Urinary proteomic and non-prefractionation quantitative phosphoproteomic analysis during pregnancy and non-pregnancy

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Zheng, Jianhua ^a   Liu, Liguo ^a   Wang, Jin ^a   Jin, Qi ^a  

^a INSTITUTE OF PATHOGEN BIOLOGY   (China)

Author keywords

Human urine; mTRAQ labeling; Pregnancy and non pregnancy; Proteomic profile; Quantitative phosphoproteomic analysis

Indexed keywords

PHOSPHOPEPTIDE; PHOSPHOPROTEIN;

ADULT; ARTICLE; CONTROLLED STUDY; DOWN REGULATION; FEMALE; GEL ELECTROPHORESIS; HUMAN; MASS SPECTROMETRY; MOLECULAR WEIGHT; NORMAL HUMAN; PREGNANCY; PREGNANT WOMAN; PROTEIN EXPRESSION; PROTEIN URINE LEVEL; PROTEOMICS; THIRD TRIMESTER PREGNANCY; UPREGULATION; URINALYSIS; VAGINAL DELIVERY;

ADULT; BIOLOGICAL MARKERS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; FEMALE; HUMANS; MASS SPECTROMETRY; PHOSPHOPROTEINS; PREGNANCY; PROTEIN BIOSYNTHESIS; PROTEOMICS; URINE;

EID: 84887359739     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-777     Document Type: Article

References (42)

