Toward a standardized urine proteome analysis methodology

Proteomics

Volumn 11, Issue 6, 2011, Pages 1160-1171

  Court, Magali ^a,b,c,d   Selevsek, Nathalie ^a,e   Matondo, Mariette ^a,e   Allory, Yves ^a,f,g   Garin, Jerome ^a,b,c,d   Masselon, Christophe D ^a,b,c,d   Domon, Bruno ^a,h  

^a DECanBio consortium ^*  (France)

^b Laboratoire d'Etude de la Dynamique des Proteomes   (France)

^c INSERM   (France)

^d UNIV GRENOBLE ALPES   (France)

^e ETH ZURICH   (Switzerland)

^f INSERM U955   (France)

^g HENRI MONDOR HOSPITAL   (France)

^h LUXEMBOURG INSTITUTE OF HEALTH   (Luxembourg)

Author keywords

AMT tag; Sample preparation; Selected reaction monitoring; Standardization; Technology; Urinary proteomics

Indexed keywords

BIOLOGICAL MARKER; PROTEOME;

ADULT; AGED; ANALYTIC METHOD; ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; EXTRACTION; FEMALE; HOSPITAL PATIENT; HUMAN; LIQUID CHROMATOGRAPHY; MALE; MASS SPECTROMETRY; METHODOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN URINE LEVEL; PROTEOMICS; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; STANDARD; STANDARDIZATION; URINALYSIS; URINE; VALIDATION PROCESS;

AMINO ACID SEQUENCE; BIOLOGICAL MARKERS; CHROMATOGRAPHY, LIQUID; DATABASES, PROTEIN; HUMANS; PEPTIDES; PROTEINURIA; PROTEOME; PROTEOMICS; QUALITY CONTROL; REFERENCE STANDARDS; TANDEM MASS SPECTROMETRY;

EID: 79952300137     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000566     Document Type: Article

References (31)

