Analysis of the human urine endogenous peptides by nanoparticle extraction and mass spectrometry identification

Analytica Chimica Acta

Volumn 829, Issue , 2014, Pages 40-47

  Yang, Xiaomin ^a   Hu, Lianghai ^a,b   Ye, Mingliang ^b   Zou, Hanfa ^b  

^a JILIN UNIVERSITY   (China)

^b DALIAN INSTITUTE OF CHEMICAL PHYSICS   (China)

Author keywords

Biomarker; Human urine; Nanoparticle; Peptidomics; Proteomics; Two dimensional

Indexed keywords

BIOMARKERS; EXTRACTION; MASS SPECTROMETRY; MOLECULAR BIOLOGY; MOLECULAR WEIGHT; NANOPARTICLES; PEPTIDES; TWO DIMENSIONAL;

BIO-MARKER DISCOVERY; HIGH MOLECULAR WEIGHT PROTEIN; HUMAN URINE; ORDERED MESOPOROUS SILICAS; ORGANIC METABOLITES; PEPTIDE DISTRIBUTIONS; PEPTIDOMICS; PROTEOMICS;

BODY FLUIDS;

NANOPARTICLE; PEPTIDE; PROTEOME; SILICON DIOXIDE; BIOLOGICAL MARKER;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; FEMALE; GEL PERMEATION CHROMATOGRAPHY; HUMAN; HYDROPHOBICITY; MALE; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR WEIGHT; PARTICLE SIZE; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROCESS DEVELOPMENT; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; SEPARATION TECHNIQUE; TANDEM MASS SPECTROMETRY; URINALYSIS; CHEMISTRY; GEL CHROMATOGRAPHY; ISOLATION AND PURIFICATION; POROSITY; REVERSED PHASE LIQUID CHROMATOGRAPHY; URINE;

BIOLOGICAL MARKERS; CHROMATOGRAPHY, GEL; CHROMATOGRAPHY, REVERSE-PHASE; HUMANS; NANOPARTICLES; PEPTIDES; POROSITY; PROTEOME; SILICON DIOXIDE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84900990297     PISSN: 00032670     EISSN: 18734324     Source Type: Journal    
DOI: 10.1016/j.aca.2014.04.040     Document Type: Article

References (57)

