Comparison of depletion strategies for the enrichment of low-Abundance proteins in urine

PLoS ONE

Volumn 10, Issue 7, 2015, Pages

  Filip, Szymon ^a,b   Vougas, Konstantinos ^a   Zoidakis, Jerome ^a   Latosinska, Agnieszka ^a,b   Mullen, William ^c   Spasovski, Goce ^d   Mischak, Harald ^c,e   Vlahou, Antonia ^a   Jankowski, Joachim ^f  

^a Academy of Athens Biomedical Research Foundation   (Greece)

^b CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^c UNIVERSITY OF GLASGOW   (United Kingdom)

^d SS CYRIL AND METHODIUS UNIVERSITY   (Macedonia)

^e MOSAIQUES DIAGNOSTICS GMBH   (Germany)

^f UNIVERSITY HOSPITAL RWTH AACHEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALBUMIN; BIOLOGICAL MARKER; IMMUNOGLOBULIN G; PROTEOME; PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; CHRONIC KIDNEY DISEASE; COMPARATIVE EFFECTIVENESS; CONTROLLED STUDY; HUMAN; IMMUNODEPLETION; INTERMETHOD COMPARISON; ION EXCHANGE; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ANALYSIS; PROTEIN CONTENT; PROTEIN DEPLETION; PROTEIN URINE LEVEL; PROTEOMICS; REPRODUCIBILITY; URINALYSIS; URINE VOLUME; CHRONIC KIDNEY FAILURE; METABOLISM; PROCEDURES; URINE;

BIOMARKERS; CHROMATOGRAPHY, LIQUID; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HUMANS; MASS SPECTROMETRY; PEPTIDES; PROTEOME; PROTEOMICS; RENAL INSUFFICIENCY, CHRONIC;

EID: 84941695660     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0133773     Document Type: Article

References (47)