1. Adachi, J., Kumar, C., Zhang, Y., Olsen, J. V. et al., The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol. 2006, 7, R80.
2. Gonzales, P. A., Pisitkun, T., Hoffert, J. D., Tchapyjnikov, D. et al., Large-scale proteomics and phosphoproteomics of urinary exosomes. J. Am. Soc. Nephrol. 2009, 20, 363-379.
3. Kentsis, A., Monigatti, F., Dorff, K., Campagne, F. et al., Urine proteomics for profiling of human disease using high accuracy mass spectrometry. Proteomics Clin. Appl. 2009, 3, 1052-1061.
4. Julian, B. A., Suzuki, H., Suzuki, Y., Tomino, Y. et al., Sources of urinary proteins and their analysis by urinary proteomics for the detection of biomarkers of disease. Proteomics Clin. Appl. 2009, 3, 1029-1043.
5. Qiu, Y., Cai, G., Su, M., Chen, T. et al., Urinary metabonomic study on colorectal cancer. J. Proteome Res. 2010, 9, 1627-1634.
6. Yap, I. K. S., Angley, M., Veselkov, K. A., Holmes, E. et al., Urinary metabolic phenotyping differentiates children with autism from their unaffected siblings and age-matched controls. J. Proteome Res. 2010, 9, 2996-3004.
7. Zimmerli, L. U., Schiffer, E., Zurbig, P., Good, D. M. et al., Urinary proteomic biomarkers in coronary artery disease. Mol. Cell. Proteomics 2008, 7, 290-298.
8. Decramer, S., Gonzalez de Peredo, A., Breuil, B., Mischak, H. et al., Urine in clinical proteomics. Mol. Cell. Proteomics 2008, 7, 1850-1862.
9. Addona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J. et al., Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 2009, 27, 633-641.
10. Thongboonkerd, V., Practical points in urinary proteomics. J. Proteome Res. 2007, 6, 3881-3890.
11. Papale, M., Pedicillo, M. C., Thatcher, B. J., Di Paolo, S. et al., Urine profiling by SELDI-TOF/MS: monitoring of the critical steps in sample collection, handling and analysis. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2007, 856, 205-213.
12. Havanapan, P., Thongboonkerd, V., Are protease inhibitors required for gel-based proteomics of kidney and urine? J. Proteome Res. 2009, 8, 3109-3117.
13. Thongboonkerd, V., Saetun, P., Bacterial overgrowth affects urinary proteome analysis: recommendation for centrifugation, temperature, duration, and the use of preservatives during sample collection. J. Proteome Res. 2007, 6, 4173-4181.
14. Thongboonkerd, V., Mungdee, S., Chiangjong, W., Should urine pH be adjusted prior to gel-based proteome analysis? J. Proteome Res. 2009, 8, 3206-3211.
15. Lee, R. S., Monigatti, F., Briscoe, A. C., Waldon, Z. et al., Optimizing sample handling for urinary proteomics. J. Proteome Res. 2008, 7, 4022-4030.
16. Mataija-Botelho, D., Murphy, P., Pinto, D. M., MacLellan, D. L. et al., A qualitative proteome investigation of the sediment portion of human urine: implications in the biom arker discovery process. Proteomics Clin. Appl. 2009, 3, 95-105.
17. Rifai, N., Gillette, M. A., Carr, S. A., Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 2006, 24, 971-983.
18. Jaquinod, M., Villiers, F., Kieffer-Jaquinod, S., Hugouvieux, V. et al., A proteomics dissection of arabidopsis thaliana vacuoles isolated from cell culture. Mol. Cell. Proteomics 2007, 6, 394-412.
19. Kraut, A., Marcellin, M., Adrait, A., Kuhn, L. et al., Peptide storage: are you getting the best return on your investment? Defining optimal storage conditions for proteomics samples. J. Proteome Res. 2009, 8, 3778-3785.
20. Elias, J. E., Gygi, S. P., Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 2007, 4, 207-214.
21. Dupierris, V., Masselon, C., Court, M., Kieffer-Jaquinod, S. et al., A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMA. Bioinformatics 2009, 25, 1980-1981.
22. Masselon, C. D., Kieffer-Jaquinod, S., Brugiere, S., Dupierris, V. et al., Influence of mass resolution on species matching in accurate mass and retention time (AMT) tag proteomics experiments. Rapid Commun. Mass Spectrom. 2008, 22, 986-992.
23. Monroe, M. E., Tolić, N., Jaitly, N., Shaw, J. L. et al., Viper: an advanced software package to support high-throughput lc-ms peptide identification. Bioinformatics 2007, 23, 2021-2023.
24. Norbeck, A. D., Monroe, M. E., Adkins, J. N., Anderson, K. K. et al., The utility of accurate mass and LC elution time information in the analysis of complex proteomes. J. Am. Soc. Mass Spectrom. 2005, 16, 1239-1249.
25. Candiano, G., Santucci, L., Petretto, A., Bruschi, M. et al., 2D-electrophoresis and the urine proteome map: where do we stand? J. Proteomics 2010, 73, 829-844.
26. Magistroni, R., Ligabue, G., Lupo, V., Furci, L. et al., Proteomic analysis of urine from proteinuric patients shows a proteolytic activity directed against albumin. Nephrol. Dial. Transplant. 2009, 24, 1672-1681.
27. Afkarian, M., Bhasin, M., Dillon, S. T., Guerrero, M. C. et al., Optimizing a proteomics platform for urine biomarker discovery. Mol. Cell. Proteomics 2010, 9, 2195-2204.
28. Thongboonkerd, V., Chutipongtanate, S., Kanlaya, R., Systematic evaluation of sample preparation methods for gel-based human urinary proteomics: quantity, quality, and variability. J. Proteome Res. 2006, 5, 183-191.
29. Tantipaiboonwong, P., Sinchaikul, S., Sriyam, S., Phutrakul, S. et al., Different techniques for urinary protein analysis of normal and lung cancer patients. Proteomics 2005, 5, 1140-1149.
30. Thongboonkerd, V., McLeish, K. R., Arthur, J. M., Klein, J. B., Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int. 2002, 62, 1461-1469.
31. Prakash, A., Tomazela, D. M., Frewen, B., Maclean, B. et al., Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. J. Proteome Res. 2009, 8, 2733-2739.