Development and characterization of novel 8-plex DiLeu isobaric labels for quantitative proteomics and peptidomics

Rapid Communications in Mass Spectrometry

Volumn 29, Issue 12, 2015, Pages 1115-1124

  Frost, Dustin C ^a   Greer, Tyler ^a   Xiang, Feng ^a   Liang, Zhidan ^a   Li, Lingjun ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BIOSYNTHESIS; COST EFFECTIVENESS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR BIOLOGY; YEAST;

CANDIDATE LIST; COST EFFECTIVE; DISEASE BIOMARKER; LABELING REAGENT; PEPTIDE PRODUCTS; PEPTIDOMICS; Q EXACTIVE; QUANTITATIVE PROTEOMICS; RELATIVE QUANTIFICATION; SYNTHESISED;

PEPTIDES;

DEUTERIUM; LEUCINE; PEPTIDE;

ANALOGS AND DERIVATIVES; CHEMISTRY; DEVICES; LIQUID CHROMATOGRAPHY; PROCEDURES; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SYNTHESIS; TANDEM MASS SPECTROMETRY;

CHROMATOGRAPHY, LIQUID; DEUTERIUM; LEUCINE; PEPTIDES; PROTEOMICS; SACCHAROMYCES CEREVISIAE; TANDEM MASS SPECTROMETRY;

EID: 84929299779     PISSN: 09514198     EISSN: 10970231     Source Type: Journal    
DOI: 10.1002/rcm.7201     Document Type: Article

References (56)

