NeuCode labels for relative protein quantification

Molecular and Cellular Proteomics

Volumn 13, Issue 9, 2014, Pages 2503-2512

  Merrill, Anna E ^a   Hebert, Alexander S ^a   MacGilvray, Matthew E ^a   Rose, Christopher M ^a   Bailey, Derek J ^a   Bradley, Joel C ^b   Wood, William W ^b   El Masri, Marwan ^b   Westphall, Michael S ^a   Gasch, Audrey P ^a   Coon, Joshua J ^a,c  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b CAMBRIDGE ISOTOPE LABORATORIES INC   (United States)

^c UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LYSINE; PROTEOME; SACCHAROMYCES CEREVISIAE PROTEIN; SODIUM CHLORIDE;

AMINO ACID SEQUENCE; AMINO ACID SYNTHESIS; ARTICLE; CELL PROLIFERATION; CHEMICAL LABELING; CONTROLLED STUDY; ENVIRONMENTAL STRESS; LIMIT OF QUANTITATION; MEASUREMENT ACCURACY; NEUTRON ENCODING; NONHUMAN; OPTICAL RESOLUTION; OSMOTIC STRESS; QUALITY CONTROL; QUANTITATIVE ANALYSIS; SALT STRESS; TANDEM MASS SPECTROMETRY; UPREGULATION; YEAST CELL; DRUG EFFECTS; METABOLISM; PHYSIOLOGICAL STRESS; PHYSIOLOGY; PROCEDURES; PROTEOMICS;

LYSINE; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE PROTEINS; SODIUM CHLORIDE; STRESS, PHYSIOLOGICAL;

EID: 84907221170     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M114.040287     Document Type: Article

References (54)

