ITRAQ-based Shotgun Neuroproteomics

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2010 Jan 9

PMID 20058174

Citations 11

Authors

Tong Liu

Jun Hu

Hong Li

Affiliations

Soon will be listed here.

Abstract

Shotgun proteomics involves the analysis of peptides obtained by enzymatic digestions of proteins and subsequent identification via tandem mass spectrometry. This approach is an effective method for studying global protein expression in neuronal systems. The method described here is a quantitative shotgun neuroproteomics method using amine-specific isobaric tags for a relative and absolute quantitation (iTRAQ)-based workflow. We will provide the technical details for sample preparation, two-dimensional liquid chromatography, tandem mass spectrometry, database search, and statistical analysis to identify differentially expressed proteins. We will use a recent study on a rat model of multiple sclerosis, experimental autoimmune encephalomyelitis to illustrate the successful application of this method.

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References

Grant J, Hu J, Liu T, Jain M, Elkabes S, Li H . Post-translational modifications in the rat lumbar spinal cord in experimental autoimmune encephalomyelitis. J Proteome Res. 2007; 6(7):2786-91. PMC: 2435290. DOI: 10.1021/pr070013c. View

Lund T, Anderson L, McCullar V, Higgins L, Yun G, Grzywacz B . iTRAQ is a useful method to screen for membrane-bound proteins differentially expressed in human natural killer cell types. J Proteome Res. 2007; 6(2):644-53. DOI: 10.1021/pr0603912. View

Wu C, MacCoss M . Shotgun proteomics: tools for the analysis of complex biological systems. Curr Opin Mol Ther. 2002; 4(3):242-50. View

Zhang B, VerBerkmoes N, Langston M, Uberbacher E, Hettich R, Samatova N . Detecting differential and correlated protein expression in label-free shotgun proteomics. J Proteome Res. 2006; 5(11):2909-18. DOI: 10.1021/pr0600273. View

Liu T, Donahue K, Hu J, Kurnellas M, Grant J, Li H . Identification of differentially expressed proteins in experimental autoimmune encephalomyelitis (EAE) by proteomic analysis of the spinal cord. J Proteome Res. 2007; 6(7):2565-75. PMC: 2430926. DOI: 10.1021/pr070012k. View

Xia Q, Wang T, Park Y, Lamont R, Hackett M . Differential quantitative proteomics of Porphyromonas gingivalis by linear ion trap mass spectrometry: non-label methods comparison, q-values and LOWESS curve fitting. Int J Mass Spectrom. 2009; 259(1-3):105-116. PMC: 2662607. DOI: 10.1016/j.ijms.2006.08.004. View

Hu J, Qian J, Borisov O, Pan S, Li Y, Liu T . Optimized proteomic analysis of a mouse model of cerebellar dysfunction using amine-specific isobaric tags. Proteomics. 2006; 6(15):4321-34. PMC: 2553677. DOI: 10.1002/pmic.200600026. View

Coombes K, Tsavachidis S, Morris J, Baggerly K, Hung M, Kuerer H . Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform. Proteomics. 2005; 5(16):4107-17. DOI: 10.1002/pmic.200401261. View

Peng J, Elias J, Thoreen C, Licklider L, Gygi S . Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res. 2003; 2(1):43-50. DOI: 10.1021/pr025556v. View

10.

Shiio Y, Aebersold R . Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nat Protoc. 2007; 1(1):139-45. DOI: 10.1038/nprot.2006.22. View

11.

McDonald W, Yates 3rd J . Shotgun proteomics and biomarker discovery. Dis Markers. 2002; 18(2):99-105. PMC: 3851423. DOI: 10.1155/2002/505397. View

12.

Liu T, DMello V, Deng L, Hu J, Ricardo M, Pan S . A multiplexed proteomics approach to differentiate neurite outgrowth patterns. J Neurosci Methods. 2006; 158(1):22-9. PMC: 2423279. DOI: 10.1016/j.jneumeth.2006.05.010. View

13.

Mann M . Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol. 2006; 7(12):952-8. DOI: 10.1038/nrm2067. View

14.

Shadforth I, Dunkley T, Lilley K, Bessant C . i-Tracker: for quantitative proteomics using iTRAQ. BMC Genomics. 2005; 6:145. PMC: 1276793. DOI: 10.1186/1471-2164-6-145. View

15.

Wu W, Wang G, Yu M, Knepper M, Shen R . Identification and quantification of basic and acidic proteins using solution-based two-dimensional protein fractionation and label-free or 18O-labeling mass spectrometry. J Proteome Res. 2007; 6(7):2447-59. DOI: 10.1021/pr060621c. View

16.

Wiese S, Reidegeld K, Meyer H, Warscheid B . Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics. 2006; 7(3):340-50. DOI: 10.1002/pmic.200600422. View