1. Y. Oda, K. Huang, F. R. Cross, D. Cowburn, B. T. Chait,. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. USA 1999, 96, 6591.
2. H. Zhu, S. Pan, S. Gu, E. M. Bradbury, X. Chen,. Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun. Mass Spectrom. 2002, 16, 2115.
3. S.-E. Ong, B. Blagoev, I. Kratchmarova, D. B. Kristensen, H. Steen, A. Pandey, M. Mann,. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376.
4. S. Pan, S. Gu, E. M. Bradbury, X. Chen,. Single peptide-based protein identification in human proteome through MALDI-TOF MS coupled with amino acids coded mass tagging. Anal. Chem. 2003, 75, 1316.
5. S. Gu, S. Pan, E. M. Bradbury, X. Chen,. Precise peptide sequencing and protein quantification in the human proteome through in vivo lysine-specific mass tagging. J. Am. Soc. Mass Spectrom. 2003, 14, 1.
6. S. P. Gygi, B. Rist, S. a. Gerber, F. Turecek, M. H. Gelb, R. Aebersold,. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17, 994.
7. M. B. Smolka, H. Zhou, S. Purkayastha, R. Aebersold,. Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Anal. Biochem. 2001, 297, 25.
8. D. K. Han, J. Eng, H. Zhou, R. Aebersold,. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 2001, 19, 946.
9. C. Ji, N. Guo, L. Li,. Differential dimethyl labeling of N-termini of peptides after guanidination for proteome analysis. J. Proteome Res. 2005, 4, 2099.
10. Q. Fu, L. Li,. Fragmentation of peptides with N-terminal dimethylation and imine/methylol adduction at the tryptophan side-chain. J. Am. Soc. Mass Spectrom. 2006, 17, 859.
11. P. J. Boersema, T. T. Aye, T. A. B. Van Veen, A. J. R. Heck, S. Mohammed,. Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates. Proteomics 2008, 8, 4624.
12. Y. Wu, F. Wang, Z. Liu, H. Qin, C. Song, J. Huang, Y. Bian, X. Wei, J. Dong, H. Zou,. Five-plex isotope dimethyl labeling for quantitative proteomics. Chem. Commun. (Camb). 2014, 50, 1708.
13. L. V. DeSouza, A. M. Taylor, W. Li, M. S. Minkoff, A. D. Romaschin, T. J. Colgan, K. W. M. Siu,. Multiple reaction monitoring of mTRAQ-labeled peptides enables absolute quantification of endogenous levels of a potential cancer marker in cancerous and normal endometrial tissues. J. Proteome Res. 2008, 7, 3525.
14. J. Y. Yoon, J. Yeom, H. Lee, K. Kim, S. Na, K. Park, E. Paek, C. Lee,. High-throughput peptide quantification using mTRAQ reagent triplex. BMC Bioinformatics 2011, 12, S46.
15. C. Y. Hwang, K. Kim, J. Y. Choi, Y. J. Bahn, S.-M. Lee, Y. K. Kim, C. Lee, K.-S. Kwon,. Quantitative proteome analysis of age-related changes in mouse gastrocnemius muscle using mTRAQ. Proteomics 2014, 14, 121.
16. P. Mertins, N. D. Udeshi, K. R. Clauser, D. R. Mani, J. Patel, S. Ong, J. D. Jaffe, S. A. Carr,. iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics. Mol. Cell. Proteomics 2012, 11, M111.014423.
17. A. S. Hebert, A. E. Merrill, D. J. Bailey, A. J. Still, M. S. Westphall, E. R. Strieter, D. J. Pagliarini, J. J. Coon,. Neutron-encoded mass signatures for multiplexed proteome quantification. Nat. Methods 2013, 10, 332.
18. C. M. Rose, A. E. Merrill, D. J. Bailey, A. S. Hebert, M. S. Westphall, J. J. Coon,. Neutron encoded labeling for peptide identification. Anal. Chem. 2013, 85, 5129.
19. A. L. Richards, C. E. Vincent, A. Guthals, C. M. Rose, M. S. Westphall, N. Bandeira, J. J. Coon,. Neutron-encoded signatures enable product ion annotation from tandem mass spectra. Mol. Cell. Proteomics 2013, 12, 3812.
20. A. E. Merrill, A. S. Hebert, M. E. MacGilvray, C. M. Rose, D. J. Bailey, J. C. Bradley, W. W. Wood, M. ElMasri, M. S. Westphall, A. P. Gasch, J. J. Coon,. NeuCode labels for relative protein quantification. Mol. Cell. Proteomics 2014, 1.
21. T. W. Rhoads, C. M. Rose, D. J. Bailey, N. M. Riley, R. C. Molden, A. J. Nestler, A. E. Merrill, L. M. Smith, A. S. Hebert, M. S. Westphall, D. J. Pagliarini, B. A. Garcia, J. J. Coon,. Neutron-encoded mass signatures for quantitative top-down proteomics. Anal. Chem. 2014, 86, 2314.
22. A. S. Hebert, A. E. Merrill, J. a. Stefely, D. J. Bailey, C. D. Wenger, M. S. Westphall, D. J. Pagliarini, J. J. Coon,. Amine-reactive neutron-encoded labels for highly plexed proteomic quantitation. Mol. Cell. Proteomics 2013, 12, 3360.
23. A. Ulbrich, A. E. Merrill, A. S. Hebert, M. S. Westphall, M. P. Keller, A. D. Attie, J. J. Coon,. Neutron-encoded protein quantification by peptide carbamylation. J. Am. Soc. Mass Spectrom. 2014, 25, 6.
24. A. Ulbrich, D. J. Bailey, M. S. Westphall, J. J. Coon,. Organic acid quantitation by NeuCode methylamidation. Anal. Chem. 2014, DOI 10.1021/ac500270q.
25. A. Thompson, J. Schäfer, K. Kuhn, S. Kienle, J. Schwarz, G. Schmidt, T. Neumann, R. Johnstone, a K. a Mohammed, C. Hamon,. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 2003, 75, 1895.
26. L. Dayon, A. Hainard, V. Licker, N. Turck, K. Kuhn, D. F. Hochstrasser, P. R. Burkhard, J. Sanchez,. Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal. Chem. 2008, 80, 2921.
27. J. Sinclair, J. F. Timms,. Quantitative profiling of serum samples using TMT protein labelling, fractionation and LC-MS/MS. Methods 2011, 54, 361.
