Automated protein turnover calculations from 15n partial metabolic labeling lc/ms shotgun proteomics data

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Lyon, David ^a   Castillejo, Maria Angeles ^a   Staudinger, Christiana ^a   Weckwerth, Wolfram ^a   Wienkoop, Stefanie ^a   Egelhofer, Volker ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

NITROGEN 15; PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; AUTOMATED PROTEIN TURNOVER CALCULATION; AUTOMATION; BARREL MEDIC; CALCULATION; COMPUTER PROGRAM; CONTROLLED STUDY; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PROTEIN DEGRADATION; PROTEIN METABOLISM; PROTEIN SYNTHESIS; PROTEOMICS; RADIOLOGICAL PARAMETERS; RELATIVE ISOTOPIC ABUNDANCE; ALGORITHM; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR GENETICS; PROCEDURES;

ALGORITHMS; AMINO ACID SEQUENCE; AUTOMATION; CHROMATOGRAPHY, LIQUID; HUMANS; ISOTOPE LABELING; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEOLYSIS; PROTEOMICS;

EID: 84899680032     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0094692     Document Type: Article

References (25)

1. Pratt JM, Petty J, Riba-Garcia I, Robertson DHL, Gaskell SJ, et al. (2002) Dynamics of Protein Turnover, a Missing Dimension in Proteomics. Mol Cell Proteomics 1: 579-591. doi:10.1074/mcp.M200046-MCP200.
2. Hoehenwarter W, Wienkoop S (2010) Spectral counting robust on high mass accuracy mass spectrometers. Rapid Commun Mass Spectrom: 3609-3614. doi:10.1002/rcm.
3. Li L, Nelson CJ, Solheim C, Whelan J, Millar AH (2012) Determining Degradation and Synthe-sis Rates of Arabidopsis Proteins Using the Kinetics of Progressive 15N Labeling of Two-dimensional Gel-separated Protein Spots. Mol Cell Proteomics 11: M111.010025. doi:10.1074/mcp.M111.010025.
4. Belle A, Tanay A, Bitincka L, Shamir R, Shea EKO, et al. (2006) Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci U S A 103: 13004-13009. doi:10.1073/pnas.0605420103.
5. Yen H-CS, Xu Q, Chou DM, Zhao Z, Elledge SJ (2008) Global protein stability profiling in mammalian cells. Science 322: 918-923. doi:10.1126/science. 1160489.
6. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, et al. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63. doi:10.1038/nature07228.
7. Maier T, Schmidt A, Güell M, Kühner S, Gavin A-C, et al. (2011) Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol 7: 511. doi:10.1038/msb.2011.38.
8. Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, et al. (2013) Corrigendum: Global quantification of mammalian gene expression control. Nature 495: 126-127. doi:10.1038/nature11848.
9. Martin SF, Munagapati VS, Salvo-Chirnside E, Kerr LE, Le Bihan T (2012) Proteome turnover in the green alga Ostreococcus tauri by time course 15N metabolic labeling mass spectrometry. J Proteome Res 11: 476-486. doi:10.1021/pr2009302.
10. Price JC, Guan S, Burlingame A, Prusiner SB, Ghaemmaghami S (2010) Analysis of proteome dynamics in the mouse brain. PNAS 2010. doi:10.1073/ pnas.1006551107/2/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas. 1006551107.
11. Zhang Y, Reckow S, Webhofer C, Boehme M, Gormanns P, et al. (2011) Proteome Scale Turno-ver Analysis in Live Animals Using Stable Isotope Metabolic Labeling. Anal Chem: 1665-1672. doi:10.1021/ac102755n.
12. Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, et al. (2013) Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell 154: 971-982. doi:10.1016/j.cell.2013.07.037.
13. Schwanhäusser B, Busse D, Li N (2011) Global quantification of mammalian gene expression control. Nature: 337-342. doi:10.1038/nature10098.
14. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26: 1367-1372. doi:10.1038/nbt.1511.
15. Savas JN, Toyama BH, Xu T, Yates JR, Hetzer MW (2012) Extremely longlived nuclear pore proteins in the rat brain. Science 335: 942. doi:10.1126/ science.1217421.
16. Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, et al. (2013) Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell 154: 971-982. doi:10.1016/j.cell.2013.07.037.
17. Park SK, Venable JD, Xu T, Iii JRY (2008) A quantitative analysis software tool for mass spec-trometry-based proteomics. 5. doi:10.1038/NMETH. 1195.
18. Zhang Y, Reckow S, Webhofer C, Boehme M, Gormanns P, et al. (2011) Proteome Scale Turno-ver Analysis in Live Animals Using Stable Isotope Metabolic Labeling. Anal Chem: 1665-1672.
19. Castillejo MA, Staudinger C, Egelhofer V, Wienkoop S (2014) Medicago truncatula proteomics for systems biology: novel rapid shotgun LC-MS approach for relative quantification based on Full-Scan Selective Peptide Extraction (Selpex). Plant Proteomics Methods Mol Biol 1072: 303-313.
20. Gustavsson N, Greber B, Kreitler T, Himmelbauer H, Lehrach H, et al. (2005) A proteomic method for the analysis of changes in protein concentrations in response to systemic perturba-tions using metabolic incorporation of stable isotopes and mass spectrometry. Proteomics 5: 3563-3570. doi:10.1002/ pmic.200401193.
21. Ong S, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, et al. (2002) Stable Isotope Label-ing by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics : 376-386. doi:10.1074/ mcp.M200025-MCP200.
22. Hebeler R, Oeljeklaus S, Reidegeld KA, Eisenacher M, Stephan C, et al. (2008) Study of early leaf senescence in Arabidopsis thaliana by quantitative proteomics using reciprocal 14N/15N la-beling and difference gel electrophoresis. Mol Cell Proteomics 7: 108-120. doi:10.1074/mcp.M700340-MCP200.
23. Li L, Nelson CJ, Solheim C, Whelan J, Millar AH (2012) Determining degradation and synthesis rates of arabidopsis proteins using the kinetics of progressive 15N labeling of two-dimensional gel-separated protein spots. Mol Cell Proteomics 11: M111.010025. doi:10.1074/mcp.M111.010025.
24. Singh U, Deb D, Singh A, Grover A (2011) Glycine-rich RNA binding protein of Oryza sativa inhibits growth of M15 E. coli cells. BMC Res Notes 4: 18. doi:10.1186/1756-0500-4-18.
25. Singh DK, McNellis TW (2011) Fibrillin protein function: the tip of the iceberg? Trends Plant Sci 16: 432-441. doi:10.1016/j.tplants.2011.03.014.