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Protein abundance profiling of the Escherichia coli cytosol.

Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D.

BMC Genomics. 2008 Feb 27;9:102.PMID: 18304323 [PubMed - indexed for MEDLINE]Related articlesFree article

Global quantitative proteomic profiling through 18O-labeling in combination with MS/MS spectra analysis.

White CA, Oey N, Emili A.

J Proteome Res. 2009 Jul;8(7):3653-65.PMID: 19400582 [PubMed - indexed for MEDLINE]Related articles

Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled "universal" reference sample.

Qian WJ, Liu T, Petyuk VA, Gritsenko MA, Petritis BO, Polpitiya AD, Kaushal A, Xiao W, Finnerty CC, Jeschke MG, Jaitly N, Monroe ME, Moore RJ, Moldawer LL, Davis RW, Tompkins RG, Herndon DN, Camp DG, Smith RD; Inflammation and the Host Response to Injury Large Scale Collaborative Research Program.

J Proteome Res. 2009 Jan;8(1):290-9.PMID: 19053531 [PubMed - indexed for MEDLINE]Related articlesFree article

Targeted proteomics of low-level proteins in human plasma by LC/MSn: using human growth hormone as a model system.

Wu SL, Amato H, Biringer R, Choudhary G, Shieh P, Hancock WS.

J Proteome Res. 2002 Sep-Oct;1(5):459-65.PMID: 12645918 [PubMed - indexed for MEDLINE]Related articles

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.

Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD.

BMC Bioinformatics. 2008 Dec 16;9:542.PMID: 19087345 [PubMed - indexed for MEDLINE]Related articlesFree article

Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale.

Silva JC, Denny R, Dorschel C, Gorenstein MV, Li GZ, Richardson K, Wall D, Geromanos SJ.

Mol Cell Proteomics. 2006 Apr;5(4):589-607. Epub 2006 Jan 5.PMID: 16399765 [PubMed - indexed for MEDLINE]Related articlesFree article

An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics.

Zerck A, Nordhoff E, Resemann A, Mirgorodskaya E, Suckau D, Reinert K, Lehrach H, Gobom J.

J Proteome Res. 2009 Jul;8(7):3239-51.PMID: 19402737 [PubMed - indexed for MEDLINE]Related articles

Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: zero-inflated Poisson regression models to predict abundance of undetected proteins.

Nie L, Wu G, Brockman FJ, Zhang W.

Bioinformatics. 2006 Jul 1;22(13):1641-7. Epub 2006 May 4.PMID: 16675466 [PubMed - indexed for MEDLINE]Related articlesFree article

Influence of protein abundance on high-throughput protein-protein interaction detection.

Ivanic J, Yu X, Wallqvist A, Reifman J.

PLoS One. 2009 Jun 5;4(6):e5815.PMID: 19503833 [PubMed - indexed for MEDLINE]Related articlesFree article

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. PMID: 15543535 [PubMed - indexed for MEDLINE]Related articles

Sequential peptide affinity purification system for the systematic isolation and identification of protein complexes from Escherichia coli.

Babu M, Butland G, Pogoutse O, Li J, Greenblatt JF, Emili A.

Methods Mol Biol. 2009;564:373-400.PMID: 19544035 [PubMed - indexed for MEDLINE]Related articles

Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein.

Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M.

Mol Cell Proteomics. 2005 Sep;4(9):1265-72. Epub 2005 Jun 14.PMID: 15958392 [PubMed - indexed for MEDLINE]Related articlesFree article

Enhanced detection of low abundance human plasma proteins using a tandem IgY12-SuperMix immunoaffinity separation strategy.

Qian WJ, Kaleta DT, Petritis BO, Jiang H, Liu T, Zhang X, Mottaz HM, Varnum SM, Camp DG 2nd, Huang L, Fang X, Zhang WW, Smith RD.

Mol Cell Proteomics. 2008 Oct;7(10):1963-73. Epub 2008 Jul 15.PMID: 18632595 [PubMed - indexed for MEDLINE]Related articlesFree article

Design and analysis of quantitative differential proteomics investigations using LC-MS technology.

Bukhman YV, Dharsee M, Ewing R, Chu P, Topaloglou T, Le Bihan T, Goh T, Duewel H, Stewart II, Wisniewski JR, Ng NF.

J Bioinform Comput Biol. 2008 Feb;6(1):107-23.PMID: 18324749 [PubMed - indexed for MEDLINE]Related articles

Reversed-phase high-performance liquid chromatographic prefractionation of immunodepleted human serum proteins to enhance mass spectrometry identification of lower-abundant proteins.

Martosella J, Zolotarjova N, Liu H, Nicol G, Boyes BE.

J Proteome Res. 2005 Sep-Oct;4(5):1522-37.PMID: 16212403 [PubMed - indexed for MEDLINE]Related articles

Significance analysis of microarray for relative quantitation of LC/MS data in proteomics.

Roxas BA, Li Q.

BMC Bioinformatics. 2008 Apr 10;9:187.PMID: 18402702 [PubMed - indexed for MEDLINE]Related articlesFree article

Mixed-effects statistical model for comparative LC-MS proteomics studies.

Daly DS, Anderson KK, Panisko EA, Purvine SO, Fang R, Monroe ME, Baker SE.

J Proteome Res. 2008 Mar;7(3):1209-17. Epub 2008 Feb 6.PMID: 18251496 [PubMed - indexed for MEDLINE]Related articles

Shotgun proteome analysis of Rhodospirillum rubrum S1H: integrating data from gel-free and gel-based peptides fractionation methods.

Mastroleo F, Leroy B, Van Houdt R, s' Heeren C, Mergeay M, Hendrickx L, Wattiez R.

J Proteome Res. 2009 May;8(5):2530-41.PMID: 19243122 [PubMed - indexed for MEDLINE]Related articles

Proteomic profiling of Escherichia coli proteins under high cell density fed-batch cultivation with overexpression of phosphogluconolactonase.

Wang Y, Wu SL, Hancock WS, Trala R, Kessler M, Taylor AH, Patel PS, Aon JC.

Biotechnol Prog. 2005 Sep-Oct;21(5):1401-11.PMID: 16209543 [PubMed - indexed for MEDLINE]Related articles

Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data.

Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, MacCoss MJ.

Anal Chem. 2008 Feb 15;80(4):961-71. Epub 2008 Jan 12.PMID: 18189369 [PubMed - indexed for MEDLINE]Related articles