期刊论文详细信息
BMC Research Notes
The Trip Adviser guide to the protein science world: a proposal to improve the awareness concerning the quality of recombinant proteins
Ario de Marco1  Tsafi Danieli2  Mario Lebendiker2 
[1] Department of Biomedical Sciences and Engineering, University of Nova Gorica, Glavni Trg 9, SI-5261 Vipava, Slovenia;Protein Expression and Purification Facilities, Wolfson Centre for Applied Structural Biology, Givat-Ram Campus - The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
关键词: Protein quality;    Data reproducibility;    Data annotation;   
Others  :  1129999
DOI  :  10.1186/1756-0500-7-585
 received in 2014-03-26, accepted in 2014-07-31,  发布年份 2014
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【 摘 要 】

In many research articles, where protein purification is required for various assays, (protein-protein interactions, activity assays, etc.), we always have access to the final results, but seldom have access to the raw data required for an accurate evaluation of the protein quality. This data is extremely important on one hand to critically evaluate the quality of the proteins used in the described research and, on the other hand, to allow other laboratories to safely use the described procedure in a reproducible manner. We herby propose to include a standardized methodology that can easily be incorporated in research papers. Moreover, this methodology can be utilized as a “quality control” ladder, where the more information given, will lead to a higher ranking of the article. This “quality control” stamp will allow researchers retrieving relevant and useful materials and methods in the field of protein research.

【 授权许可】

   
2014 Lebendiker et al.; licensee BioMed Central Ltd.

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【 参考文献 】
  • [1]Bauerlein M, Gad-el-Hak M, Grody W, McKelvey B, Trimble SV: We must stop the avalanche of low-quality research. Chron Higher Educ 2010., 57June 13. http://chronicle.com/article/We-Must-Stop-the-Avalanche-of/65890/ webcite
  • [2]Chafen JJ, Newberry SJ, Riedl MA, Bravata DM, Maglione M, Suttorp MJ, Sundaram V, Paige NM, Towfigh A, Hulley BJ, Shekelle PG: Diagnosing and managing common food allergies: a systematic review. JAMA 2010, 303:1848-1856.
  • [3]de Marco A: Reagent validation: an underestimated issue in lab praxis. J Mol Recognit 2011, 24:136.
  • [4]Rich RL, Myszka DG: Grading the commercial optical biosensor literature – Class of 2008: “The Mighty Binders”. J Mol Recognit 2010, 23:1-64.
  • [5]Rich RL, Myszka DG: Survey of the 2009 commercial optical biosensor literature. J Mol Recognit 2011, 24:892-914.
  • [6]Garwood J: Academic truth or biotech bullshit? LabTimes 2012, 3:40-44.
  • [7]Prinz F, Schlange T, Asadullah K: Believe or not: how much can we rely on published data on potential drug targets. Nature Rev Drug Discov 2011, 10:712-713.
  • [8]Begley CG, Ellis LM: Raise standards for preclinical cancer research. Nature 2012, 483:531-533.
  • [9]Ball CA, Sherlock G, Brazma A: Funding high-throughput data sharing. Nat Biotechnol 2004, 22:1179-1183.
  • [10]Cusick ME, Yu H, Smolyar A, Venkatesan K, Carvunis A-R, Simonis N, Rual J-F, Borick H, Braun P, Dreze M, Vandenhaute J, Galli M, Yazaki J, Hill DE, Ecker JR, Roth FP, Vidal M: Literature-curated protein interaction datasets. Nat Methods 2009, 6:39-46.
  • [11]Leitner F, Chatr-aryamontri A, Mardis SA, Ceol A, Krallinger M, Licata L, Hirschman L, Cesareni G, Valencia A: The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. Nat Biotechnol 2010, 28:897-899.
  • [12]Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D: Toward interoperable bioscience data. Nat Genetics 2012, 44:121-126.
  • [13]Kettner C, Field D, Sansone S-A, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL: Meeting report from the second “Minimum Information about a Biological or Biomedical Investigation” (MIBBI) workshop. Standards Genomic Sci 2010, 3:3.
  • [14]Tenenbaum JD, Sansone SA, Haendel M: A sea of standards for omics data: sink or swim? J Am Med Inform Assoc 2013. doi:10.1136/amiajnl-2013-002066
  • [15]Buckle AM, Bate MA, Androulakis S, Cinquanta M, Basquin J, Bonneau F, Chatterjee DK, Cittaro D, Gräslund S, Gruszka A, Page R, Suppmann S, Wheeler JX, Agostini D, Taussig M, Taylor CF, Bottomley SP, Villaverde A, de Marco A: Recombinant protein quality evaluation: proposal for a Minimal Information standard. Standards Genomic Sci 2011, 5:195-197.
  • [16]Schroter S, Black N, Evans S, Godlee F, Osorio L, Smith R: What errors do peer reviewers detect, and does training improve their ability to detect them? J R Soc Med 2008, 101:507-514.
  • [17]Hrynaszkiewicz I: A call for BMC Research Notes contributions promoting best practice in data standardization, sharing and publication. BMC Res Notes 2010, 3:235. BioMed Central Full Text
  • [18]Sala E, de Marco A: Screening optimized protein purification protocols by coupling small-scale expression and mini-size exclusion chromatography. Prot Expr Purif 2010, 74:231-235.
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