1. Altelaar, A. F., Munoz, J., and Heck, A. J. (2013) Next-generation proteomics: towards an integrative view of proteome dynamics. Nat. Rev. Genet. 14, 35-48
2. Ahmad, Y., and Lamond, A. I. (2014) A perspective on proteomics in cell biology. Trends Cell Biol. 24, 257-264
3. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999
4. Washburn, M. P., Wolters, D., and Yates, J. R., 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247
5. Syka, J. E., Marto, J. A., Bai, D. L., Horning, S., Senko, M. W., Schwartz, J. C., Ueberheide, B., Garcia, B., Busby, S., Muratore, T., Shabanowitz, J., and Hunt, D. F. (2004) Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J. Proteome Res. 3, 621-626
6. Jiang, H., and English, A. M. (2002) Quantitative analysis of the yeast proteome by incorporation of isotopically labeled leucine. J. Proteome Res. 1, 345-350
7. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386
8. Zhu, H., Pan, S., Gu, S., Bradbury, E. M., and Chen, X. (2002) Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun. Mass Spectrom. 16, 2115-2123
9. Molina, H., Yang, Y., Ruch, T., Kim, J. W., Mortensen, P., Otto, T., Nalli, A., Tang, Q. Q., Lane, M. D., Chaerkady, R., and Pandey, A. (2009) Temporal profiling of the adipocyte proteome during differentiation using a fiveplex SILAC based strategy. J. Proteome Res. 8, 48-58
10. Tzouros, M., Golling, S., Avila, D., Lamerz, J., Berrera, M., Ebeling, M., Langen, H., and Augustin, A. (2013) Development of a 5-plex SILAC method tuned for the quantitation of tyrosine phosphorylation dynamics. Mol. Cell. Proteomics 12, 3339-3349
11. Thompson, A., Schafer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., Neumann, T., Johnstone, R., Mohammed, A. K., and Hamon, C. (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75, 1895-1904
12. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., Purkayastha, S., Juhasz, P., Martin, S., Bartlet-Jones, M., He, F., Jacobson, A., and Pappin, D. J. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154-1169
13. McAlister, G. C., Huttlin, E. L., Haas, W., Ting, L., Jedrychowski, M. P., Rogers, J. C., Kuhn, K., Pike, I., Grothe, R. A., Blethrow, J. D., and Gygi, S. P. (2012) Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses. Anal. Chem. 84, 7469-7478
14. Werner, T., Becher, I., Sweetman, G., Doce, C., Savitski, M. M., and Bantscheff, M. (2012) High-resolution enabled TMT 8-plexing. Anal. Chem. 84, 7188-7194
15. Ow, S. Y., Salim, M., Noirel, J., Evans, C., Rehman, I., and Wright, P. C. (2009) iTRAQ underestimation in simple and complex mixtures: "the good, the bad and the ugly." J. Proteome Res. 8, 5347-5355
16. Wenger, C. D., Lee, M. V., Hebert, A. S., McAlister, G. C., Phanstiel, D. H., Westphall, M. S., and Coon, J. J. (2011) Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nat. Methods 8, 933-935
17. Ting, L., Rad, R., Gygi, S. P., and Haas, W. (2011) MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat. Methods 8, 937-940
18. Hebert, A. S., Merrill, A. E., Bailey, D. J., Still, A. J., Westphall, M. S., Strieter, E. R., Pagliarini, D. J., and Coon, J. J. (2013) Neutron-encoded mass signatures for multiplexed proteome quantification. Nat. Methods 10, 332-334
19. Sleno, L. (2012) The use of mass defect in modern mass spectrometry. J. Mass Spectrom. 47, 226-236
20. Schaub, T. M., Hendrickson, C. L., Horning, S., Quinn, J. P., Senko, M. W., and Marshall, A. G. (2008) High-performance mass spectrometry: Fourier transform ion cyclotron resonance at 14.5 Tesla. Anal. Chem. 80, 3985-3990
21. Denisov, E., Damoc, E., Lange, O., and Makarov, A. (2012) Orbitrap mass spectrometry with resolving powers above 1,000,000. Int. J. Mass Spectrom. 325-327, 80-85
22. Brachmann, C. B., Davies, A., Cost, G. J., Caputo, E., Li, J., Hieter, P., and Boeke, J. D. (1998) Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCRmediated gene disruption and other applications. Yeast 14, 115-132
23. Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B., Arkin, A. P., Astromoff, A., El-Bakkoury, M., Bangham, R., Benito, R., Brachat, S., Campanaro, S., Curtiss, M., Davis, K., Deutschbauer, A., Entian, K. D., Flaherty, P., Foury, F., Garfinkel, D. J., Gerstein, M., Gotte, D., Guldener, U., Hegemann, J. H., Hempel, S., Herman, Z., Jaramillo, D. F., Kelly, D. E., Kelly, S. L., Kotter, P., LaBonte, D., Lamb, D. C., Lan, N., Liang, H., Liao, H., Liu, L., Luo, C., Lussier, M., Mao, R., Menard, P., Ooi, S. L., Revuelta, J. L., Roberts, C. J., Rose, M., Ross-Macdonald, P., Scherens, B., Schimmack, G., Shafer, B., Shoemaker, D. D., Sookhai-Mahadeo, S., Storms, R. K., Strathern, J. N., Valle, G., Voet, M., Volckaert, G., Wang, C. Y., Ward, T. R., Wilhelmy, J., Winzeler, E. A., Yang, Y., Yen, G., Youngman, E., Yu, K., Bussey, H., Boeke, J. D., Snyder, M., Philippsen, P., Davis, R. W., and Johnston, M. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391
24. Lee, M. V., Topper, S. E., Hubler, S. L., Hose, J., Wenger, C. D., Coon, J. J., and Gasch, A. P. (2011) A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol. Syst. Biol. 7, 514
25. Sherman, F. (2002) Getting started with yeast. Methods Enzymol. 350, 3-41
26. Julius, D., Blair, L., Brake, A., Sprague, G., and Thorner, J. (1983) Yeast alpha factor is processed from a larger precursor polypeptide: the essential role of a membrane-bound dipeptidyl aminopeptidase. Cell 32, 839-852
27. Lewis, J. A., and Gasch, A. P. (2012) Natural variation in the yeast glucosesignaling network reveals a new role for the Mig3p transcription factor. G3 2, 1607-1612
