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proteomics 20091218


22899

Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis.
Griffin NM, Yu J, Long F, Oh P, Shore S, Li Y, Koziol JA, Schnitzer JE.
Nat Biotechnol. . [Epub ahead of print]PMID: 20010810
プロテオミクスで定量化


Comparative analysis to guide quality improvements in proteomics.
Mann M.
Nat Methods. 2009 Oct;6(10):717-19. No abstract available. PMID: 19953682

Quantitative proteomic analysis of purified yeast kinetochores identifies a PP1 regulatory subunit
Akiyoshi B, Nelson CR, Ranish JA, Biggins S.
Genes Dev. 2009 Nov 30. [Epub ahead of print]PMID: 19948764
キネトコアのタンパク質複合体を精製してプロテオミクス


Recurated protein interaction datasets.
Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H.
Nat Methods. 2009 Dec;6(12):860-861. No abstract available.
PMID: 19935838
再展示されるデータセット

Regulation of the osteoblast-specific transcription factor Osterix by NO66, a Jumonji family histone demethylase.
Sinha KM, Yasuda H, Coombes MM, Dent SY, de Crombrugghe B.
EMBO J. 2009 Nov 19.
PMID: 19927124
骨芽細胞特異的転写因子はヒストンの脱メチル化活性あり


The Proteomics Identifications database: 2010 update.
Vizcaino JA, Cote R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L.
Nucleic Acids Res. 2009 Nov 11.
PMID: 19906717
データベースの更新


Spin filter-based sample preparation for shotgun proteomics.
Liebler DC, Ham AJ.
Nat Methods. 2009 Nov;6(11):785; author reply 785-6. No abstract available
PMID: 19876013
スピンカラムでサンプル調製

Sequestosome-1/p62 is the key intracellular target of innate defense regulator peptide.
Yu HB, Kielczewska A, Rozek A, Takenaka S, Li Y, Thorson L, Hancock RE, Guarna MM, North JR, Foster LJ, Donini O, Finlay BB.
J Biol Chem. 2009 Oct 22.
PMID: 19850933
調節因子ペプチド


Quantitative proteomic analysis of single pancreatic islets.
Waanders LF, Chwalek K, Monetti M, Kumar C, Lammert E, Mann M.
Proc Natl Acad Sci U S A. 2009 Oct 21.
PMID: 19846766
一つの膵島の定量プロテオミクス

Visual proteomics of the human pathogen Leptospira interrogans.
Beck M, Malmstrom JA, Lange V, Schmidt A, Deutsch EW, Aebersold R.
Nat Methods. 2009 Oct 18.
PMID: 19838170
プロテオミクス解析結果の可視化


Snapshots of kinase activities.
Munoz J, Heck AJ.
Nat Biotechnol. 2009 Oct;27(10):912-3. No abstract available.
PMID: 19816446
リン酸化の解析、コメント

The kinase TNIK is an essential activator of Wnt target genes.
Mahmoudi T, Li VS, Ng SS, Taouatas N, Vries RG, Mohammed S, Heck AJ, Clevers H.
EMBO J. 2009 Oct 8.
PMID: 19816403
リン酸化の解析

New citizens for the life sciences.
Bonetta L.
Cell. 2009 Sep 18;138(6):1043-5.
PMID: 19766554
リポート


Protein quantification across hundreds of experimental conditions.
Khan Z, Bloom JS, Garcia BA, Singh M, Kruglyak L.
Proc Natl Acad Sci U S A. 2009 Aug 26.
PMID: 19717460
実験条件を変えた時の、タンパク質発現量を計算

Applying mass spectrometry-based proteomics to genetics, genomics and network biology.
Gstaiger M, Aebersold R.
Nat Rev Genet. 2009 Sep;10(9):617-27.
PMID: 19687803
レビュー


Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions.
Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther T, Olsen JV, Mann M
.Science. 2009 Jul 16.
PMID: 19608861
タンパク質中のリジンのアセチル化の重要性

PRIDE Converter: making proteomics data-sharing easy.
Barsnes H, Vizcaino JA, Eidhammer I, Martens L.
Nat Biotechnol. 2009 Jul;27(7):598-9.
PMID: 19587657


Algorithms and databases.
Martens L, Apweiler R.
Methods Mol Biol. 2009;564:245-59.
レビュー この号にプロテオミクス特集あり


Unbiased RNA-protein interaction screen by quantitative proteomics.
Butter F, Scheibe M, Morl M, Mann M.
Proc Natl Acad Sci U S A. 2009 Jun 16.
PMID: 19541640
RNAに結合するたんぱく質をプロテオミクス


