Longitudinal Urinary Protein Variability in Participants of the Space Flight Simulation Program

Journal of Proteome Research

Volumn 15, Issue 1, 2016, Pages 114-124

  Khristenko, Nina A ^a,b   Larina, Irina M ^c   Domon, Bruno ^a,b  

^a LUXEMBOURG INSTITUTE OF HEALTH   (Luxembourg)

^b UNIVERSITY OF LUXEMBOURG   (Luxembourg)

^c INSTITUTE OF BIOMEDICAL PROBLEMS   (Russian Federation)

Author keywords

normal protein concentration; quantification; spectral library; Targeted proteomics; urine

Indexed keywords

PROTEIN; PEPTIDE FRAGMENT; PROTEOME;

AMINO ACID SEQUENCE; ARTICLE; COLORIMETRY; COSMONAUT; ELECTROPHORESIS; ELUTION; HOMEOSTASIS; HUMAN; ION MONITORING; MASS SPECTROMETER; MASS SPECTROMETRY; MICROGRAVITY; NORMAL HUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN URINE LEVEL; PROTEOMICS; SPACE FLIGHT; URINALYSIS; URINE VOLUME; ADULT; CHEMISTRY; LONGITUDINAL STUDY; MALE; METABOLISM; MOLECULAR GENETICS; PROCEDURES; PROTEIN DEGRADATION; STANDARD; STANDARDS; TANDEM MASS SPECTROMETRY;

ADULT; AMINO ACID SEQUENCE; HUMANS; LONGITUDINAL STUDIES; MALE; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEOLYSIS; PROTEOME; PROTEOMICS; REFERENCE STANDARDS; SPACE FLIGHT; TANDEM MASS SPECTROMETRY; URINALYSIS;

EID: 84953277779     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00594     Document Type: Article

References (47)

