High-resolution Proteome/peptidome Analysis of Peptides and Low-molecular-weight Proteins in Urine

Overview

Journal Proteomics Clin Appl

Specialty Biochemistry

Date 2010 Jan 29

PMID 20107618

Citations 25

Authors

Harald Mischak

Bruce A Julian

Jan Novak

Affiliations

Soon will be listed here.

Abstract

All organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance diagnosis and therapy of specific diseases. The low-molecular-weight proteome, also termed peptidome, provides a rich source of information. Due to its unique features, the technical challenges differ somewhat from those in "common" proteomics. In this manuscript, we focus on the low-molecular-weight urinary proteome. We review the methodological aspects of sample collection, preparation, analysis, and subsequent data evaluation. In the second part of this review, we summarize the recent progress in the definition and identification of clinically relevant polypeptide markers.

Citing Articles

Urinary matrix Gla protein is associated with mortality risk in Flemish population: A prospective study.

Wei D, Melgarejo J, Vanassche T, Van Aelst L, Janssens S, Verhamme P Front Cardiovasc Med. 2022; 9:894447.

PMID: 35935627 PMC: 9353515. DOI: 10.3389/fcvm.2022.894447.

Urinary Proteomic Profile of Arterial Stiffness Is Associated With Mortality and Cardiovascular Outcomes.

Wei D, Melgarejo J, Thijs L, Temmerman X, Vanassche T, Van Aelst L J Am Heart Assoc. 2022; 11(8):e024769.

PMID: 35411793 PMC: 9238473. DOI: 10.1161/JAHA.121.024769.

Peptidomics and Capillary Electrophoresis.

Stepanova S, Kasicka V Adv Exp Med Biol. 2021; 1336:87-104.

PMID: 34628628 DOI: 10.1007/978-3-030-77252-9_5.

Gastrointestinal Digestion Model Assessment of Peptide Diversity and Microbial Fermentation Products of Collagen Hydrolysates.

Larder C, Iskandar M, Kubow S Nutrients. 2021; 13(8).

PMID: 34444880 PMC: 8401164. DOI: 10.3390/nu13082720.

Candidate Urine Peptide Biomarkers for IgA Nephropathy: Where Are We Now?.

Marek-Bukowiec K, Konieczny A, Ratajczyk K, Witkiewicz W Dis Markers. 2018; 2018:5205831.

PMID: 29606986 PMC: 5827886. DOI: 10.1155/2018/5205831.

References

Thongboonkerd V, Malasit P . Renal and urinary proteomics: current applications and challenges. Proteomics. 2005; 5(4):1033-42. DOI: 10.1002/pmic.200401012. View

Mischak H, Apweiler R, Banks R, Conaway M, Coon J, Dominiczak A . Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics Clin Appl. 2010; 1(2):148-56. DOI: 10.1002/prca.200600771. View

Neususs C, Pelzing M, Macht M . A robust approach for the analysis of peptides in the low femtomole range by capillary electrophoresis-tandem mass spectrometry. Electrophoresis. 2002; 23(18):3149-59. DOI: 10.1002/1522-2683(200209)23:18<3149::AID-ELPS3149>3.0.CO;2-8. View

Decramer S, Wittke S, Mischak H, Zurbig P, Walden M, Bouissou F . Predicting the clinical outcome of congenital unilateral ureteropelvic junction obstruction in newborn by urinary proteome analysis. Nat Med. 2006; 12(4):398-400. DOI: 10.1038/nm1384. View

Issaq H . The role of separation science in proteomics research. Electrophoresis. 2001; 22(17):3629-38. DOI: 10.1002/1522-2683(200109)22:17<3629::AID-ELPS3629>3.0.CO;2-O. View

Yanagida M . Functional proteomics; current achievements. J Chromatogr B Analyt Technol Biomed Life Sci. 2002; 771(1-2):89-106. DOI: 10.1016/s1570-0232(02)00074-0. View