Perspective: Proteomic approach to detect biomarkers of human growth hormone.
Ding J, List EO, Okada S, Kopchick JJ.
Growth Horm IGF Res. 2009 Jun 3.
PMID: 19501004
血中の成長ホルモンのプロテオミクス


Analysis of insoluble proteins.
Trimpin S, Brizzard B.
Biotechniques. 2009 Apr;46(5):321-6.
PMID: 19480627
不溶化たんぱく質の解析方法、レビュー

Quantitative proteomics reveals a dynamic interactome and phase-specific phosphorylation in the Neurospora circadian clock.
Baker CL, Kettenbach AN, Loros JJ, Gerber SA, Dunlap JC.
Mol Cell. 2009 May 15;34(3):354-63.
PMID: 19450533
日周リズムに関与するタンパク質のリン酸化を解析


A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.
Bell AW et al
Nat Methods. 2009 May 17
PMID: 19448641
測定エラーよりも解析エラーに注意


Fbxo45 forms a novel ubiquitin ligase complex and is required for neuronal development.
Saiga T, Fukuda T, Matsumoto M, Tada H, Okano HJ, Okano H, Nakayama KI.
Mol Cell Biol. 2009 Apr 27.
PMID: 19398581
ユビキチン化と神経の発生

Universal sample preparation method for proteome analysis.
Wi?niewski JR, Zougman A, Nagaraj N, Mann M.
Nat Methods. 2009 Apr 19.
PMID: 19377485
サンプルの調製方法


Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation.
Xu P, Duong DM, Seyfried NT, Cheng D, Xie Y, Robert J, Rush J, Hochstrasser M, Finley D, Peng J.
Cell. 2009 Apr 3;137(1):133-45.
PMID: 19345192
ユビキチン化とタンパク質分解の流れ


Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics.
Boersema PJ, Raijmakers R, Lemeer S, Mohammed S, Heck AJ.
Nat Protoc. 2009;4(4):484-94.
PMID: 19300442
安定同位体でラベルして定量プロテオミクス


Identifying the proteins to which small-molecule probes and drugs bind in cells.
Ong SE, Schenone M, Margolin AA, Li X, Do K, Doud MK, Mani DR, Kuai L, Wang X, Wood JL, Tolliday NJ, Koehler AN, Marcaurelle LA, Golub TR, Gould RJ, Schreiber SL, Carr SA.
Proc Natl Acad Sci U S A. 2009 Mar 2.
PMID: 19255428
細胞内で薬剤に結合するたんぱく質の同定

From the Cover: Cytokinins modulate auxin-induced organogenesis in plants via regulation of the auxin efflux.
Pernisova M, Klima P, Horak J, Valkova M, Malbeck J, Soucek P, Reichman P, Hoyerova K, Dubova J, Friml J, Za Zimalova E, Hejatko J.
Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3609-14. Epub 2009 Feb 11.
PMID: 19211794

Cytokinins modulate auxin-induced organogenesis in plants via regulation of the auxin efflux.
Pernisova M, Klima P, Horak J, Valkova M, Malbeck J, Soucek P, Reichman P, Hoyerova K, Dubova J, Friml J, Zazimalova E, Hejatko J.
Proc Natl Acad Sci U S A. 2009 Feb 11.
PMID: 19211794
植物ホルモンの影響を解析

Purification of proteins associated with specific genomic Loci.
Dejardin J, Kingston RE.
Cell. 2009 Jan 9;136(1):175-86.
PMID: 19135898
ゲノムの特定の領域に結合する因子を解析

Functional Proteomics of Arabidopsis thaliana Guard Cells Uncovers New Stomatal Signaling Pathways.
Zhao Z, Zhang W, Stanley BA, Assmann SM.
Plant Cell. 2008 Dec 29.
PMID: 19114538


Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics.
Maruyama Y, Wakamatsu A, Kawamura Y, Kimura K, Yamamoto J, Nishikawa T, Kisu Y, Sugano S, Goshima N, Isogai T, Nomura N.
Nucleic Acids Res. 2009 Jan;37(Database issue):D762-6.
PMID: 19073703
実験結果を取り入れたデーターベース

Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation.
Kang R, Wan J, Arstikaitis P, Takahashi H, Huang K, Bailey AO, Thompson JX, Roth AF, Drisdel RC, Mastro R, Green WN, Yates JR 3rd, Davis NG, El-Husseini A.
Nature. 2008 Dec 18;456(7224):904-9.
PMID: 19092927

Combining RNA interference mutants and comparative proteomics to identify protein components and dependencies in a eukaryotic flagellum.
Portman N, Lacomble S, Thomas B, McKean PG, Gull K.
J Biol Chem. 2008 Dec 11. [Epub ahead of print]
PMID: 19074134