1. Nagaraj, N.; Mann, M. Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome J. Proteome Res. 2011, 10 (2) 637-45 10.1021/pr100835s
2. He, W.; Huang, C.; Luo, G.; Pra, I. D.; Feng, J.; Chen, W.; Ma, L.; Wang, Y.; Chen, X.; Tan, J.; Zhang, X.; Armato, U.; Wu, J. A stable panel comprising 18 urinary proteins in the human healthy population Proteomics 2012, 12 (7) 1059-72 10.1002/pmic.201100400
3. Pirmoradian, M.; Budamgunta, H.; Chingin, K.; Zhang, B.; Astorga-Wells, J.; Zubarev, R. A. Rapid and deep human proteome analysis by single-dimension shotgun proteomics Mol. Cell. Proteomics 2013, 12 (11) 3330-8 10.1074/mcp.O113.028787
4. Tabb, D. L.; Vega-Montoto, L.; Rudnick, P. A.; Variyath, A. M.; Ham, A. J.; Bunk, D. M.; Kilpatrick, L. E.; Billheimer, D. D.; Blackman, R. K.; Cardasis, H. L.; Carr, S. A.; Clauser, K. R.; Jaffe, J. D.; Kowalski, K. A.; Neubert, T. A.; Regnier, F. E.; Schilling, B.; Tegeler, T. J.; Wang, M.; Wang, P.; Whiteaker, J. R.; Zimmerman, L. J.; Fisher, S. J.; Gibson, B. W.; Kinsinger, C. R.; Mesri, M.; Rodriguez, H.; Stein, S. E.; Tempst, P.; Paulovich, A. G.; Liebler, D. C.; Spiegelman, C. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry J. Proteome Res. 2010, 9 (2) 761-76 10.1021/pr9006365
5. Selevsek, N.; Chang, C. Y.; Gillet, L. C.; Navarro, P.; Bernhardt, O. M.; Reiter, L.; Cheng, L. Y.; Vitek, O.; Aebersold, R. Reproducible and Consistent Quantification of the Saccharomyces cerevisiae Proteome by SWATH-mass spectrometry Mol. Cell. Proteomics 2015, 14 (3) 739-49 10.1074/mcp.M113.035550
6. Liu, Y.; Huttenhain, R.; Surinova, S.; Gillet, L. C.; Mouritsen, J.; Brunner, R.; Navarro, P.; Aebersold, R. Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS Proteomics 2013, 13 (8) 1247-56 10.1002/pmic.201200417
7. Domon, B.; Aebersold, R. Options and considerations when selecting a quantitative proteomics strategy Nat. Biotechnol. 2010, 28 (7) 710-21 10.1038/nbt.1661
8. Ellis, M. J.; Gillette, M.; Carr, S. A.; Paulovich, A. G.; Smith, R. D.; Rodland, K. K.; Townsend, R. R.; Kinsinger, C.; Mesri, M.; Rodriguez, H.; Liebler, D. C. Clinical Proteomic Tumor Analysis, C., Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium Cancer Discovery 2013, 3 (10) 1108-12 10.1158/2159-8290.CD-13-0219
9. Chen, Y. T.; Chen, H. W.; Domanski, D.; Smith, D. S.; Liang, K. H.; Wu, C. C.; Chen, C. L.; Chung, T.; Chen, M. C.; Chang, Y. S.; Parker, C. E.; Borchers, C. H.; Yu, J. S. Multiplexed quantification of 63 proteins in human urine by multiple reaction monitoring-based mass spectrometry for discovery of potential bladder cancer biomarkers J. Proteomics 2012, 75 (12) 3529-45 10.1016/j.jprot.2011.12.031
10. Gallien, S.; Duriez, E.; Crone, C.; Kellmann, M.; Moehring, T.; Domon, B. Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer Mol. Cell. Proteomics 2012, 11 (12) 1709-23 10.1074/mcp.O112.019802
11. Peterson, A. C.; Russell, J. D.; Bailey, D. J.; Westphall, M. S.; Coon, J. J. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics Mol. Cell. Proteomics 2012, 11 (11) 1475-88 10.1074/mcp.O112.020131
12. Gallien, S.; Peterman, S.; Kiyonami, R.; Souady, J.; Duriez, E.; Schoen, A.; Domon, B. Highly multiplexed targeted proteomics using precise control of peptide retention time Proteomics 2012, 12 (8) 1122-33 10.1002/pmic.201100533
13. Gallien, S.; Bourmaud, A.; Kim, S. Y.; Domon, B. Technical considerations for large-scale parallel reaction monitoring analysis J. Proteomics 2014, 100, 147-59 10.1016/j.jprot.2013.10.029
14. Carr, S. A.; Abbatiello, S. E.; Ackermann, B. L.; Borchers, C.; Domon, B.; Deutsch, E. W.; Grant, R. P.; Hoofnagle, A. N.; Huttenhain, R.; Koomen, J. M.; Liebler, D. C.; Liu, T.; MacLean, B.; Mani, D. R.; Mansfield, E.; Neubert, H.; Paulovich, A. G.; Reiter, L.; Vitek, O.; Aebersold, R.; Anderson, L.; Bethem, R.; Blonder, J.; Boja, E.; Botelho, J.; Boyne, M.; Bradshaw, R. A.; Burlingame, A. L.; Chan, D.; Keshishian, H.; Kuhn, E.; Kinsinger, C.; Lee, J. S.; Lee, S. W.; Moritz, R.; Oses-Prieto, J.; Rifai, N.; Ritchie, J.; Rodriguez, H.; Srinivas, P. R.; Townsend, R. R.; Van Eyk, J.; Whiteley, G.; Wiita, A.; Weintraub, S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach Mol. Cell. Proteomics 2014, 13 (3) 907-17 10.1074/mcp.M113.036095