Kolch W, Neususs C, Pelzing M, Mischak H . Capillary electrophoresis-mass spectrometry as a powerful tool in clinical diagnosis and biomarker discovery. Mass Spectrom Rev. 2005; 24(6):959-77. DOI: 10.1002/mas.20051. View

Comper W, Osicka T, Clark M, MacIsaac R, Jerums G . Earlier detection of microalbuminuria in diabetic patients using a new urinary albumin assay. Kidney Int. 2004; 65(5):1850-5. DOI: 10.1111/j.1523-1755.2004.00585.x. View

Orvisky E, Drake S, Martin B, Abdel-Hamid M, Ressom H, Varghese R . Enrichment of low molecular weight fraction of serum for MS analysis of peptides associated with hepatocellular carcinoma. Proteomics. 2006; 6(9):2895-902. DOI: 10.1002/pmic.200500443. View

10.

Vestergaard P, LEVERETT R . Constancy of urinary creatinine excretion. J Lab Clin Med. 1958; 51(2):211-8. View

11.

Kislinger T, Gramolini A, MacLennan D, Emili A . Multidimensional protein identification technology (MudPIT): technical overview of a profiling method optimized for the comprehensive proteomic investigation of normal and diseased heart tissue. J Am Soc Mass Spectrom. 2005; 16(8):1207-20. DOI: 10.1016/j.jasms.2005.02.015. View

12.

Baggerly K, Morris J, Edmonson S, Coombes K . Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J Natl Cancer Inst. 2005; 97(4):307-9. DOI: 10.1093/jnci/dji008. View

13.

Schiffer E, Mischak H, Novak J . High resolution proteome/peptidome analysis of body fluids by capillary electrophoresis coupled with MS. Proteomics. 2006; 6(20):5615-27. DOI: 10.1002/pmic.200600230. View

14.

Soldi M, Sarto C, Valsecchi C, Magni F, Proserpio V, Ticozzi D . Proteome profile of human urine with two-dimensional liquid phase fractionation. Proteomics. 2005; 5(10):2641-7. DOI: 10.1002/pmic.200401269. View

15.

Schulz-Knappe P, Schrader M, Standker L, Richter R, Hess R, Jurgens M . Peptide bank generated by large-scale preparation of circulating human peptides. J Chromatogr A. 1997; 776(1):125-32. DOI: 10.1016/s0021-9673(97)00152-0. View

16.

Morrison R, Kinoshita Y, Johnson M, Uo T, Ho J, McBee J . Proteomic analysis in the neurosciences. Mol Cell Proteomics. 2002; 1(8):553-60. DOI: 10.1074/mcp.r200004-mcp200. View

17.

Fricke K, Schulz A, John H, Forssmann W, Maronde E . Isolation and characterization of a novel proopiomelanocortin-derived peptide from hemofiltrate of chronic renal failure patients. Endocrinology. 2005; 146(4):2060-8. DOI: 10.1210/en.2004-1097. View

18.

Liu W, Guan M, Wu D, Zhang Y, Wu Z, Xu M . Using tree analysis pattern and SELDI-TOF-MS to discriminate transitional cell carcinoma of the bladder cancer from noncancer patients. Eur Urol. 2005; 47(4):456-62. DOI: 10.1016/j.eururo.2004.10.006. View

19.

Weissinger E, Wittke S, Kaiser T, Haller H, Bartel S, Krebs R . Proteomic patterns established with capillary electrophoresis and mass spectrometry for diagnostic purposes. Kidney Int. 2004; 65(6):2426-34. DOI: 10.1111/j.1523-1755.2004.00659.x. View

20.

Rogers M, Clarke P, Noble J, Munro N, Paul A, Selby P . Proteomic profiling of urinary proteins in renal cancer by surface enhanced laser desorption ionization and neural-network analysis: identification of key issues affecting potential clinical utility. Cancer Res. 2003; 63(20):6971-83. View