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1:

Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system.

de Godoy LM, Olsen JV, de Souza GA, Li G, Mortensen P, Mann M.

Genome Biol. 2006;7(6):R50.

PMID: 16784548 [PubMed - indexed for MEDLINE]

2:

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast.

de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Fröhlich F, Walther TC, Mann M.

Nature. 2008 Oct 30;455(7217):1251-4. Epub 2008 Sep 28.

PMID: 18820680 [PubMed - indexed for MEDLINE]

3:

Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry.

Gruhler A, Schulze WX, Matthiesen R, Mann M, Jensen ON.

Mol Cell Proteomics. 2005 Nov;4(11):1697-709. Epub 2005 Aug 8.

PMID: 16088002 [PubMed - indexed for MEDLINE]

5:

Evaluation of shotgun sequencing for proteomic analysis of human plasma using HPLC coupled with either ion trap or Fourier transform mass spectrometry.

Wu SL, Choudhary G, Ramström M, Bergquist J, Hancock WS.

J Proteome Res. 2003 Jul-Aug;2(4):383-93.

PMID: 12938928 [PubMed - indexed for MEDLINE]

6:

Depth of proteome issues: a yeast isotope-coded affinity tag reagent study.

Parker KC, Patterson D, Williamson B, Marchese J, Graber A, He F, Jacobson A, Juhasz P, Martin S.

Mol Cell Proteomics. 2004 Jul;3(7):625-59. Epub 2004 Mar 28.

PMID: 15047794 [PubMed - indexed for MEDLINE]

7:

Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.

Gruhler A, Olsen JV, Mohammed S, Mortensen P, Faergeman NJ, Mann M, Jensen ON.

Mol Cell Proteomics. 2005 Mar;4(3):310-27. Epub 2005 Jan 22.

PMID: 15665377 [PubMed - indexed for MEDLINE]

8:

Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer.

Venable JD, Wohlschlegel J, McClatchy DB, Park SK, Yates JR 3rd.

Anal Chem. 2007 Apr 15;79(8):3056-64. Epub 2007 Mar 17.

PMID: 17367114 [PubMed - indexed for MEDLINE]

9:

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.

PMID: 17533220 [PubMed - indexed for MEDLINE]

10:

Making broad proteome protein measurements in 1-5 min using high-speed RPLC separations and high-accuracy mass measurements.

Shen Y, Strittmatter EF, Zhang R, Metz TO, Moore RJ, Li F, Udseth HR, Smith RD, Unger KK, Kumar D, Lubda D.

Anal Chem. 2005 Dec 1;77(23):7763-73.

PMID: 16316187 [PubMed - indexed for MEDLINE]

11:

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.

PMID: 18045802 [PubMed - indexed for MEDLINE]

12:

High-throughput analysis of rat liver plasma membrane proteome by a nonelectrophoretic in-gel tryptic digestion coupled with mass spectrometry identification.

Cao R, He Q, Zhou J, He Q, Liu Z, Wang X, Chen P, Xie J, Liang S.

J Proteome Res. 2008 Feb;7(2):535-45. Epub 2008 Jan 1.

PMID: 18166008 [PubMed - indexed for MEDLINE]

13:

Double standards in quantitative proteomics: direct comparative assessment of difference in gel electrophoresis and metabolic stable isotope labeling.

Kolkman A, Dirksen EH, Slijper M, Heck AJ.

Mol Cell Proteomics. 2005 Mar;4(3):255-66. Epub 2005 Jan 4.

PMID: 15632418 [PubMed - indexed for MEDLINE]

14:

The use of accurate mass tags for high-throughput microbial proteomics.

Smith RD, Anderson GA, Lipton MS, Masselon C, Pasa-Tolic L, Shen Y, Udseth HR.

OMICS. 2002;6(1):61-90. Review.

PMID: 11881835 [PubMed - indexed for MEDLINE]

15:

Proteome analysis by mass spectrometry.

Ferguson PL, Smith RD.

Annu Rev Biophys Biomol Struct. 2003;32:399-424. Epub 2003 Jan 28. Review.

PMID: 12574065 [PubMed - indexed for MEDLINE]

16:

Pox proteomics: mass spectrometry analysis and identification of Vaccinia virion proteins.

Yoder JD, Chen TS, Gagnier CR, Vemulapalli S, Maier CS, Hruby DE.

Virol J. 2006 Mar 1;3:10.

PMID: 16509968 [PubMed - indexed for MEDLINE]

17:

Development and application of proteomics technologies in Saccharomyces cerevisiae.

Kolkman A, Slijper M, Heck AJ.

Trends Biotechnol. 2005 Dec;23(12):598-604. Epub 2005 Oct 3. Review.

PMID: 16202464 [PubMed - indexed for MEDLINE]

18:

Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry.

Smolka M, Zhou H, Aebersold R.

Mol Cell Proteomics. 2002 Jan;1(1):19-29.

PMID: 12096137 [PubMed - indexed for MEDLINE]

19:

Expression clustering reveals detailed co-expression patterns of functionally related proteins during B cell differentiation: a proteomic study using a combination of one-dimensional gel electrophoresis, LC-MS/MS, and stable isotope labeling by amino acids in cell culture (SILAC).

Romijn EP, Christis C, Wieffer M, Gouw JW, Fullaondo A, van der Sluijs P, Braakman I, Heck AJ.

Mol Cell Proteomics. 2005 Sep;4(9):1297-310. Epub 2005 Jun 15.

PMID: 15961381 [PubMed - indexed for MEDLINE]

20:

Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response.

Li J, Steen H, Gygi SP.

Mol Cell Proteomics. 2003 Nov;2(11):1198-204. Epub 2003 Sep 23.

PMID: 14506205 [PubMed - indexed for MEDLINE]

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