM) mapped, and assess their abundances. This is central to modern biology and has relevance for research ranging from human disease to evolution.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM080148-06
Application #
8237677
Study Section
Enabling Bioanalytical and Imaging Technologies Study Section (EBIT)
Program Officer
Edmonds, Charles G
Project Start
2007-03-01
Project End
2016-02-29
Budget Start
2012-06-01
Budget End
2013-02-28
Support Year
6
Fiscal Year
2012
Total Cost
$351,494
Indirect Cost
$107,503
Name
University of Wisconsin Madison
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
161202122
City
Madison
State
WI
Country
United States
Zip Code
53715
Richards, Alicia L; Merrill, Anna E; Coon, Joshua J (2015) Proteome sequencing goes deep. Curr Opin Chem Biol 24:7-Nov
Rhoads, Timothy W; Rose, Christopher M; Bailey, Derek J et al. (2014) Neutron-encoded mass signatures for quantitative top-down proteomics. Anal Chem 86:2314-9
Merrill, Anna E; Hebert, Alexander S; MacGilvray, Matthew E et al. (2014) NeuCode labels for relative protein quantification. Mol Cell Proteomics 13:2503-12
Ulbrich, Arne; Merrill, Anna E; Hebert, Alexander S et al. (2014) Neutron-encoded protein quantification by peptide carbamylation. J Am Soc Mass Spectrom 25:6-9
Brumbaugh, Justin; Russell, Jason D; Yu, Pengzhi et al. (2014) NANOG is multiply phosphorylated and directly modified by ERK2 and CDK1 in vitro. Stem Cell Reports 2:18-25
Chasman, Deborah; Ho, Yi-Hsuan; Berry, David B et al. (2014) Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. Mol Syst Biol 10:759
Hebert, Alexander S; Richards, Alicia L; Bailey, Derek J et al. (2014) The one hour yeast proteome. Mol Cell Proteomics 13:339-47
Rose, Christopher M; Merrill, Anna E; Bailey, Derek J et al. (2013) Neutron encoded labeling for peptide identification. Anal Chem 85:5129-37
Vincent, Catherine E; Potts, Gregory K; Ulbrich, Arne et al. (2013) Segmentation of precursor mass range using "tiling" approach increases peptide identifications for MS1-based label-free quantification. Anal Chem 85:2825-32
Wenger, Craig D; Coon, Joshua J (2013) A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. J Proteome Res 12:1377-86

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