Operator- and software-related post-experimental variability and source of error in 2-DE analysis

Amino Acids

Volumn 42, Issue 5, 2012, Pages 1583-1590

  Millioni, Renato ^a   Puricelli, Lucia ^a   Sbrignadello, Stefano ^a,b   Iori, Elisabetta ^a   Murphy, Ellen ^a   Tessari, Paolo ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b CNR   (Italy)

Author keywords

2 DE; Pixelbased method; Post experimental variability; Spot based method

Indexed keywords

ANALYTICAL ERROR; ANALYTICAL PARAMETERS; COMPUTER PROGRAM; EXPERIMENT; EXPERIMENT SIZE; IMAGE ANALYSIS; IMAGE PROCESSING; NORMAL DISTRIBUTION; OPERATOR; POST EXPERIMENTAL VARIABILITY; PRIORITY JOURNAL; REVIEW; STATISTICAL ANALYSIS; TIME; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; PROTEOME; PROTEOMICS; QUALITY CONTROL; SOFTWARE;

EID: 84862771027     PISSN: 09394451     EISSN: 14382199     Source Type: Journal    
DOI: 10.1007/s00726-011-0873-7     Document Type: Review

References (41)

1. Ahmad N, Zhang J, Brown PJ, James DC, Birch JR, Racher AJ, Smales CM (2006) On the statistical analysis of the GS-NS0 cell proteome: imputation, clustering and variability testing. Biochim Biophys Acta 1764:1179-1187 (Pubitemid 44080864)
2. Albrecht D, Kniemeyer O, Brakhage AA, Guthke R (2010) Missing values in gel-based proteomics. Proteomics 10:1202-1211
3. Appel RD, Vargas JR, Palagi PM, Walther D, Hochstrasser DF (1997) Melanie II-a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms. Electrophoresis 18:2735-2748 (Pubitemid 28059945)
4. Berth M, Moser FM, Kolbe M, Bernhardt J (2007) The state of the art in the analysis of two-dimensional gel electrophoresis images. Appl Microbiol Biotechnol 76:1223-1243 (Pubitemid 47459790)
5. Bettens E (1999) Peak characterisation using parameter estimation methods. Ph.D thesis, University of Antwerp. http://visielab.ua.ac.be/exstaff/ bettens/thesis.html
6. Biron DG, Brun C, Lefevre T, Lebarbenchon C, Loxdale HD, Chevenet F, Brizard JP, Thomas F (2006) The pitfalls of proteomics experiments without the correct use of bioinformatics tools. Proteomics 6:5577-5596 (Pubitemid 44683222)
7. Canas B, Pineiro C, Calvo E, Lopez-Ferrer D, Gallardo JM (2007) Trends in sample preparation for classical and second generation proteomics. J Chromatogr A 1153:235-258 (Pubitemid 46755189)
8. Cannistraci CV, Montevecchi FM, Alessio M (2009) Medianmodified Wiener filter provides efficient denoising, preserving spot edge and morphology in 2-DE image processing. Proteomics 9:4908-4919
9. Choe LH, Lee KH (2000) A comparison of three commercially available isoelectric focusing units for proteome analysis: the multiphor, the IPGphor and the protean IEF cell. Electrophoresis 21:993-1000 (Pubitemid 30194080)
10. Clark BN, Gutstein HB (2008) The myth of automated, highthroughput two-dimensional gel analysis. Proteomics 8:1197-1203 (Pubitemid 351462925)
11. Damodaran S, Rabin RA (2007) Minimizing variability in twodimensional electrophoresis gel image analysis. Omics 11:225-230 (Pubitemid 47016182)
12. Dowsey AW, English J, Pennington K, Cotter D, Stuehler K, Marcus K, Meyer HE, Dunn MJ, Yang GZ (2006) Examination of 2-DE in the Human Proteome Organisation Brain Proteome Project pilot studies with the new RAIN gel matching technique. Proteomics 6:5030-5047 (Pubitemid 44483897)
13. Engelen K, Sifrim A, Van de Plas B, Laukens K, Arckens L, Marchal K (2010) Alternative experimental design with an applied normalization scheme can improve statistical power in 2D-DIGE experiments. J Proteome Res 9:4919-4926
14. Fodor IK, Nelson DO, Alegria-Hartman M, Robbins K, Langlois RG, Turteltaub KW, Corzett TH, McCutchen-Maloney SL (2005) Statistical challenges in the analysis of two-dimensional difference gel electrophoresis experiments using DeCyder. Bioinformatics 21:3733-3740 (Pubitemid 41535521)
15. Fuxius S, Eravci M, Broedel O, Weist S, Mansmann U, Eravci S, Baumgartner A (2008) Technical strategies to reduce the amount of "false significant" results in quantitative proteomics. Proteomics 8:1780-1784 (Pubitemid 351678277)
16. Grove H, Hollung K, Uhlen AK, Martens H, Faergestad EM (2006) Challenges related to analysis of protein spot volumes from twodimensional gel electrophoresis as revealed by replicate gels. J Proteome Res 5:3399-3410 (Pubitemid 44904331)
17. Jessen F, Lametsch R, Bendixen E, Kjaersgard IVH, Jorgensen BM (2002) Extracting information from two-dimensional electrophoresis gels by partial least squares regression. Proteomics 2:32-35 (Pubitemid 34273096)