1. Gonzalez-Buitrago J.M., Ferreira L., Lorenzo I. Urinary proteomics. Clinica Chimica Acta 2007, 375:49-56.
2. Siwy J., Mullen W., Golovko I., Franke J., Zuerbig P. Human urinary peptide database for multiple disease biomarker discovery. Proteomics Clinical Applications 2011, 5:367-374.
3. Frantzi M., Zoidakis J., Papadopoulos T., Zuerbig P., Katafigiotis I., Stravodimos K., Lazaris A., Giannopoulou I., Ploumidis A., Mischak H., Mullen W., Vlahou A. IMAC fractionation in combination with LC-MS reveals H2B and NIF-1 peptides as potential bladder cancer biomarkers. Journal of Proteome Research 2013, 12:3969-3979.
4. Vitzthum F., Behrens F., Anderson N.L., Shaw J.H. Proteomics: from basic research to diagnostic application. A review of requirements and needs. Journal of Proteome Research 2005, 4:1086-1097.
5. Tyan Y.C., Guo H.R., Liu C.Y., Liao P.C. Proteomic profiling of human urinary proteome using nano-high performance liquid chromatography/electrospray ionization tandem mass spectrometry. Analytica Chimica Acta 2006, 579:158-176.
6. Sun W., Li F.X., Wu S.Z., Wang X.R., Zheng D.X., Wang J., Gao Y.H. Human urine proteome analysis by three separation approaches. Proteomics 2005, 5:4994-5001.
7. Hong S.S., Kwon S.W. Profiling of urinary proteins by nano-high performance liquid chromatography/tandem mass spectrometry. Journal of Liquid Chromatography & Related Technologies 2005, 28:805-822.
8. Chen W.H., Lee S.C., Sabu S., Fang H.C., Chung S.C., Han C.C., Chang H.C. Solid-phase extraction and elution on diamond (SPEED): a fast and general platform for proteome analysis with mass spectrometry. Analytical Chemistry 2006, 78:4228-4234.
9. Pang J.X., Ginanni N., Dongre A.R., Hefta S.A., Opiteck G.J. Biomarker discovery in urine by proteomics. Journal of Proteome Research 2002, 1:161-169.
10. Thongboonkerd V., Chutipongtanate S., Kanlaya R. Systematic evaluation of sample preparation methods for gel-based human urinary proteomics: quantity, quality, and variability. Journal of Proteome Research 2006, 5:183-191.
11. Ru Q.H.C., Katenhusen R.A., Zhu L., Silberman J., Yang S., Orchard T.J., Brzeski H., Liebman M., Ellsworth D.L. Proteomic profiling of human urine using multi-dimensional protein identification technology. Journal of Chromatography A 2006, 1111:166-174.
12. Pieper R., Gatlin C.L., McGrath A.M., Makusky A.J., Mondal M., Seonarain M., Field E., Schatz C.R., Estock M.A., Ahmed N., Anderson N.G., Steiner S. Characterization of the human urinary proteome: a method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots. Proteomics 2004, 4:1159-1174.
13. Adachi J., Kumar C., Zhang Y.L., Olsen J.V., Mann M. The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biology 2006, 7(9). R80.
14. Schulz-Knappe P., Zucht H.D., Heine C., Jurgens M., Hess R., Schrader M. Peptidomics: the comprehensive analysis of peptides in complex biological mixtures. Combinatorial Chemistry & High Throughput Screening 2001, 4:207-217.
15. Schrader M., Schulz-Knappe P. Peptidomics technologies for human body fluids. Trends in Biotechnology 2001, 19:S55-S60.
16. Tammen H., Schulte L., Hess R., Menzel C., Kellmann M., Mohring T., Schulz-Knappe P. Peptidomic analysis of human blood specimens: comparison between plasma specimens and serum by differential peptide display. Proteomics 2005, 5:3414-3422.
17. Hortin G.L., Shen R.F., Martin B.M., Remaley A.T. Diverse range of small peptides associated with high-density lipoprotein. Biochemical and Biophysical Research Communications 2006, 340:909-915.
18. Geho D.H., Liotta L.A., Petricoin E.F., Zhao W.D., Araujo R.P. The amplified peptidome: the new treasure chest of candidate biomarkers. Current Opinion in Chemical Biology 2006, 10:50-55.
19. Soloviev M., Finch P. Peptidomics: bridging the gap between proteome and metabolome. Proteomics 2006, 6:744-747.
20. Tirumalai R.S., Chan K.C., Prieto D.A., Issaq H.J., Conrads T.P., Veenstra T.D. Characterization of the low molecular weight human serum proteome. Molecular & Cellular Proteomics 2003, 2:1096-1103.
