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Title: Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry

Authors:
; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1152564
Resource Type:
Journal Article
Resource Relation:
Journal Name: Genome Research; Journal Volume: 17; Journal Issue: 3
Country of Publication:
United States
Language:
English

Citation Formats

Petyuk, V. A., Qian, W. -J., Chin, M. H., Wang, H., Livesay, E. A., Monroe, M. E., Adkins, J. N., Jaitly, N., Anderson, D. J., Camp, D. G., Smith, D. J., and Smith, R. D. Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry. United States: N. p., 2007. Web. doi:10.1101/gr.5799207.
Petyuk, V. A., Qian, W. -J., Chin, M. H., Wang, H., Livesay, E. A., Monroe, M. E., Adkins, J. N., Jaitly, N., Anderson, D. J., Camp, D. G., Smith, D. J., & Smith, R. D. Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry. United States. doi:10.1101/gr.5799207.
Petyuk, V. A., Qian, W. -J., Chin, M. H., Wang, H., Livesay, E. A., Monroe, M. E., Adkins, J. N., Jaitly, N., Anderson, D. J., Camp, D. G., Smith, D. J., and Smith, R. D. Tue . "Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry". United States. doi:10.1101/gr.5799207.
@article{osti_1152564,
title = {Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry},
author = {Petyuk, V. A. and Qian, W. -J. and Chin, M. H. and Wang, H. and Livesay, E. A. and Monroe, M. E. and Adkins, J. N. and Jaitly, N. and Anderson, D. J. and Camp, D. G. and Smith, D. J. and Smith, R. D.},
abstractNote = {},
doi = {10.1101/gr.5799207},
journal = {Genome Research},
number = 3,
volume = 17,
place = {United States},
year = {Tue Feb 06 00:00:00 EST 2007},
month = {Tue Feb 06 00:00:00 EST 2007}
}
  • Temporally and spatially resolved mapping of protein abundance patterns within the mammalian brain is of significant interest for understanding brain function and molecular etiologies of neurodegenerative diseases; however, such imaging efforts have been greatly challenged by complexity of the proteome, throughput and sensitivity of applied analytical methodologies, and accurate quantitation of protein abundances across the brain. Here, we describe a methodology for comprehensive spatial proteome mapping that addresses these challenges by employing voxelation integrated with automated microscale sample processing, high-throughput LC system coupled with high resolution Fourier transform ion cyclotron mass spectrometer and a “universal” stable isotope labeled reference samplemore » approach for robust quantitation. We applied this methodology as a proof-of-concept trial for the analysis of protein distribution within a single coronal slice of a C57BL/6J mouse brain. For relative quantitation of the protein abundances across the slice, an 18O-isotopically labeled reference sample, derived from a whole control coronal slice from another mouse, was spiked into each voxel sample and stable isotopic intensity ratios were used to obtain measures of relative protein abundances. In total, we generated maps of protein abundance patterns for 1,028 proteins. The significant agreement of the protein distributions with previously reported data supports the validity of this methodology, which opens new opportunities for studying the spatial brain proteome and its dynamics during the course of disease progression and other important biological and associated health aspects in a discovery-driven fashion.« less
  • Voxelation creates expression atlases by high-throughput analysis of spatially registered cubes or voxels harvested from the brain. The modality independence of voxelation allows a variety of bioanalytical techniques to be used to map abundance. Protein expression patterns in the brain can be obtained using liquid chromatography (LC) combined with mass spectrometry (MS). Here we describe the methodology of voxelation as it pertains particularly to LC-MS proteomic analysis: sample preparation, instrumental set up and analysis, peptide identification and protein relative abundance quantitation. We also briefly describe some of the advantages, limitations and insights into the brain that can be obtained usingmore » combined proteomic and transcriptomic maps« less
  • We report on the design and application of a high-efficiency multiple-capillary liquid chromatography (LC) system for high-throughput proteome analysis. The multiple-capillary LC system was operated at the pressure of 10,000 psi using commercial LC pumps to deliver the mobile phase and newly developed passive feedback valves to switch the mobile phase flow and introduce samples. The multiple-capillary LC system was composed of several serially connected dual-capillary column devices. The dual-capillary column approach was designed to eliminate the time delay for regeneration (or equilibrium) of the capillary column after its use under the mobile phase gradient condition (i.e. one capillary columnmore » was used in separation and the other was washed using mobile phase A). The serially connected dual-capillary columns and ESI sources were operated independently, and could be used for either''backup'' operation or with other mass spectrometer(s). This high-efficiency multiple-capillary LC system uses switching valves for all operations and is highly amenable to automation. The separations efficiency of dual-capillary column device, optimal capillary dimensions (column length and packed particle size), suitable mobile phases for electrospray, and the capillary re-generation were investigated. A high magnetic field (11.5 tesla) Fourier transform ion cyclotron resonance (FTICR) mass spectrometer was coupled on-line with this high-efficiency multiple-capillary LC system through an electrospray ionization source. The capillary LC provided a peak capacity of {approx}600, and the 2-D capillary LC-FTICR provided a combined resolving power of > 6 x 10 7 polypeptide isotopic distributions. For yeast cellular tryptic digests, > 100,000 polypeptides were typically detected, and {approx}1,000 proteins can be characterized in a single run.« less