Prefractionation of intact proteins by reversed-phase and anion-exchange chromatography for the differential proteomic analysis of saccharomyces cerevisiae

Journal of Proteome Research

Volumn 12, Issue 2, 2013, Pages 626-636

  Stobaugh, Jordan T ^a   Fague, Kaitlin M ^a   Jorgenson, James W ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

anion exchange chromatography; intact protein prefractionation; label free proteomics; LC MS; mass spectrometry; multidimensional liquid chromatography; reversed phase chromatography

Indexed keywords

GLUCOSE; GLYCEROL;

ANION EXCHANGE CHROMATOGRAPHY; ARTICLE; CARBON SOURCE; ENZYME DEGRADATION; FUNGUS GROWTH; GLYCOLYSIS; IONIC STRENGTH; LIMIT OF DETECTION; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; PRODUCTIVITY; PROTEIN ANALYSIS; PROTEIN PROCESSING; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; SACCHAROMYCES CEREVISIAE; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY; VALIDITY;

CHEMICAL FRACTIONATION; CHROMATOGRAPHY, ION EXCHANGE; CHROMATOGRAPHY, REVERSE-PHASE; FERMENTATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GLUCOSE; GLYCEROL; PEPTIDE FRAGMENTS; PROTEOLYSIS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84873359716     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr300701x     Document Type: Article

References (33)