21. Zheng X.Y., Baker H., Hancock W.S. Analysis of the low molecular weight serum peptidome using ultrafiltration and a hybrid ion trap-Fourier transform mass spectrometer. Journal of Chromatography A 2006, 1120:173-184.
22. Liotta L.A., Ferrari M., Petricoin E. Written in blood. Nature 2003, 425:905.
23. Novak K. Biomarkers: taking out the trash. Nature Reviews Cancer 2006, 6:92.
24. Petricoin E.F., Belluco C., Araujo R.P., Liotta L.A. The blood peptidome: a higher dimension of information content for cancer biomarker discovery. Nature Reviews Cancer 2006, 6:961-967.
25. Liotta L.A., Petricoin E.F. Serum peptidome for cancer detection: spinning biologic trash into diagnostic gold. Journal of Clinical Investigation 2006, 116:26-30.
26. Petricoin E.F., Ardekani A.M., Hitt B.A., Levine P.J., Fusaro V.A., Steinberg S.M., Mills G.B., Simone C., Fishman D.A., Kohn E.C., Liotta L.A. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002, 359:572-577.
27. Villanueva J., Shaffer D.R., Philip J., Chaparro C.A., Erdjument-Bromage H., Olshen A.B., Fleisher M., Lilja H., Brogi E., Boyd J., Sanchez-Carbayo M., Holland E.C., Cordon-Cardo C., Scher H.I., Tempst P. Differential exoprotease activities confer tumor-specific serum peptidome patterns. Journal of Clinical Investigation 2006, 116:271-284.
28. Wittke S., Fliser D., Haubitz M., Bartel S., Krebs R., Hausadel F., Hillmann M., Golovko I., Koester P., Haller H., Kaiser T., Mischak H., Weissinger E.M. Determination of peptides and proteins in human urine with capillary electrophoresis-mass spectrometry, a suitable tool for the establishment of new diagnostic markers. Journal of Chromatography A 2003, 1013:173-181.
29. Jurgens M., Appel A., Heine G., Neitz S., Menzel C., Tammen H., Zucht H.D. Towards characterization of the human urinary peptidome. Combinatorial Chemistry & High Throughput Screening 2005, 8:757-765.
30. Heine G., Raida M., Forssmann W.G. Mapping of peptides and protein fragments in human urine using liquid chromatography mass spectrometry. Journal of Chromatography A 1997, 776:117-124.
31. Cutillas P.R., Norden A.G.W., Cramer R., Burlingame A.L., Unwin R.J. Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome. Clinical Science 2003, 104:483-490.
32. Greive K.A., Balazs N.D.H., Comper W.D. Protein fragments in urine have been considerably underestimated by various protein assays. Clinical Chemistry 2001, 47:1717-1719.
33. Strong K.J., Osicka T.M., Comper W.D. Urinary-peptide excretion by patients with and volunteers without diabetes. Journal of Laboratory and Clinical Medicine 2005, 145:239-246.
34. Gaspari M., Cheng M.M.C., Terracciano R., Liu X.W., Nijdam A.J., Vaccari L., di Fabrizio E., Petricoin E.F., Liotta L.A., Cuda G., Venuta S., Ferrari M. Nanoporous surfaces as harvesting agents for mass spectrometric analysis of peptides in human plasma. Journal of Proteome Research 2006, 5:1261-1266.
35. Terracciano R., Gaspari M., Testa F., Pasqua L., Tagliaferri P., Cheng M.M.C., Nijdam A.J., Petricoin E.F., Liotta L.A., Cuda G., Ferrari M., Venuta S. Selective binding and enrichment for low-molecular weight biomarker molecules in human plasma after exposure to nanoporous silica particles. Proteomics 2006, 6:3243-3250.
36. Kresge C.T., Leonowicz M.E., Roth W.J., Vartuli J.C., Beck J.S. Ordered mesoporous molecular-sieves synthesized by a liquid-crystal template mechanism. Nature 1992, 359:710-712.
37. Zhao D.Y., Feng J.L., Huo Q.S., Melosh N., Fredrickson G.H., Chmelka B.F., Stucky G.D. Triblock copolymer syntheses of mesoporous silica with periodic 50 to 300 angstrom pores. Science 1998, 279:548-552.
38. Yiu H.H.P., Botting C.H., Botting N.P., Wright P.A. Size selective protein adsorption on thiol-functionalised SBA-15 mesoporous molecular sieve. Physical Chemistry Chemical Physics 2001, 3:2983-2985.
39. Tian R.J., Zhang H., Ye M.L., Jiang X.G., Hu L.H., Li X., Bao X.H., Zou H.F. Selective extraction of peptides from human plasma by highly ordered mesoporous silica particles for peptidome analysis. Angewandte Chemie International Edition 2007, 46:962-965.