28. Wohlbach, D. J., Kuo, A., Sato, T. K., Potts, K. M., Salamov, A. A., Labutti, K. M., Sun, H., Clum, A., Pangilinan, J. L., Lindquist, E. A., Lucas, S., Lapidus, A., Jin, M., Gunawan, C., Balan, V., Dale, B. E., Jeffries, T. W., Zinkel, R., Barry, K. W., Grigoriev, I. V., and Gasch, A. P. (2011) Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. Proc. Natl. Acad. Sci. U.S.A. 108, 13212-13217
29. Boersema, P. J., Raijmakers, R., Lemeer, S., Mohammed, S., and Heck, A. J. (2009) Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat. Protoc. 4, 484-494
30. Elias, J. E., and Gygi, S. P. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214
31. Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M., Maynard, D. M., Yang, X., Shi, W., and Bryant, S. H. (2004) Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964
32. Wenger, C. D., Phanstiel, D. H., Lee, M. V., Bailey, D. J., and Coon, J. J. (2011) COMPASS: a suite of pre-and post-search proteomics software tools for OMSSA. Proteomics 11, 1064-1074
33. Nesvizhskii, A. I., and Aebersold, R. (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 4, 1419-1440
34. Aranda, A., and del Olmo Ml, M. (2003) Response to acetaldehyde stress in the yeast Saccharomyces cerevisiae involves a strain-dependent regulation of several ALD genes and is mediated by the general stress response pathway. Yeast 20, 747-759
35. Cox, B., Kislinger, T., Wigle, D. A., Kannan, A., Brown, K., Okubo, T., Hogan, B., Jurisica, I., Frey, B., Rossant, J., and Emili, A. (2007) Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes. Mol. Syst. Biol. 3, 109
36. de Nadal, E., and Posas, F. (2010) Multilayered control of gene expression by stress-activated protein kinases. EMBO J. 29, 4-13
37. Meggio, F., and Pinna, L. A. (2003) One-thousand-and-one substrates of protein kinase CK2? FASEB J. 17, 349-368
38. Garre, E., Romero-Santacreu, L., De Clercq, N., Blasco-Angulo, N., Sunnerhagen, P., and Alepuz, P. (2012) Yeast mRNA cap-binding protein Cbc1/Sto1 is necessary for the rapid reprogramming of translation after hyperosmotic shock. Mol. Biol. Cell 23, 137-150
39. Teige, M., Scheikl, E., Reiser, V., Ruis, H., and Ammerer, G. (2001) Rck2, a member of the calmodulin-protein kinase family, links protein synthesis to high osmolarity MAP kinase signaling in budding yeast. Proc. Natl. Acad. Sci. U.S.A. 98, 5625-5630
40. Lippman, S. I., and Broach, J. R. (2009) Protein kinase A and TORC1 activate genes for ribosomal biogenesis by inactivating repressors encoded by Dot6 and its homolog Tod6. Proc. Natl. Acad. Sci. U.S.A. 106, 19928-19933
41. Alepuz, P. M., Jovanovic, A., Reiser, V., and Ammerer, G. (2001) Stressinduced map kinase Hog1 is part of transcription activation complexes. Mol. Cell 7, 767-777
42. Proft, M., Mas, G., de Nadal, E., Vendrell, A., Noriega, N., Struhl, K., and Posas, F. (2006) The stress-activated Hog1 kinase is a selective transcriptional elongation factor for genes responding to osmotic stress. Mol. Cell 23, 241-250
43. Rep, M., Krantz, M., Thevelein, J. M., and Hohmann, S. (2000) The transcriptional response of Saccharomyces cerevisiae to osmotic shock. Hot1p and Msn2p/Msn4p are required for the induction of subsets of high osmolarity glycerol pathway-dependent genes. J. Biol. Chem. 275, 8290-8300
44. Kruger, M., Moser, M., Ussar, S., Thievessen, I., Luber, C. A., Forner, F., Schmidt, S., Zanivan, S., Fassler, R., and Mann, M. (2008) SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134, 353-364
45. Geiger, T., Cox, J., Ostasiewicz, P., Wisniewski, J. R., and Mann, M. (2010) Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat. Methods 7, 383-385
46. Monetti, M., Nagaraj, N., Sharma, K., and Mann, M. (2011) Large-scale phosphosite quantification in tissues by a spike-in SILAC method. Nat. Methods 8, 655-658
47. Hebert, A. S., Merrill, A. E., Stefely, J. A., Bailey, D. J., Wenger, C. D., Westphall, M. S., Pagliarini, D. J., and Coon, J. J. (2013) Amine-reactive neutron-encoded labels for highly plexed proteomic quantitation. Mol. Cell. Proteomics 12, 3360-3369
48. Ulbrich, A., Merrill, A. E., Hebert, A. S., Westphall, M. S., Keller, M. P., Attie, A. D., and Coon, J. J. (2014) Neutron-encoded protein quantification by peptide carbamylation. J. Am. Soc. Mass Spectrom. 25, 6-9
49. Zhou, Y., Shan, Y., Wu, Q., Zhang, S., Zhang, L., and Zhang, Y. (2013) Mass defect-based pseudo-isobaric dimethyl labeling for proteome quantification. Anal. Chem. 85, 10658-10663
50. Bamberger, C., Pankow, S., Park, S. K., and Yates, J. R. (2014) Interference-free proteome quantification with MS/MS-based isobaric isotopologue detection. J. Proteome Res. 13, 1494-1501
51. Hebert, A. S., Richards, A. L., Bailey, D. J., Ulbrich, A., Coughlin, E. E., Westphall, M. S., and Coon, J. J. (2013) The one hour yeast proteome. Mol. Cell. Proteomics 13, 339-347
52. Senko, M. W., Remes, P. M., Canterbury, J. D., Mathur, R., Song, Q., Eliuk, S. M., Mullen, C., Earley, L., Hardman, M., Blethrow, J. D., Bui, H., Specht, A., Lange, O., Denisov, E., Makarov, A., Horning, S., and Zabrouskov, V. (2013) Novel parallelized quadrupole/linear ion trap/Orbitrap tribrid mass spectrometer improving proteome coverage and peptide identification rates. Anal. Chem. 85, 11710-11714
53. Mitchell, D. W., and Smith, R. D. (1995) Cyclotron motion of two Coulombically interacting ion clouds with implications to Fourier-transform ion cyclotron resonance mass spectrometry. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics 52, 4366-4386
54. Gorshkov, M. V., Fornelli, L., and Tsybin, Y. O. (2012) Observation of ion coalescence in Orbitrap Fourier transform mass spectrometry. Rapid Commun. Mass Spectrom. 26, 1711-1717