28. J. P. Murphy, R. A. Everley, J. L. Coloff, S. P. Gygi,. Combining amine metabolomics and quantitative proteomics of cancer cells using derivatization with isobaric tags. Anal. Chem. 2014, 86, 3585.
29. P. L. Ross, Y. N. Huang, J. N. Marchese, B. Williamson, K. Parker, S. Hattan, N. Khainovski, S. Pillai, S. Dey, S. Daniels, S. Purkayastha, P. Juhasz, S. Martin, M. Bartlet-Jones, et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3, 1154.
30. L. DeSouza, G. Diehl, M. J. Rodrigues, J. Guo, A. D. Romaschin, T. J. Colgan, K. W. M. Siu,. Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J. Proteome Res. 2005, 4, 377.
31. Y. Guo, P. A. Singleton, A. Rowshan, M. Gucek, R. N. Cole, D. R. M. Graham, J. E. Van Eyk, J. G. N. Garcia,. Quantitative proteomics analysis of human endothelial cell membrane rafts: evidence of MARCKS and MRP regulation in the sphingosine 1-phosphate-induced barrier enhancement. Mol. Cell. Proteomics 2007, 6, 689.
32. L. Choe, M. D'Ascenzo, N. R. Relkin, D. Pappin, P. Ross, B. Williamson, S. Guertin, P. Pribil, K. H. Lee,. 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease. Proteomics 2007, 7, 3651.
33. P. Pichler, T. Köcher, J. Holzmann, M. Mazanek, T. Taus, G. Ammerer, K. Mechtler,. Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap. Anal. Chem. 2010, 82, 6549.
34. N. Dephoure, S. P. Gygi,. Hyperplexing: a method for higher-order multiplexed quantitative proteomics provides a map of the dynamic response to rapamycin in yeast. Sci. Signal. 2012, 5, rs2.
35. R. A. Everley, R. C. Kunz, F. E. McAllister, S. P. Gygi,. Increasing throughput in targeted proteomics assays: 54-plex quantitation in a single mass spectrometry run. Anal. Chem. 2013, 85, 5340.
36. R. A. S. Robinson, A. R. Evans,. Enhanced sample multiplexing for nitrotyrosine-modified proteins using combined precursor isotopic labeling and isobaric tagging. Anal. Chem. 2012, 84, 4677.
37. 3 acquisition. Proteomics 2013, 13, 3267.
38. T. Werner, I. Becher, G. Sweetman, C. Doce, M. M. Savitski, M. Bantscheff,. High-resolution enabled TMT 8-plexing. Anal. Chem. 2012, 84, 7188.
39. G. C. McAlister, E. L. Huttlin, W. Haas, L. Ting, M. P. Jedrychowski, J. C. Rogers, K. Kuhn, I. Pike, R. A. Grothe, J. D. Blethrow, S. P. Gygi,. Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses. Anal. Chem. 2012, 84, 7469.
40. F. Xiang, H. Ye, R. Chen, Q. Fu, L. Li,. N,N-dimethyl leucines as novel isobaric tandem mass tags for quantitative proteomics and peptidomics. Anal. Chem. 2010, 82, 2817.
41. L. Hui, F. Xiang, Y. Zhang, L. Li,. Mass spectrometric elucidation of the neuropeptidome of a crustacean neuroendocrine organ. Peptides 2012, 36, 230.
42. M. Zhao, L. Bi, W. Wang, C. Wang, M. Baudy-Floc'h, J. Ju, S. Peng,. Synthesis and cytotoxic activities of beta-carboline amino acid ester conjugates. Bioorg. Med. Chem. 2006, 14, 6998.
43. C. B. Lietz, Q. Yu, L. Li,. Large-scale collision cross-section profiling on a traveling wave ion mobility mass spectrometer. J. Am. Soc. Mass Spectrom. 2014, DOI: 10.1007/s13361.
44. L. Käll, J. D. Canterbury, J. Weston, W. S. Noble, M. J. MacCoss,. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 2007, 4, 923.
45. I. P. Shadforth, T. P. J. Dunkley, K. S. Lilley, C. Bessant,. i-Tracker: for quantitative proteomics using iTRAQ. BMC Genomics 2005, 6, 145.
46. M. Fauré-Tromeur, S. Zard,. A practical synthesis of benzyl esters and related derivatives. Tetrahedron Lett. 1998, 39, 7301.
47. J. Tummatorn, P. A. Albiniak, G. B. Dudley,. Synthesis of benzyl esters using 2-benzyloxy-1-methylpyridinium triflate. J. Org. Chem. 2007, 72, 8962.
48. S. S. Lopez, G. B. Dudley,. Convenient method for preparing benzyl ethers and esters using 2-benzyloxypyridine. Beilstein J. Org. Chem. 2008, 4. DOI: 10.3762/bjoc.4.44.
49. P. G. M. Wuts, T. W. Greene,. Greene's Protective Groups in Organic Synthesis. John Wiley & Sons, Inc., Hoboken, NJ, USA, 2006.
50. S. Y. Ow, M. Salim, J. Noirel, C. Evans, I. Rehman, P. C. Wright,. iTRAQ underestimation in simple and complex mixtures: "the good, the bad and the ugly". J. Proteome Res. 2009, 8, 5347.
51. R. Zhang, C. S. Sioma, S. Wang, F. E. Regnier,. Fractionation of isotopically labeled peptides in quantitative proteomics. Anal. Chem. 2001, 73, 5142.
52. R. Zhang, C. S. Sioma, R. a. Thompson, L. Xiong, F. E. Regnier,. Controlling deuterium isotope effects in comparative proteomics. Anal. Chem. 2002, 74, 3662.
53. J. M. Boutilier, H. Warden, A. a. Doucette, P. D. Wentzell,. Chromatographic behaviour of peptides following dimethylation with H2/D2-formaldehyde: implications for comparative proteomics. J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci. 2012, 908, 59.
54. R. M. Sturm, C. B. Lietz, L. Li,. Improved isobaric tandem mass tag quantification by ion mobility mass spectrometry. Rapid Commun. Mass Spectrom. 2014, 28, 1051.
55. 3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat. Methods 2011, 8, 937.
56. C. D. Wenger, M. V. Lee, A. S. Hebert, G. C. McAlister, D. H. Phanstiel, M. S. Westphall, J. J. Coon,. Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nat. Methods 2011, 8, 933.