18. Klose J, Kobalz U (1995) Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis 16:1034-1059
19. Kreil DP, Karp NA, Lilley KS (2004) DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results. Bioinformatics 20:2026-2034 (Pubitemid 39236554)
20. Lefkovits I, Kettman JR, Frey JR (2000) Global analysis of gene expression in cells of the immune system I. Analytical limitations in obtaining sequence information on polypeptides in twodimensional gel spots. Electrophoresis 21:2688-2693
21. Lopez JL (2007) Two-dimensional electrophoresis in proteome expression analysis. J Chromatogr B Analyt Technol Biomed Life Sci 849:190-202 (Pubitemid 46529329)
22. Luhn S, Berth M, Hecker M, Bernhardt J (2003) Using standard positions and image fusion to create proteome maps from collections of two-dimensional gel electrophoresis images. Proteomics 3:1117-1127 (Pubitemid 36929534)
23. Maurer MH, Feldmann RE, Bromme JO, Kalenka A (2005) Comparison of statistical approaches for the analysis of proteome expression data of differentiating neural stem cells. J Proteome Res 4:96-100 (Pubitemid 40344461)
24. Meunier B, Bouley J, Piec I, Bernard C, Picard B, Hocquette JF (2005) Data analysis methods for detection of differential protein expression in two-dimensional gel electrophoresis. Anal Biochem 340:226-230 (Pubitemid 40544861)
25. Millioni R, Miuzzo M, Sbrignadello S, Murphy E, Puricelli L, Tura A, Bertacco E, Rattazzi M, Iori E, Tessari P (2010a) Delta2D and Proteomweaver: performance evaluation of two different approaches for 2-DE analysis. Electrophoresis 31:1311-1317
26. Millioni R, Sbrignadello S, Tura A, Iori E, Murphy E, Tessari P (2010b) The inter- and intra-operator variability in manual spot segmentation and its effect on spot quantitation in two-dimensional electrophoresis analysis. Electrophoresis 31:1739-1742
27. Polaskova V, Kapur A, Khan A, Molloy MP, Baker MS (2010) Highabundance protein depletion: comparison of methods for human plasma biomarker discovery. Electrophoresis 31:471-482
28. Raman B, Cheung A, Marten MR (2002) Quantitative comparison and evaluation of two commercially available, two-dimensional electrophoresis image analysis software packages, Z3 and Melanie. Electrophoresis 23:2194-2202
29. Rogers M, Graham J, Tonge RP (2003a) Statistical models of shape for the analysis of protein spots in two-dimensional electrophoresis gel images. Proteomics 3:887-896 (Pubitemid 36801675)
30. Rogers M, Graham J, Tonge RP (2003b) Using statistical image models for objective evaluation of spot detection in twodimensional gels. Proteomics 3:879-886 (Pubitemid 36801674)
31. Rosengren AT, Salmi JM, Aittokallio T, Westerholm J, Lahesmaa R, Nyman TA, Nevalainen OS (2003) Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels. Proteomics 3:1936-1946 (Pubitemid 37305888)
32. Rye MB, Faergestad EM, Alsberg BK (2008) A new method for assigning common spot boundaries for multiple gels in twodimensional gel electrophoresis. Electrophoresis 29:1359-1368 (Pubitemid 351461091)
33. Silva E, O'Gorman M, Becker S, Auer G, Eklund A, Grunewald J, Wheelock AM (2010) In the eye of the beholder: does the master see the SameSpots as the novice? J Proteome Res 9:1522-1532
34. Smales CM, Birch JR, Racher AJ, Marshall CT, James DC (2003) Evaluation of individual protein errors in silver-stained twodimensional gels. Biochem Biophys Res Commun 306:1050-1055 (Pubitemid 36776237)
35. Smit S, Hoefsloot HCJ, Smilde AK (2008) Statistical data processing in clinical proteomics. J Chromatogr B 866:77-88 (Pubitemid 351491683)
36. Stessl M, Noe CR, Lachmann B (2009) Influence of image-analysis software on quantitation of two-dimensional gel electrophoresis data. Electrophoresis 30:325-328
37. Taylor RC, Coorssen JR (2006) Proteome resolution by twodimensional gel electrophoresis varies with the commercial source of IPG strips. J Proteome Res 5:2919-2927 (Pubitemid 44749210)
38. Tsakanikas P, Manolakos ES (2009) Improving 2-DE gel image denoising using contourlets. Proteomics 9:3877-3888
39. Westermeier R, Scheibe B (2008) Difference gel electrophoresis based on lys/cys tagging. Methods Mol Biol 424:73-85
40. Wheelock AM, Buckpitt AR (2005) Software-induced variance in two-dimensional gel electrophoresis image analysis. Electrophoresis 26:4508-4520 (Pubitemid 41819575)
41. Zhan X, Desiderio DM (2003) Differences in the spatial and quantitative reproducibility between two second-dimensional gel electrophoresis systems. Electrophoresis 24:1834-1846 (Pubitemid 38088971)