title: Mass spectrometry based proteomics in urine biomarker discovery.
abstract: All organisms contain 1,000s of proteins and peptides in their body fluids, which undergo disease-specific changes. Advances in the understanding of the functional relevance of these polypeptides under different (patho)physiological conditions and the identification of indicative changes with disease would greatly enhance diagnosis and therapy. The low-molecular-weight proteome, also termed peptidome, provides a rich source of information. Due to its lower molecular weight, the peptidome can be assessed without the need for sample manipulation like tryptic digests. This advantage facilitates comparative analysis but it also raises technical challenges differing from those in proteomics. The first part of this manuscript, is focused on the low-molecular-weight urinary proteome and reviews methodological aspects of sample collection, preparation, analysis, and data evaluation. The second part summarizes the recent progress in the definition and identification of clinically relevant polypeptide markers.
authors: Department of Molecular Physiology, University of Virginia, Charlottesville, USA.
authors: Dan
authors: D
authors: Theodorescu
authors: Harald
authors: H
authors: Mischak
mesh_terms: D015415:Biomarkers / Q000652:urine; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D014556:Urine / Q000737:chemistry* / Q000502:physiology
chemical_list: D015415:Biomarkers; D020543:Proteome
references: Mol Cell Proteomics. 2006 Jun;5(6):1095-104
references: 16546996
references: Electrophoresis. 2002 Sep;23(17):3048-61
references: 12207315
references: Mass Spectrom Rev. 2005 Nov-Dec;24(6):959-77
references: 15747373
references: Clin Chem. 1979 Jul;25(7):1199-210
references: 455639
references: J Proteome Res. 2006 Nov;5(11):3038-47
references: 17081055
references: Mol Cell Proteomics. 2006 Oct;5(10):1760-71
references: 16837576
references: Lancet Oncol. 2006 Mar;7(3):230-40
references: 16510332
references: J Mass Spectrom. 2002 Mar;37(3):241-53
references: 11921364
references: World J Gastroenterol. 2006 Dec 21;12(47):7604-12
references: 17171788
references: Am J Transplant. 2005 Apr;5(4 Pt 1):729-38
references: 15760396
references: Annu Rev Med. 2004;55:97-112
references: 14746511
references: Electrophoresis. 2001 Oct;22(17):3629-38
references: 11699900
references: J Biotechnol. 2006 Aug 5;124(4):758-87
references: 16600411
references: J Proteome Res. 2005 Sep-Oct;4(5):1757-67
references: 16212430
references: Lancet. 2002 Feb 16;359(9306):572-7
references: 11867112
references: Biochem Biophys Res Commun. 2002 Apr 5;292(3):587-92
references: 11922607
references: Kidney Int. 2004 Jan;65(1):323-32
references: 14675066
references: Electrophoresis. 2002 Sep;23(18):3182-92
references: 12298090
references: Rapid Commun Mass Spectrom. 2004;18(2):149-56
references: 14745763
references: J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Jan 5;814(1):11-9
references: 15607703
references: J Chromatogr A. 2006 Apr 14;1111(2):166-74
references: 16569576
references: Kidney Int. 2005 Jun;67(6):2313-20
references: 15882273
references: Proteomics. 2005 Aug;5(13):3226-45
references: 16104056
references: J Chromatogr A. 2006 Jun 2;1117(1):87-93
references: 16620839
references: Proteomics Clin Appl. 2007 Feb;1(2):148-56
references: 21136664
references: Curr Opin Mol Ther. 2004 Dec;6(6):616-23
references: 15663326
references: Rapid Commun Mass Spectrom. 2005;19(2):162-8
references: 15593243
references: Mass Spectrom Rev. 1998 Jan-Feb;17(1):1-35
references: 9768511