1. Wiśniewski, J. R.; Mann, M. Consecutive Proteolytic Digestion in an Enzyme Reactor Increases Depth of Proteomic and Phosphoproteomic Analysis Anal. Chem. 2012, 84 (6) 2631-2637
2. Kocher, T.; Pichler, P.; Schutzbier, M.; Stingl, C.; Kaul, A.; Teucher, N.; Hasenfuss, G.; Penninger, J. M.; Mechtler, K. High Precision Quantitative Proteomics Using iTRAQ on an LTQ Orbitrap: A New Mass Spectrometric Method Combining the Benefits of All J. Proteome Res. 2009, 8 (10) 4743-4752
3. Li, Z.; Adams, R. M.; Chourey, K.; Hurst, G. B.; Hettich, R. L.; Pan, C. Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos J. Proteome Res. 2011, 11 (3) 1582-1590
4. Qian, W.-J.; Monroe, M. E.; Liu, T.; Jacobs, J. M.; Anderson, G. A.; Shen, Y.; Moore, R. J.; Anderson, D. J.; Zhang, R.; Calvano, S. E.; Lowry, S. F.; Xiao, W.; Moldawer, L. L.; Davis, R. W.; Tompkins, R. G.; Camp, D. G.; Smith, R. D. Quantitative Proteome Analysis of Human Plasma following in Vivo Lipopolysaccharide Administration Using 16O/18O Labeling and the Accurate Mass and Time Tag Approach Mol. Cell. Proteomics 2005, 4 (5) 700-709
5. Roy, S. M.; Anderle, M.; Lin, H.; Becker, C. H. Differential expression profiling of serum proteins and metabolites for biomarker discovery Int. J. Mass Spectrom. 2004, 238 (2) 163-171
6. Monteoliva, L.; Albar, J. P. Differential proteomics: An overview of gel and non-gel based approaches Briefings Funct. Genomics Proteomics 2004, 3 (3) 220-239
7. Yates, J. R.; Ruse, C. I.; Nakorchevsky, A. Proteomics by Mass Spectrometry: Approaches, Advances, and Applications Annu. Rev. Biomed. Eng. 2009, 11 (1) 49-79
8. Wolters, D. A.; Washburn, M. P.; Yates, J. R. An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics Anal. Chem. 2001, 73 (23) 5683-5690
9. Washburn, M. P.; Ulaszek, R.; Deciu, C.; Schieltz, D. M.; Yates, J. R. Analysis of Quantitative Proteomic Data Generated via Multidimensional Protein Identification Technology Anal. Chem. 2002, 74 (7) 1650-1657
10. Gilar, M.; Olivova, P.; Daly, A. E.; Gebler, J. C. Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions J. Sep. Sci. 2005, 28 (14) 1694-1703
11. Staub, A.; Guillarme, D.; Schappler, J.; Veuthey, J.-L.; Rudaz, S. Intact protein analysis in the biopharmaceutical field J. Pharm. Biomed. Anal. 2011, 55 (4) 810-822
12. Tran, J. C.; Zamdborg, L.; Ahlf, D. R.; Lee, J. E.; Catherman, A. D.; Durbin, K. R.; Tipton, J. D.; Vellaichamy, A.; Kellie, J. F.; Li, M.; Wu, C.; Sweet, S. M. M.; Early, B. P.; Siuti, N.; LeDuc, R. D.; Compton, P. D.; Thomas, P. M.; Kelleher, N. L. Mapping intact protein isoforms in discovery mode using top-down proteomics Nature 2011, 480 (7376) 254-258
13. Vellaichamy, A.; Tran, J. C.; Catherman, A. D.; Lee, J. E.; Kellie, J. F.; Sweet, S. M. M.; Zamdborg, L.; Thomas, P. M.; Ahlf, D. R.; Durbin, K. R.; Valaskovic, G. A.; Kelleher, N. L. Size-Sorting Combined with Improved Nanocapillary Liquid Chromatography-Mass Spectrometry for Identification of Intact Proteins up to 80 kDa Anal. Chem. 2010, 82 (4) 1234-1244
14. Tran, J. C.; Doucette, A. A. Gel-Eluted Liquid Fraction Entrapment Electrophoresis: An Electrophoretic Method for Broad Molecular Weight Range Proteome Separation Anal. Chem. 2008, 80 (5) 1568-1573
15. Martosella, J.; Zolotarjova, N.; Liu, H.; Nicol, G.; Boyes, B. E. Reversed-Phase High-Performance Liquid Chromatographic Prefractionation of Immunodepleted Human Serum Proteins to Enhance Mass Spectrometry Identification of Lower-Abundant Proteins J. Proteome Res. 2005, 4 (5) 1522-1537
16. Dowell, J. A.; Frost, D. C.; Zhang, J.; Li, L. Comparison of Two-Dimensional Fractionation Techniques for Shotgun Proteomics Anal. Chem. 2008, 80 (17) 6715-6723
17. Melchior, K.; Tholey, A.; Heisel, S.; Keller, A.; Lenhof, H.-P.; Meese, E.; Huber, C. G. Protein- versus peptide fractionation in the first dimension of two-dimensional high-performance liquid chromatography-matrix-assisted laser desorption/ionization tandem mass spectrometry for qualitative proteome analysis of tissue samples J. Chromatogr., A 2010, 1217 (40) 6159-6168
18. Searle, B. C. Scaffold: A bioinformatic tool for validating MS/MS-based proteomic studies Proteomics 2010, 10 (6) 1265-1269
19. Eng, J. K.; Searle, B. C.; Clauser, K. R.; Tabb, D. L., A Face in the Crowd: Recognizing Peptides Through Database Search. Mol. Cell. Proteomics 2011, 10 (11).
20. Dillon, T. M.; Bondarenko, P. V.; Rehder, D. S.; Pipes, G. D.; Kleemann, G. R.; Speed, R. M. Optimization of a reversed-phase high-performance liquid chromatography/mass spectrometry method for characterizing recombinant antibody heterogeneity and stability J. Chromatogr., A 2006, 1120 (1) 112-120
21. Wagner, A. Energy Constraints on the Evolution of Gene Expression Mol. Biol. Evol. 2005, 22 (6) 1365-1374
22. Fraenkel, D. G. Carbohydrate metabolism [in yeast] Cold Spring Harbor Monogr. Ser. 1982, 11B, 1-37
23. Sprague, G. F.; Cronan, J. E. Isolation and characterization of Saccharomyces cerevisiae mutants defective in glycerol catabolism J. Bacteriol. 1977, 129 (3) 1335-1342
24. Grauslund, M.; Lopes, J. M.; Rønnow, B. Expression of GUT1, which encodes glycerol kinase in Saccharomyces cerevisiae, is controlled by the positive regulators Adr1p, Ino2p and Ino4p and the negative regulator Opi1p in a carbon source-dependent fashion Nucleic Acids Res. 1999, 27 (22) 4391-4398
25. Cronwright, G. R.; Rohwer, J. M.; Prior, B. A. Metabolic Control Analysis of Glycerol Synthesis in Saccharomyces cerevisiae Appl. Environ. Microbiol. 2002, 68 (9) 4448-4456
26. ter Schure, E. G.; Flikweert, M. T.; van Dijken, J. P.; Pronk, J. T.; Verrips, C. T. Pyruvate Decarboxylase Catalyzes Decarboxylation of Branched-Chain 2-Oxo Acids but Is Not Essential for Fusel Alcohol Production by Saccharomyces cerevisiae Appl. Environ. Microbiol. 1998, 64 (4) 1303-1307
27. Brewster, N. K.; Val, D. L.; Walker, M. E.; Wallace, J. C. Regulation of Pyruvate Carboxylase Isozyme (PYC1, PYC2) Gene Expression in Saccharomyces cerevisiae during Fermentative and Nonfermentative Growth Arch. Biochem. Biophys. 1994, 311 (1) 62-71
28. Pavlik, P.; Simon, M.; Schuster, T.; Ruis, H. The glycerol kinase (GUT1) gene of Saccharomyces cerevisiae cloning and characterization Curr. Genet. 1993, 24 (1) 21-25
29. Blumberg, H.; Hartshorne, T. A.; Young, E. T. Regulation of expression and activity of the yeast transcription factor ADR1 Mol. Cell. Biol. 1988, 8 (5) 1868-1876
30. Kratzer, S.; Schüller, H.-J. Transcriptional control of the yeast acetyl-CoA synthetase gene, ACS1, by the positive regulators CAT8 and ADR1 and the pleiotropic repressor UME6 Mol. Microbiol. 1997, 26 (4) 631-641
31. Simon, M.; Binder, M.; Adam, G.; Hartig, A.; Ruis, H. Control of peroxisome proliferation in Saccharomyces cerevisiae by ADR1, SNF1 (CAT1, CCR1) and SNF4 (CAT3) Yeast 1992, 8 (4) 303-309
32. Kellis, M.; Patterson, N.; Endrizzi, M.; Birren, B.; Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 2003, 423 (6937) 241-254
33. Gu, H.; Huang, Y.; Carr, P. W. Peak capacity optimization in comprehensive two dimensional liquid chromatography: A practical approach J. Chromatogr., A 2011, 1218 (1) 64-73