1. Decramer S, de Peredo Gonzalez A, Breuil B, Mischak H, Monsarrat B, Bascands JL, Schanstra JP. Urine in clinical proteomics. Mol Cell Proteomics 2008, 7(10):1850-1862. 10.1074/mcp.R800001-MCP200, 18667409.
2. Li QR, Fan KX, Li RX, Dai J, Wu CC, Zhao SL, Wu JR, Shieh CH, Zeng R. A comprehensive and non-prefractionation on the protein level approach for the human urinary proteome: touching phosphorylation in urine. Rapid Commun Mass Spectrom 2010, 24(6):823-832. 10.1002/rcm.4441, 20187088.
3. Marimuthu A, O'Meally RN, Chaerkady R, Subbannayya Y, Nanjappa V, Kumar P, Kelkar DS, Pinto SM, Sharma R, Renuse S, et al. A comprehensive map of the human urinary proteome. J Proteome Res 2011, 10(6):2734-2743. 10.1021/pr2003038, 21500864.
4. Lee RS, Monigatti F, Briscoe AC, Waldon Z, Freeman MR, Steen H. Optimizing sample handling for urinary proteomics. J Proteome Res 2008, 7(9):4022-4030. 10.1021/pr800301h, 18662026.
5. Kentsis A, Monigatti F, Dorff K, Campagne F, Bachur R, Steen H. Urine proteomics for profiling of human disease using high accuracy mass spectrometry. Proteomics Clin Appl 2009, 3(9):1052-1061. 10.1002/prca.200900008, 2994589, 21127740.
6. 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 Biol 2006, 7(9):R80. 10.1186/gb-2006-7-9-r80, 1794545, 16948836.
7. Bakun M, Niemczyk M, Domanski D, Jazwiec R, Perzanowska A, Niemczyk S, Kistowski M, Fabijanska A, Borowiec A, Paczek L, et al. Urine proteome of autosomal dominant polycystic kidney disease patients. Clin Proteomics 2012, 9(1):13. 10.1186/1559-0275-9-13, 3607978, 23228063.
8. Castagna A, Cecconi D, Sennels L, Rappsilber J, Guerrier L, Fortis F, Boschetti E, Lomas L, Righetti PG. Exploring the hidden human urinary proteome via ligand library beads. J Proteome Res 2005, 4(6):1917-1930. 10.1021/pr050153r, 16335936.
9. Khan A, Packer NH. Simple urinary sample preparation for proteomic analysis. J Proteome Res 2006, 5(10):2824-2838. 10.1021/pr060305y, 17022654.
10. Kolla V, Jeno P, Moes S, Lapaire O, Hoesli I, Hahn S. Quantitative proteomic (iTRAQ) analysis of 1st trimester maternal plasma samples in pregnancies at risk for preeclampsia. J Biomed Biotechnol 2012, 2012:305964. 3335425, 22570525.
11. Pawson T, Nash P. Assembly of cell regulatory systems through protein interaction domains. Science 2003, 300(5618):445-452. 10.1126/science.1083653, 12702867.
12. Hu P, Shimoji S, Hart GW. Site-specific interplay between O-GlcNAcylation and phosphorylation in cellular regulation. FEBS Lett 2010, 584(12):2526-2538. 10.1016/j.febslet.2010.04.044, 20417205.
13. Hao P, Guo T, Sze SK. Simultaneous analysis of proteome, phospho- and glycoproteome of rat kidney tissue with electrostatic repulsion hydrophilic interaction chromatography. PLoS One 2011, 6(2):e16884. 10.1371/journal.pone.0016884, 3044146, 21373199.
14. Duan X, Young R, Straubinger RM, Page B, Cao J, Wang H, Yu H, Canty JM, Qu J. A straightforward and highly efficient precipitation/on-pellet digestion procedure coupled with a long gradient nano-LC separation and Orbitrap mass spectrometry for label-free expression profiling of the swine heart mitochondrial proteome. J Proteome Res 2009, 8(6):2838-2850. 10.1021/pr900001t, 2734143, 19290621.
15. Cristobal A, Hennrich ML, Giansanti P, Goerdayal SS, Heck AJ, Mohammed S. In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis. Analyst 2012, 137(15):3541-3548. 10.1039/c2an35445d, 22728655.
16. Kocher T, Swart R, Mechtler K. Ultra-high-pressure RPLC hyphenated to an LTQ-Orbitrap Velos reveals a linear relation between peak capacity and number of identified peptides. Anal Chem 2011, 83(7):2699-2704. 10.1021/ac103243t, 21388192.
17. Wittke S, Fliser D, Haubitz M, Bartel S, Krebs R, Hausadel F, Hillmann M, Golovko I, Koester P, Haller H, et al. Determination of peptides and proteins in human urine with capillary electrophoresis-mass spectrometry, a suitable tool for the establishment of new diagnostic markers. J Chromatogr A 2003, 1013(1-2):173-181.
18. Zhou L, Ying W, Han Y, Chen M, Yan Y, Li L, Zhu Z, Zheng Z, Jia W, Yang R, et al. A proteome reference map and virulence factors analysis of Yersinia pestis 91001. J Proteomics 2012, 75(3):894-907. 10.1016/j.jprot.2011.10.004, 22040741.
19. 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. 10.1002/pmic.201100212, 22140069.
20. Zerefos PG, Vougas K, Dimitraki P, Kossida S, Petrolekas A, Stravodimos K, Giannopoulos A, Fountoulakis M, Vlahou A. Characterization of the human urine proteome by preparative electrophoresis in combination with 2-DE. Proteomics 2006, 6(15):4346-4355. 10.1002/pmic.200500671, 16807940.
21. Smith G, Barratt D, Rowlinson R, Nickson J, Tonge R. Development of a high-throughput method for preparing human urine for two-dimensional electrophoresis. Proteomics 2005, 5(9):2315-2318. 10.1002/pmic.200401267, 15887186.