15. Desiere, F.; Deutsch, E. W.; King, N. L.; Nesvizhskii, A. I.; Mallick, P.; Eng, J.; Chen, S.; Eddes, J.; Loevenich, S. N.; Aebersold, R. The PeptideAtlas project Nucleic Acids Res. 2006, 34, D655-8 10.1093/nar/gkj040
16. Kim, Y. J.; Gallien, S.; van Oostrum, J.; Domon, B. Targeted proteomics strategy applied to biomarker evaluation Proteomics: Clin. Appl. 2013, 7 (11-12) 739-47 10.1002/prca.201300070
17. Larina, I. M.; Pastushkova, L.; Tiys, E. S.; Kireev, K. S.; Kononikhin, A. S.; Starodubtseva, N. L.; Popov, I. A.; Custaud, M. A.; Dobrokhotov, I. V.; Nikolaev, E. N.; Kolchanov, N. A.; Ivanisenko, V. A. Permanent proteins in the urine of healthy humans during the Mars-500 experiment J. Bioinf. Comput. Biol. 2015, 13 (1) 1540001 10.1142/S0219720015400016
18. Court, M.; Selevsek, N.; Matondo, M.; Allory, Y.; Garin, J.; Masselon, C. D.; Domon, B. Toward a standardized urine proteome analysis methodology Proteomics 2011, 11 (6) 1160-71 10.1002/pmic.201000566
19. Selevsek, N.; Matondo, M.; Sanchez Carbayo, M.; Aebersold, R.; Domon, B. Systematic quantification of peptides/proteins in urine using selected reaction monitoring Proteomics 2011, 11 (6) 1135-47 10.1002/pmic.201000599
20. Khristenko, N.; Domon, B. Quantification of proteins in urine samples using targeted mass spectrometry methods Methods Mol. Biol. 2015, 1243, 207-20 10.1007/978-1-4939-1872-0-12
21. Gallien, S.; Kim, S. Y.; Domon, B. Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring Mol. Cell. Proteomics 2015, 14, 1630-44 10.1074/mcp.O114.043968
22. MacLean, B.; Tomazela, D. M.; Shulman, N.; Chambers, M.; Finney, G. L.; Frewen, B.; Kern, R.; Tabb, D. L.; Liebler, D. C.; MacCoss, M. J. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments Bioinformatics 2010, 26 (7) 966-8 10.1093/bioinformatics/btq054
23. Chang, C. Y.; Picotti, P.; Huttenhain, R.; Heinzelmann-Schwarz, V.; Jovanovic, M.; Aebersold, R.; Vitek, O. Protein significance analysis in selected reaction monitoring (SRM) measurements Mol. Cell. Proteomics 2012, 11 (4) M111.014662 10.1074/mcp.M111.014662
24. Callister, S. J.; Barry, R. C.; Adkins, J. N.; Johnson, E. T.; Qian, W. J.; Webb-Robertson, B. J.; Smith, R. D.; Lipton, M. S. Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics J. Proteome Res. 2006, 5 (2) 277-86 10.1021/pr050300l
25. Schafer, A.; von Toerne, C.; Becker, S.; Sarioglu, H.; Neschen, S.; Kahle, M.; Hauck, S. M.; Ueffing, M. Two-dimensional peptide separation improving sensitivity of selected reaction monitoring-based quantitative proteomics in mouse liver tissue: comparing off-gel electrophoresis and strong cation exchange chromatography Anal. Chem. 2012, 84 (20) 8853-62 10.1021/ac3023026
26. Nichols, A. M.; White, F. M. Manual validation of peptide sequence and sites of tyrosine phosphorylation from MS/MS spectra Methods Mol. Biol. 2009, 492, 143-60 10.1007/978-1-59745-493-3-8
27. Wang, X.; Li, Y.; Wu, Z.; Wang, H.; Tan, H.; Peng, J. JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy Mol. Cell. Proteomics 2014, 13, 3663-73 10.1074/mcp.O114.039586
28. Mann, M.; Wilm, M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags Anal. Chem. 1994, 66 (24) 4390-9 10.1021/ac00096a002
29. Ivanov, M. V.; Levitsky, L. I.; Lobas, A. A.; Panic, T.; Laskay, U. A.; Mitulovic, G.; Schmid, R.; Pridatchenko, M. L.; Tsybin, Y. O.; Gorshkov, M. V. Empirical multidimensional space for scoring peptide spectrum matches in shotgun proteomics J. Proteome Res. 2014, 13 (4) 1911-20 10.1021/pr401026y
30. Curran, T. G.; Bryson, B. D.; Reigelhaupt, M.; Johnson, H.; White, F. M. Computer aided manual validation of mass spectrometry-based proteomic data Methods 2013, 61 (3) 219-26 10.1016/j.ymeth.2013.03.004