references: Proteomics. 2006 May;6(9):2895-902
references: 16586431
references: Electrophoresis. 2005 Jul;26(14):2797-808
references: 15981297
references: Technol Cancer Res Treat. 2002 Aug;1(4):273-80
references: 12625786
references: Electrophoresis. 2004 Mar;25(6):809-16
references: 15004840
references: Clin Chim Acta. 2000 Jul;297(1-2):251-60
references: 10841926
references: Bioinformatics. 2004 Mar 22;20(5):735-41
references: 14751989
references: Mol Cell Proteomics. 2002 Aug;1(8):553-60
references: 12376570
references: Mass Spectrom Rev. 2004 Jan-Feb;23(1):34-44
references: 14625891
references: Clin Chim Acta. 2006 Apr;366(1-2):249-56
references: 16332361
references: Biochem Biophys Res Commun. 2003 Sep 12;309(1):18-25
references: 12943657
references: Electrophoresis. 2005 Apr;26(7-8):1209-20
references: 15776480
references: Proteomics. 2005 Jul;5(10):2641-7
references: 15912557
references: Mol Cell Proteomics. 2005 Jul;4(7):1002-8
references: 15863400
references: J Lab Clin Med. 1958 Feb;51(2):211-8
references: 13514226
references: Electrophoresis. 2003 Dec;24(22-23):3837-67
references: 14661221
references: J Am Soc Mass Spectrom. 2004 Jul;15(7):1099-108
references: 15234368
references: Bioinformatics. 2004 Mar 22;20(5):777-85
references: 14751995
references: Biotechniques. 2006 Jun;40(6):783-9
references: 16774122
references: Electrophoresis. 2005 Apr;26(7-8):1254-90
references: 15776483
references: Electrophoresis. 2000 Apr;21(6):1164-77
references: 10786889
references: Electrophoresis. 2006 Jan;27(1):3-34
references: 16315165
references: J Natl Cancer Inst. 2005 Feb 16;97(4):307-9
references: 15713966
references: Electrophoresis. 2002 Sep;23(18):3149-59
references: 12298087
references: Blood. 2007 Jun 15;109(12):5511-9
references: 17339419
references: J Chromatogr B Analyt Technol Biomed Life Sci. 2002 May 5;771(1-2):89-106
references: 12015994
references: Nature. 2004 Jun 3;429(6991):496-7
references: 15175721
references: Curr Opin Biotechnol. 2004 Dec;15(6):599-606
references: 15560988
references: Kidney Int. 2004 Jun;65(6):2426-34
references: 15149356
references: Proteomics. 2006 Oct;6(20):5615-27
references: 16991199
references: Mass Spectrom Rev. 2005 Mar-Apr;24(2):126-34
references: 15389861
references: Proteomics. 2006 Nov;6(22):5903-14
references: 17051648
references: Proc Natl Acad Sci U S A. 2005 Jul 5;102(27):9463-8
references: 15983376
references: J Am Soc Mass Spectrom. 2005 Aug;16(8):1207-20
references: 15979338
references: Electrophoresis. 2006 Jun;27(11):2111-25
references: 16645980
references: Kidney Int. 2006 Apr;69(8):1471-6
references: 16501490
references: Mass Spectrom Rev. 2003 Jan-Feb;22(1):57-77
references: 12768604
references: Electrophoresis. 2004 Jul;25(14):2257-81
references: 15274009
references: Mol Cell Proteomics. 2006 Jan;5(1):14-25
references: 16236702
references: FEBS Lett. 2003 Dec 4;555(2):358-62
references: 14644442
references: Electrophoresis. 2001 Aug;22(14):2898-902
references: 11565785
references: J Biol Chem. 2005 May 13;280(19):19136-45
references: 15728186
references: Mol Cell Proteomics. 2006 Jan;5(1):53-6
references: 16272560
references: Toxicol Pathol. 2005;33(3):343-55
references: 15805072
references: Proteomics. 2005 Jun;5(9):2381-4
references: 15880814
references: Biochem Biophys Res Commun. 2002 Feb 1;290(4):1328-35
references: 11812009
references: Genome Biol. 2006;7(9):R80
references: 16948836
references: Rapid Commun Mass Spectrom. 2004;18(19):2365-6
references: 15384161
references: Electrophoresis. 2005 Apr;26(7-8):1500-12
references: 15765480