40. 3+-immobilized mesoporous nanoparticles of MCM-41 for MALDI and nano-LC-MS/MS analysis. Journal of Proteome Research 2006, 5:3114-3124.
41. Jiang X.N., Ye M.L., Zou H.F. Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics. BMC Bioinformatics 2007, 8(323):1-12.
42. Gudehithlu K.P., Pegoraro A.A., Dunea G., Arruda J.A.L., Singh A.K. Degradation of albumin by the renal proximal tubule cells and the subsequent fate of its fragments. Kidney International 2004, 65:2113-2122.
43. Singh A., Gudehithlu K.P., Le G., Litbarg N.O., Khalili V., Vernik J., Hart P., Arruda J.A.L., Dunea G. Decreased urinary peptide excretion in patients with renal disease. American Journal of Kidney Diseases 2004, 44:1031-1038.
44. Schaub S., Wilkins J.A., Antonovici M., Krokhin O., Weiler T., Rush D., Nickerson P. Proteomic-based identification of cleaved urinary beta 2-microglobulin as a potential marker for acute tubular injury in renal allografts. American Journal of Transplantation 2005, 5:729-738.
45. Shu Z.S., Jiang Y.S. Research development of urinary trypsin inhibitor. World Clinical Drugs 1991, 12:203-205.
46. Richter R., Schulz-Knappe P., Schrader M., Standker L., Jurgens M., Tammen H., Forssmann W.G. Composition of the peptide fraction in human blood plasma: database of circulating human peptides. Journal of Chromatography B 1999, 726:25-35.
47. Tian R.J., Ye M.L., Hu L.H., Li X., Zou H.F. Selective extraction of peptides in acidic human plasma by porous silica nanoparticles for peptidome analysis with 2-D LC-MS/MS. Journal of Separation Science 2007, 30:2204-2209.
48. Hu L.H., Li X., Jiang X.N., Jiang X.G., Zhou H.J., Kong L., Ye M.L., Zou H.F. Comprehensive peptidome analysis of mouse livers by size exclusion chromatography prefractionation and nanoLC-MS/MS identification. Journal of Proteome Research 2007, 6:801-808.
49. Mohring T., Kellmann M., Jurgens M., Schrader M. Top-down identification of endogenous peptides up to 9kDa in cerebrospinal fluid and brain tissue by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry. Journal of Mass Spectrometry 2005, 40:214-226.
50. Wu S.L., Jardine I., Hancock W.S., Karger B.L. A new and sensitive on-line liquid chromatography/mass spectrometric approach for top-down protein analysis: the comprehensive analysis of human growth hormone in an E. coli lysate using a hybrid linear ion trap/Fourier transform ion cyclotron resonance mass spectrometer. Rapid Communications in Mass Spectrometry 2004, 18:2201-2207.
51. Rawlings N.D., Morton F.R., Barrett A.J. MEROPS: the peptidase database. Nucleic Acids Research 2006, 34:D270-D272.
52. Klein J., Eales J., Zuerbig P., Vlahou A., Mischak H., Stevens R. Proteasix: a tool for automated and large-scale prediction of proteases involved in naturally occurring peptide generation. Proteomics 2013, 13:1077-1082.
53. Yamamoto H., Yamada T., Itoh Y. Probable involvement of cathepsin D in the degradation of beta(2)-microglobulin in acidic urine. Clinical Chemistry and Laboratory Medicine 2000, 38:495-499.
54. Muchmore A.V., Decker J.M. Uromodulin: a unique 85-kilodalton immunosuppressive glycoprotein isolated from urine of pregnant women. Science 1985, 229:479-481.
55. Hart T.C., Gorry M.C., Hart P.S., Woodard A.S., Shihabi Z., Sandhu J., Shirts B., Xu L., Zhu H., Barmada M.M., Bleyer A.J. Mutations of the UMOD gene are responsible for medullary cystic kidney disease 2 and familial juvenile hyperuricaemic nephropathy. Journal of Medical Genetics 2002, 39:882-892.
56. Schittek B., Hipfel R., Sauer B., Bauer J., Kalbacher H., Stevanovic S., Schirle M., Schroeder K., Blin N., Meier F., Rassner G., Garbe C. Dermcidin: a novel human antibiotic peptide secreted by sweat glands. Nature Immunology 2001, 2:1133-1137.
57. Kimata H. Increase in dermcidin-derived peptides in sweat of patients with atopic eczema caused by a humorous video. Journal of Psychosomatic Research 2007, 62:57-79.