31. 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
32. Gonzales, P. A.; Pisitkun, T.; Hoffert, J. D.; Tchapyjnikov, D.; Star, R. A.; Kleta, R.; Wang, N. S.; Knepper, M. A. Large-scale proteomics and phosphoproteomics of urinary exosomes J. Am. Soc. Nephrol. 2009, 20 (2) 363-79 10.1681/ASN.2008040406
33. Li, Q. R.; Fan, K. X.; Li, R. X.; Dai, J.; Wu, C. C.; Zhao, S. L.; Wu, J. R.; Shieh, C. H.; 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) 823-32 10.1002/rcm.4441
34. Marimuthu, A.; O'Meally, R. N.; Chaerkady, R.; Subbannayya, Y.; Nanjappa, V.; Kumar, P.; Kelkar, D. S.; Pinto, S. M.; Sharma, R.; Renuse, S.; Goel, R.; Christopher, R.; Delanghe, B.; Cole, R. N.; Harsha, H. C.; Pandey, A. A comprehensive map of the human urinary proteome J. Proteome Res. 2011, 10 (6) 2734-43 10.1021/pr2003038
35. Adachi, J.; Kumar, C.; Zhang, Y.; Olsen, J. V.; 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
36. Santucci, L.; Candiano, G.; Petretto, A.; Bruschi, M.; Lavarello, C.; Inglese, E.; Righetti, P. G.; Ghiggeri, G. M. From hundreds to thousands: widening the normal human Urinome (1) J. Proteomics 2015, 112, 53-62 10.1016/j.jprot.2014.07.021
37. Dalluge, J.; Vreuls, R.; van Iperen, D.; van Rijn, M.; Brinkman, U. A. T. Resistively heated gas chromatography coupled to quadrupole mass spectrometry J. Sep. Sci. 2002, 25, 608-14 10.1002/1615-9314(20020601)25:9<608::AID-JSSC608>3.0.CO;2-R
38. Nagaraj, N.; Kulak, N. A.; Cox, J.; Neuhauser, N.; Mayr, K.; Hoerning, O.; Vorm, O.; Mann, M. System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap Mol. Cell. Proteomics 2012, 11 (3) M111.013722 10.1074/mcp.M111.013722
39. Huttenhain, R.; Soste, M.; Selevsek, N.; Rost, H.; Sethi, A.; Carapito, C.; Farrah, T.; Deutsch, E. W.; Kusebauch, U.; Moritz, R. L.; Nimeus-Malmstrom, E.; Rinner, O.; Aebersold, R. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics Sci. Transl. Med. 2012, 4 (142) 142ra94 10.1126/scitranslmed.3003989
40. Strewe, C.; Muckenthaler, F.; Feuerecker, M.; Yi, B.; Rykova, M.; Kaufmann, I.; Nichiporuk, I.; Vassilieva, G.; Horl, M.; Matzel, S.; Schelling, G.; Thiel, M.; Morukov, B.; Chouker, A. Functional changes in neutrophils and psychoneuroendocrine responses during 105 days of confinement J. Appl. Physiol. 2015, 118 (9) 1122-7 10.1152/japplphysiol.00755.2014
41. Gemignani, A.; Piarulli, A.; Menicucci, D.; Laurino, M.; Rota, G.; Mastorci, F.; Gushin, V.; Shevchenko, O.; Garbella, E.; Pingitore, A.; Sebastiani, L.; Bergamasco, M.; L'Abbate, A.; Allegrini, P.; Bedini, R. How stressful are 105 days of isolation? Sleep EEG patterns and tonic cortisol in healthy volunteers simulating manned flight to Mars Int. J. Psychophysiol 2014, 93 (2) 211-9 10.1016/j.ijpsycho.2014.04.008
42. Gushin, V.; Shved, D.; Vinokhodova, A.; Vasylieva, G.; Nitchiporuk, I.; Ehmann, B.; Balazs, L. Some psychophysiological and behavioral aspects of adaptation to simulated autonomous Mission to Mars Acta Astronaut. 2012, 70, 52-57 10.1016/j.actaastro.2011.07.020
43. Schneider, S.; Brummer, V.; Carnahan, H.; Kleinert, J.; Piacentini, M. F.; Meeusen, R.; Struder, H. K. Exercise as a countermeasure to psycho-physiological deconditioning during long-term confinement Behav. Brain Res. 2010, 211 (2) 208-14 10.1016/j.bbr.2010.03.034
44. Hortin, G. L.; Sviridov, D.; Anderson, N. L. High-abundance polypeptides of the human plasma proteome comprising the top 4 logs of polypeptide abundance Clin. Chem. 2008, 54 (10) 1608-16 10.1373/clinchem.2008.108175
45. Zerefos, P. G.; 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
46. Worboys, J. D.; Sinclair, J.; Yuan, Y.; Jorgensen, C. Systematic evaluation of quantotypic peptides for targeted analysis of the human kinome Nat. Methods 2014, 11 (10) 1041-4 10.1038/nmeth.3072
47. Bouter, A.; Carmeille, R.; Gounou, C.; Bouvet, F.; Degrelle, S. A.; Evain-Brion, D.; Brisson, A. R. Review: Annexin-A5 and cell membrane repair Placenta 2015, 36, S43-9 10.1016/j.placenta.2015.01.193