Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus. Abraham, P., Giannone, J, R., Adams, M, R., Kalluri, U., Tuskan, A, G., Hettich, & L, R. Mol. Cell. Proteomics, 12(1):106–119, 14 pp., 2013. doi abstract bibtex High-performance mass spectrometry (MS)-based proteomics enabled the construction of a detailed proteome atlas for Populus, a woody perennial plant model organism. Optimization of exptl. procedures and implementation of current state-of-the-art instrumentation afforded the most detailed look into the predicted proteome space of Populus, offering varying proteome perspectives: (1) network-wide, (2) pathway-specific, and (3) protein-level viewpoints. Together, enhanced protein retrieval through a detergent-based lysis approach and maximized peptide sampling via the dual-pressure linear ion trap mass spectrometer (LTQ Velos), have resulted in the identification of 63,056 tryptic peptides. The technol. advancements, specifically spectral-acquisition and sequencing speed, afforded the deepest look into the Populus proteome, with peptide abundances spanning 6 orders of magnitude and mapping to ∼25% of the predicted proteome space. In total, tryptic peptides mapped to 11,689 protein assignments across four organ-types: mature (fully expanded, leaf plastichronic index (LPI) 10-12) leaf, young (juvenile, LPI 4-6) leaf, root, and stem. To resolve protein ambiguity, identified proteins were grouped by sequence similarity (≥90%), thereby reducing the protein assignments into 7538 protein groups. In addn., this large-scale data set features the first systems wide survey of protein expression across different Populus organs. As a demonstration of the precision and comprehensiveness of the semiquant. anal., we were able to contrast two stages of leaf development, mature vs. young leaf. Statistical comparison through ANOVA anal. revealed 1432 protein groups that exhibited statistically significant (p \textless 0.01) differences in protein abundance. Exptl. validation of the metabolic circuitry expected in mature leaf (characterized by photosynthesis and carbon fixation) compared with young leaf (characterized by rapid growth and moderate photosynthetic activities) strongly testifies to the credibility of the approach. Instead of quant. comparing a few proteins, a systems view of all the changes assocd. with a given cellular perturbation could be made. [on SciFinder(R)]
@article{ abraham_putting_2013,
title = {Putting the pieces together: high-performance {LC-MS/MS} provides network-, pathway-, and protein-level perspectives in Populus.},
volume = {12},
issn = {1535-9484},
doi = {10.1074/mcp.M112.022996},
abstract = {High-performance mass spectrometry ({MS)-based} proteomics enabled the construction of a detailed proteome atlas for Populus, a woody perennial plant model organism. Optimization of exptl. procedures and implementation of current state-of-the-art instrumentation afforded the most detailed look into the predicted proteome space of Populus, offering varying proteome perspectives: (1) network-wide, (2) pathway-specific, and (3) protein-level viewpoints. Together, enhanced protein retrieval through a detergent-based lysis approach and maximized peptide sampling via the dual-pressure linear ion trap mass spectrometer ({LTQ} Velos), have resulted in the identification of 63,056 tryptic peptides. The technol. advancements, specifically spectral-acquisition and sequencing speed, afforded the deepest look into the Populus proteome, with peptide abundances spanning 6 orders of magnitude and mapping to ∼25% of the predicted proteome space. In total, tryptic peptides mapped to 11,689 protein assignments across four organ-types: mature (fully expanded, leaf plastichronic index ({LPI)} 10-12) leaf, young (juvenile, {LPI} 4-6) leaf, root, and stem. To resolve protein ambiguity, identified proteins were grouped by sequence similarity (≥90%), thereby reducing the protein assignments into 7538 protein groups. In addn., this large-scale data set features the first systems wide survey of protein expression across different Populus organs. As a demonstration of the precision and comprehensiveness of the semiquant. anal., we were able to contrast two stages of leaf development, mature vs. young leaf. Statistical comparison through {ANOVA} anal. revealed 1432 protein groups that exhibited statistically significant (p {\textless} 0.01) differences in protein abundance. Exptl. validation of the metabolic circuitry expected in mature leaf (characterized by photosynthesis and carbon fixation) compared with young leaf (characterized by rapid growth and moderate photosynthetic activities) strongly testifies to the credibility of the approach. Instead of quant. comparing a few proteins, a systems view of all the changes assocd. with a given cellular perturbation could be made. [on {SciFinder(R)]}},
number = {1},
journal = {Mol. Cell. Proteomics},
author = {Abraham, Paul and Giannone, Richard J and Adams, Rachel M and Kalluri, Udaya and Tuskan, Gerald A and Hettich, Robert L},
year = {2013},
keywords = {Populus, chromatog, liq, mass, network, pathway, protein, spectrometry},
pages = {106–119, 14 pp.}
}
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