1. Yates JR, Ruse CI, Nakorchevsky A. Proteomics by mass spectrometry: approaches, advances, and applications. Annual review of biomedical engineering. 2009; 11:49-79. doi: 10.1146/annurev-bioeng-061008-124934.
2. Law KP, Lim YP. Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring. Expert review of proteomics. 2013; 10(6):551-66. doi: 10.1586/14789450.2013. 858022.
3. Fliser D, Novak J, Thongboonkerd V, Argiles A, Jankowski V, Girolami MA, et al. Advances in urinary proteome analysis and biomarker discovery. Journal of the American Society of Nephrology: JASN. 2007; 18(4):1057-71. doi: 10.1681/ASN.2006090956.
4. Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Molecular &cellular proteomics: MCP. 2002; 1(11):845-67..
5. Thomas R, Kanso A, Sedor JR. Chronic kidney disease and its complications. Primary care. 2008; 35 (2):329-44, vii. doi: 10.1016/j.pop.2008.01.008
6. Filip S, Pontillo C, Peter Schanstra J, Vlahou A, Mischak H, Klein J. Urinary proteomics and molecular determinants of chronic kidney disease: possible link to proteases. Expert review of proteomics. 2014:1-14. doi: 10.1586/14789450.2014.926224.
7. Perkins BA, Ficociello LH, Roshan B, Warram JH, Krolewski AS. In patients with type 1 diabetes and new-onset microalbuminuria the development of advanced chronic kidney disease may not require progression to proteinuria. Kidney international. 2010; 77(1):57-64. doi: 10.1038/ki.2009.399
8. Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nature biotechnology. 2006; 24(8):971-83. doi: 10.1038/nbt1235.
9. Decramer S, Gonzalez de Peredo A, Breuil B, Mischak H, Monsarrat B, Bascands JL, et al. Urine in clinical proteomics. Molecular &cellular proteomics: MCP. 2008; 7(10):1850-62. doi: 10.1074/mcp. R800001-MCP200.
10. Hortin GL, Sviridov D. Diagnostic potential for urinary proteomics. Pharmacogenomics. 2007; 8 (3):237-55. doi: 10.2217/14622416.8.3.237.
11. Doucette AA, Tran JC, Wall MJ, Fitzsimmons S. Intact proteome fractionation strategies compatible with mass spectrometry. Expert review of proteomics. 2011; 8(6):787-800. doi: 10.1586/epr.11.67
12. Jungbauer A, Hahn R. Ion-exchange chromatography. Methods in enzymology. 2009; 463:349-71. doi: 10.1016/S0076-6879(09)63022-6.
13. Duong-Ly KC, Gabelli SB. Gel filtration chromatography (size exclusion chromatography) of proteins. Methods in enzymology. 2014; 541:105-14. doi: 10.1016/B978-0-12-420119-4.00009-4
14. Cheung RC, Wong JH, Ng TB. Immobilized metal ion affinity chromatography: a review on its applications. Applied microbiology and biotechnology. 2012; 96(6):1411-20. doi: 10.1007/s00253-012-4507-0
15. Moser AC, Hage DS. Immunoaffinity chromatography: an introduction to applications and recent developments. Bioanalysis. 2010; 2(4):769-90. doi: 10.4155/bio.10.31
16. Urh M, Simpson D, Zhao K. Affinity chromatography: general methods. Methods in enzymology. 2009; 463:417-38. doi: 10.1016/S0076-6879(09)63026-3.
17. Filip S, Zoidakis J, Vlahou A, Mischak H. Advances in urinary proteome analysis and applications in systems biology. Bioanalysis. 2014; 6(19):2549-69. doi: 10.4155/bio.14.210.
18. Righetti PG, Candiano G, Citterio A, Boschetti E. Combinatorial Peptide ligand libraries as a "trojan horse" in deep discovery proteomics. Analytical chemistry. 2015; 87(1):293-305. doi: 10.1021/ac502171b.
19. Righetti PG, Boschetti E. The ProteoMiner and the FortyNiners: searching for gold nuggets in the proteomic arena. Mass spectrometry reviews. 2008; 27(6):596-608. doi: 10.1002/mas.20178
20. Boschetti E, Giorgio Righetti P. Hexapeptide combinatorial ligand libraries: the march for the detection of the low-Abundance proteome continues. BioTechniques. 2008; 44(5):663-5. doi: 10.2144/000112762.
21. Righetti PG, Boschetti E. Sample treatment methods involving combinatorial Peptide ligand libraries for improved proteomes analyses. Methods in molecular biology. 2015; 1243:55-82. doi: 10.1007/978-1-4939-1872-0-4.
22. Millioni R, Tolin S, Puricelli L, Sbrignadello S, Fadini GP, Tessari P, et al. High abundance proteins depletion vs low abundance proteins enrichment: comparison of methods to reduce the plasma proteome complexity. PloS one. 2011; 6(5):e19603. doi: 10.1371/journal.pone.0019603
23. Granger J, Siddiqui J, Copeland S, Remick D. Albumin depletion of human plasma also removes low abundance proteins including the cytokines. Proteomics. 2005; 5(18):4713-8. doi: 10.1002/pmic. 200401331.
24. Fountoulakis M, Juranville JF, Jiang L, Avila D, Roder D, Jakob P, et al. Depletion of the high-Abundance plasma proteins. Amino acids. 2004; 27(3-4):249-59. doi: 10.1007/s00726-004-0141-1
25. Stempfer R, Kubicek M, Lang IM, Christa N, Gerner C. Quantitative assessment of human serum highabundance protein depletion. Electrophoresis. 2008; 29(21):4316-23. doi: 10.1002/elps.200800211