22. Oh J, Pyo JH, Jo EH, Hwang SI, Kang SC, Jung JH, Park EK, Kim SY, Choi JY, Lim J. Establishment of a near-standard two-dimensional human urine proteomic map. Proteomics 2004, 4(11):3485-3497. 10.1002/pmic.200401018, 15529407.
23. Kim KH, Moon MH. High speed two-dimensional protein separation without gel by isoelectric focusing-asymmetrical flow field flow fractionation: application to urinary proteome. J Proteome Res 2009, 8(9):4272-4278. 10.1021/pr900363s, 19653698.
24. Sun W, Li F, Wu S, Wang X, Zheng D, Wang J, Gao Y. Human urine proteome analysis by three separation approaches. Proteomics 2005, 5(18):4994-5001. 10.1002/pmic.200401334, 16281181.
25. Pisitkun T, Shen RF, Knepper MA. Identification and proteomic profiling of exosomes in human urine. Proc Natl Acad Sci U S A 2004, 101(36):13368-13373. 10.1073/pnas.0403453101, 516573, 15326289.
26. Gonzales PA, Pisitkun T, Hoffert JD, Tchapyjnikov D, Star RA, Kleta R, Wang NS, Knepper MA. Large-scale proteomics and phosphoproteomics of urinary exosomes. J Am Soc Nephrol 2009, 20(2):363-379. 10.1681/ASN.2008040406, 2637050, 19056867.
27. Zheng J, Liu L, Wei C, Leng W, Yang J, Li W, Wang J, Jin Q. A comprehensive proteomic analysis of Mycobacterium bovis bacillus Calmette-Guerin using high resolution Fourier transform mass spectrometry. J Proteomics 2012, 77:357-371.
28. Frese CK, Altelaar AF, Hennrich ML, Nolting D, Zeller M, Griep-Raming J, Heck AJ, Mohammed S. Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos. J Proteome Res 2011, 10(5):2377-2388. 10.1021/pr1011729, 21413819.
29. Chae JI, Kim J, Lee SG, Koh MW, Jeon YJ, Kim DW, Ko SM, Seo KS, Lee HK, Choi NJ, et al. Quantitative proteomic analysis of pregnancy-related proteins from peripheral blood mononuclear cells during pregnancy in pigs. Anim Reprod Sci 2012, 134(3-4):164-176.
30. Jedrychowski MP, Huttlin EL, Haas W, Sowa ME, Rad R, Gygi SP. Evaluation of HCD- and CID-type fragmentation within their respective detection platforms for murine phosphoproteomics. Mol Cell Proteomics 2011, 10(12):M111 009910. 3237076, 21917720.
31. Liu L, Liu X, Sun W, Li M, Gao Y. Unrestrictive identification of post-translational modifications in the urine proteome without enrichment. Proteome Sci 2013, 11(1):1. 10.1186/1477-5956-11-1, 3585864, 23317149.
32. Dickson IR, Poole AR, Veis A. Localisation of plasma alpha2HS glycoprotein in mineralising human bone. Nature 1975, 256(5516):430-432. 10.1038/256430a0, 49853.
33. Haglund AC, Ek B, Ek P. Phosphorylation of human plasma alpha2-Heremans-Schmid glycoprotein (human fetuin) in vivo. Biochem J 2001, 357(Pt 2):437-445. 1221970, 11439093.
34. Kalabay L, Cseh K, Pajor A, Baranyi E, Csakany GM, Melczer Z, Speer G, Kovacs M, Siller G, Karadi I, et al. Correlation of maternal serum fetuin/alpha2-HS-glycoprotein concentration with maternal insulin resistance and anthropometric parameters of neonates in normal pregnancy and gestational diabetes. Eur J Endocrinol 2002, 147(2):243-248. 10.1530/eje.0.1470243, 12153747.
35. Li P, Qian J, Yu G, Chen Y, Liu K, Li J, Wang J. Down-regulated SPARCL1 is associated with clinical significance in human gastric cancer. J Surg Oncol 2012, 105(1):31-37. 10.1002/jso.22025, 22161898.
36. Esposito I, Kayed H, Keleg S, Giese T, Sage EH, Schirmacher P, Friess H, Kleeff J. Tumor-suppressor function of SPARC-like protein 1/Hevin in pancreatic cancer. Neoplasia 2007, 9(1):8-17. 10.1593/neo.06646, 1803032, 17325739.
37. Turtoi A, Musmeci D, Naccarato AG, Scatena C, Ortenzi V, Kiss R, Murtas D, Patsos G, Mazzucchelli G, De Pauw E, et al. Sparc-like protein 1 is a new marker of human glioma progression. J Proteome Res 2012, 11(10):5011-5021. 10.1021/pr3005698, 22909274.
38. Johnson GA, Burghardt RC, Joyce MM, Spencer TE, Bazer FW, Pfarrer C, Gray CA. Osteopontin expression in uterine stroma indicates a decidualization-like differentiation during ovine pregnancy. Biol Reprod 2003, 68(6):1951-1958.
39. Christensen B, Petersen TE, Sorensen ES. Post-translational modification and proteolytic processing of urinary osteopontin. Biochem J 2008, 411(1):53-61. 10.1042/BJ20071021, 18072945.
40. Christensen B, Nielsen MS, Haselmann KF, Petersen TE, Sorensen ES. Post-translationally modified residues of native human osteopontin are located in clusters: identification of 36 phosphorylation and five O-glycosylation sites and their biological implications. Biochem J 2005, 390(Pt 1):285-292. 1184582, 15869464.
41. Zheng J, Ren X, Wei C, Yang J, Hu Y, Liu L, Xu X, Wang J, Jin Q. Analysis of the secretome and identification of novel constituents from culture filtrate of bacillus Calmette-Guerin using high-resolution mass spectrometry. Mol Cell Proteomics 2013, 12(8):2081-2095. 10.1074/mcp.M113.027318, 23616670.
42. Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008, 26(12):1367-1372. 10.1038/nbt.1511, 19029910.