The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales - PubMed (original) (raw)
Review
The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales
Jianhua Hu et al. Brief Funct Genomic Proteomic. 2005 Feb.
Abstract
Proteomic expression patterns derived from mass spectrometry have been put forward as potential biomarkers for the early diagnosis of cancer and other diseases. This approach has generated much excitement and has led to a large number of new experiments and vast amounts of new data. The data, derived at great expense, can have very little value if careful attention is not paid to the experimental design and analysis. Using examples from surface-enhanced laser desorption/ionisation time-of-flight (SELDI-TOF) and matrix-assisted laser desorption-ionisation/time-of-flight (MALDI-TOF) experiments, we describe several experimental design issues that can corrupt a dataset. Fortunately, the problems we identify can be avoided if attention is paid to potential sources of bias before the experiment is run. With an appropriate experimental design, proteomics technology can be a useful tool for discovering important information relating protein expression to disease.
Similar articles
- Advances in clinical cancer proteomics: SELDI-ToF-mass spectrometry and biomarker discovery.
Seibert V, Ebert MP, Buschmann T. Seibert V, et al. Brief Funct Genomic Proteomic. 2005 May;4(1):16-26. doi: 10.1093/bfgp/4.1.16. Brief Funct Genomic Proteomic. 2005. PMID: 15975261 Review. - Clinical proteomics in breast cancer: a review.
Gast MC, Schellens JH, Beijnen JH. Gast MC, et al. Breast Cancer Res Treat. 2009 Jul;116(1):17-29. doi: 10.1007/s10549-008-0263-3. Epub 2008 Dec 11. Breast Cancer Res Treat. 2009. PMID: 19082706 Review. - Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.
Brozkova K, Budinska E, Bouchal P, Hernychova L, Knoflickova D, Valik D, Vyzula R, Vojtesek B, Nenutil R. Brozkova K, et al. Breast Cancer Res. 2008;10(3):R48. doi: 10.1186/bcr2101. Epub 2008 May 29. Breast Cancer Res. 2008. PMID: 18510725 Free PMC article. - Opportunities and limitations of SELDI-TOF-MS in biomedical research: practical advices.
Poon TC. Poon TC. Expert Rev Proteomics. 2007 Feb;4(1):51-65. doi: 10.1586/14789450.4.1.51. Expert Rev Proteomics. 2007. PMID: 17288515 Review. - MALDI/SELDI protein profiling of serum for the identification of cancer biomarkers.
Cazares LH, Diaz JI, Drake RR, Semmes OJ. Cazares LH, et al. Methods Mol Biol. 2008;428:125-40. doi: 10.1007/978-1-59745-117-8_7. Methods Mol Biol. 2008. PMID: 18287771
Cited by
- Searching for early breast cancer biomarkers by serum protein profiling of pre-diagnostic serum; a nested case-control study.
Opstal-van Winden AW, Krop EJ, Kåredal MH, Gast MC, Lindh CH, Jeppsson MC, Jönsson BA, Grobbee DE, Peeters PH, Beijnen JH, van Gils CH, Vermeulen RC. Opstal-van Winden AW, et al. BMC Cancer. 2011 Aug 26;11:381. doi: 10.1186/1471-2407-11-381. BMC Cancer. 2011. PMID: 21871081 Free PMC article. - Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale.
Buhule OD, Minster RL, Hawley NL, Medvedovic M, Sun G, Viali S, Deka R, McGarvey ST, Weeks DE. Buhule OD, et al. Front Genet. 2014 Oct 13;5:354. doi: 10.3389/fgene.2014.00354. eCollection 2014. Front Genet. 2014. PMID: 25352862 Free PMC article. - Probing the prostate tumour microenvironment II: Impact of hypoxia on a cell model of prostate cancer progression.
Tonry C, Armstrong J, Pennington S. Tonry C, et al. Oncotarget. 2017 Feb 28;8(9):15307-15337. doi: 10.18632/oncotarget.14574. Oncotarget. 2017. PMID: 28410543 Free PMC article. - Bayesian analysis of mass spectrometry proteomic data using wavelet-based functional mixed models.
Morris JS, Brown PJ, Herrick RC, Baggerly KA, Coombes KR. Morris JS, et al. Biometrics. 2008 Jun;64(2):479-89. doi: 10.1111/j.1541-0420.2007.00895.x. Epub 2007 Sep 20. Biometrics. 2008. PMID: 17888041 Free PMC article. - Integrative proteomic analysis of serum and peritoneal fluids helps identify proteins that are up-regulated in serum of women with ovarian cancer.
Amon LM, Law W, Fitzgibbon MP, Gross JA, O'Briant K, Peterson A, Drescher C, Martin DB, McIntosh M. Amon LM, et al. PLoS One. 2010 Jun 15;5(6):e11137. doi: 10.1371/journal.pone.0011137. PLoS One. 2010. PMID: 20559444 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Other Literature Sources