26. Tu C, Rudnick PA, Martinez MY, Cheek KL, Stein SE, Slebos RJ, et al. Depletion of abundant plasma proteins and limitations of plasma proteomics. Journal of proteome research. 2010; 9(10):4982-91. doi: 10.1021/pr100646w
27. Echan LA, Tang HY, Ali-Khan N, Lee K, Speicher DW. Depletion of multiple high-Abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics. 2005; 5(13):3292-303. doi: 10.1002/pmic.200401228.
28. Kullolli M, Warren J, Arampatzidou M, Pitteri SJ. Performance evaluation of affinity ligands for depletion of abundant plasma proteins. Journal of chromatography B, Analytical technologies in the biomedical and life sciences. 2013; 939:10-6. doi: 10.1016/j.jchromb.2013.09.008.
29. Magistroni R, Ligabue G, Lupo V, Furci L, Leonelli M, Manganelli L, et al. Proteomic analysis of urine from proteinuric patients shows a proteolitic activity directed against albumin. Nephrology, dialysis, transplantation: official publication of the European Dialysis and Transplant Association-European Renal Association. 2009; 24(5):1672-81. doi: 10.1093/ndt/gfp020.
30. Kushnir MM, Mrozinski P, Rockwood AL, Crockett DK. A depletion strategy for improved detection of human proteins from urine. Journal of biomolecular techniques: JBT. 2009; 20(2):101-8
31. Afkarian M, Bhasin M, Dillon ST, Guerrero MC, Nelson RG, Knowler WC, et al. Optimizing a proteomics platform for urine biomarker discovery. Molecular &cellular proteomics: MCP. 2010; 9(10):2195-204. doi: 10.1074/mcp.M110.000992
32. Magagnotti C, Fermo I, Carletti RM, Ferrari M, Bachi A. Comparison of different depletion strategies for improving resolution of the human urine proteome. Clinical chemistry and laboratory medicine: CCLM /FESCC. 2010; 48(4):531-5. doi: 10.1515/CCLM.2010.109.
33. Chen CL, Lin TS, Tsai CH, Wu CC, Chung T, Chien KY, et al. Identification of potential bladder cancer markers in urine by abundant-protein depletion coupled with quantitative proteomics. Journal of proteomics. 2013; 85:28-43. doi: 10.1016/j.jprot.2013.04.024.
34. Chevallet M, Luche S, Rabilloud T. Silver staining of proteins in polyacrylamide gels. Nature protocols. 2006; 1(4):1852-8. doi: 10.1038/nprot.2006.288
35. Wisniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nature methods. 2009; 6(5):359-62. doi: 10.1038/nmeth.1322.
36. Serang O, Noble W. A review of statistical methods for protein identification using tandem mass spectrometry. Statistics and its interface. 2012; 5(1):3-20
37. Goo YA, Cain K, Jarrett M, Smith L, Voss J, Tolentino E, et al. Urinary proteome analysis of irritable bowel syndrome (IBS) symptom subgroups. Journal of proteome research. 2012; 11(12):5650-62. doi: 10.1021/pr3004437
38. Goo YA, Tsai YS, Liu AY, Goodlett DR, Yang CC. Urinary proteomics evaluation in interstitial cystitis/painful bladder syndrome: a pilot study. International braz j urol: official journal of the Brazilian Society of Urology. 2010; 36(4):464-78; discussion 78-9, 79..
39. Martin-Lorenzo M, Gonzalez-Calero L, Zubiri I, Diaz-Payno PJ, Sanz-Maroto A, Posada-Ayala M, et al. Urine 2DE proteome analysis in healthy condition and kidney disease. Electrophoresis. 2014; 35 (18):2634-41. doi: 10.1002/elps.201300601.
40. Polaskova V, Kapur A, Khan A, Molloy MP, Baker MS. High-Abundance protein depletion: comparison of methods for human plasma biomarker discovery. Electrophoresis. 2010; 31(3):471-82. doi: 10.1002/elps.200900286.
41. Zerefos PG, Aivaliotis M, Baumann M, Vlahou A. Analysis of the urine proteome via a combination of multi-dimensional approaches. Proteomics. 2012; 12(3):391-400. doi: 10.1002/pmic.201100212
42. Mischak H, Kolch W, Aivaliotis M, Bouyssie D, Court M, Dihazi H, et al. Comprehensive human urine standards for comparability and standardization in clinical proteome analysis. Proteomics Clinical applications. 2010; 4(4):464-78. doi: 10.1002/prca.200900189
43. Adachi J, Kumar C, Zhang Y, Olsen JV, Mann M. The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome biology. 2006; 7(9):R80. doi: 10.1186/gb-2006-7-9-R80
44. Brott DA, Adler SH, Arani R, Lovick SC, Pinches M, Furlong ST. Characterization of renal biomarkers for use in clinical trials: biomarker evaluation in healthy volunteers. Drug design, development and therapy. 2014; 8:227-37. doi: 10.2147/DDDT.S54956
45. Fassett RG, Venuthurupalli SK, Gobe GC, Coombes JS, Cooper MA, Hoy WE. Biomarkers in chronic kidney disease: a review. Kidney international. 2011; 80(8):806-21. doi: 10.1038/ki.2011.198
46. Mischak H, Delles C, Vlahou A, Vanholder R. Proteomic biomarkers in kidney disease: issues in development and implementation. Nature reviews Nephrology. 2015; 11(4):221-32. doi: 10.1038/nrneph. 2014.247.
47. Available: . http://bioinformatics.psb.ugent.be/webtools/Venn/