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High resolution quantitative proteomics of HeLa cells protein species using stable isotope labeling with amino acids in cell culture(SILAC), two-dimensional gel electrophoresis(2DE) and nano-liquid chromatograpohy coupled to an LTQ-OrbitrapMass spectrometer.

Thiede B, Koehler CJ, Strozynski M, Treumann A, Stein R, Zimny-Arndt U, Schmid M, Jungblut PR.

Mol Cell Proteomics. 2013 Feb;12(2):529-38. doi: 10.1074/mcp.M112.019372. Epub 2012 Oct 1. Erratum in: Mol Cell Proteomics. 2014 Jul;13(7):1900.


Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins.

Graumann J, Hubner NC, Kim JB, Ko K, Moser M, Kumar C, Cox J, Schöler H, Mann M.

Mol Cell Proteomics. 2008 Apr;7(4):672-83. Epub 2007 Nov 28.


Systematic analysis of protein pools, isoforms, and modifications affecting turnover and subcellular localization.

Ahmad Y, Boisvert FM, Lundberg E, Uhlen M, Lamond AI.

Mol Cell Proteomics. 2012 Mar;11(3):M111.013680. doi: 10.1074/mcp.M111.013680. Epub 2011 Oct 16.


Comparing SILAC- and stable isotope dimethyl-labeling approaches for quantitative proteomics.

Lau HT, Suh HW, Golkowski M, Ong SE.

J Proteome Res. 2014 Sep 5;13(9):4164-74. doi: 10.1021/pr500630a. Epub 2014 Aug 12.


Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer.

Collier TS, Hawkridge AM, Georgianna DR, Payne GA, Muddiman DC.

Anal Chem. 2008 Jul 1;80(13):4994-5001. doi: 10.1021/ac800254z. Epub 2008 May 31.


A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics.

Cox J, Matic I, Hilger M, Nagaraj N, Selbach M, Olsen JV, Mann M.

Nat Protoc. 2009;4(5):698-705. doi: 10.1038/nprot.2009.36.


Current two-dimensional electrophoresis technology for proteomics.

Görg A, Weiss W, Dunn MJ.

Proteomics. 2004 Dec;4(12):3665-85. Review. Erratum in: Proteomics. 2005 Feb;5(3):826-7.


Assessing factors for reliable quantitative proteomics based on two-dimensional gel electrophoresis.

Fiévet J, Dillmann C, Lagniel G, Davanture M, Negroni L, Labarre J, de Vienne D.

Proteomics. 2004 Jul;4(7):1939-49.


In-Gel Stable-Isotope Labeling (ISIL): a strategy for mass spectrometry-based relative quantification.

Asara JM, Zhang X, Zheng B, Christofk HH, Wu N, Cantley LC.

J Proteome Res. 2006 Jan;5(1):155-63.


Quantitative, time-resolved proteomic analysis by combining bioorthogonal noncanonical amino acid tagging and pulsed stable isotope labeling by amino acids in cell culture.

Bagert JD, Xie YJ, Sweredoski MJ, Qi Y, Hess S, Schuman EM, Tirrell DA.

Mol Cell Proteomics. 2014 May;13(5):1352-8. doi: 10.1074/mcp.M113.031914. Epub 2014 Feb 21.


Nano-high-performance liquid chromatography in combination with nano-electrospray ionization Fourier transform ion-cyclotron resonance mass spectrometry for proteome analysis.

Ihling C, Berger K, Höfliger MM, Führer D, Beck-Sickinger AG, Sinz A.

Rapid Commun Mass Spectrom. 2003;17(12):1240-6.


Performance of isobaric and isotopic labeling in quantitative plant proteomics.

Nogueira FC, Palmisano G, Schwämmle V, Campos FA, Larsen MR, Domont GB, Roepstorff P.

J Proteome Res. 2012 May 4;11(5):3046-52. doi: 10.1021/pr300192f. Epub 2012 Apr 9.


Stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomics study of a thyroid hormone-regulated secretome in human hepatoma cells.

Chen CY, Chi LM, Chi HC, Tsai MM, Tsai CY, Tseng YH, Lin YH, Chen WJ, Huang YH, Lin KH.

Mol Cell Proteomics. 2012 Apr;11(4):M111.011270. doi: 10.1074/mcp.M111.011270. Epub 2011 Dec 14.


Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endothelial cells.

Bouyssié D, Gonzalez de Peredo A, Mouton E, Albigot R, Roussel L, Ortega N, Cayrol C, Burlet-Schiltz O, Girard JP, Monsarrat B.

Mol Cell Proteomics. 2007 Sep;6(9):1621-37. Epub 2007 May 28.


Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology.

Schmidt F, Donahoe S, Hagens K, Mattow J, Schaible UE, Kaufmann SH, Aebersold R, Jungblut PR.

Mol Cell Proteomics. 2004 Jan;3(1):24-42. Epub 2003 Oct 13.


How many proteins can be identified in a 2-DE gel spot within an analysis of a complex human cancer tissue proteome?

Zhan X, Yang H, Peng F, Li J, Mu Y, Long Y, Cheng T, Huang Y, Li Z, Lu M, Li N, Li M, Liu J, Jungblut PR.

Electrophoresis. 2017 Dec 4. doi: 10.1002/elps.201700330. [Epub ahead of print]


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