Human serum proteins fractionated by preparative partition chromatography prior to LC-ESI-MS/MS

Journal of Proteome Research

Volumn 8, Issue 3, 2009, Pages 1143-1155

  Tucholska, Monika ^a   Bowden, Peter ^a   Jacks, Kellie ^a   Zhu, Peihong ^a   Furesz, Shirley ^a   Dumbrovsky, Mila ^a   Marshall, John ^a  

^a RYERSON UNIVERSITY   (Canada)

Author keywords

Human serum; LC MS MS; Liquid chromatography; Preparative chromatography; Tryptic digest; XITANDEM

Indexed keywords

2 DIETHYLAMINOETHANOL; AMINE; CONCANAVALIN A; HEPARIN; HYDROXYAPATITE; PHENOL; PLASMA PROTEIN; PROTEIN G; RESIN;

ARTICLE; CONTROLLED STUDY; ELECTROPHORESIS; ELECTROSPRAY; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PARTITION CHROMATOGRAPHY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DETERMINATION;

BLOOD PROTEINS; CHROMATOGRAPHY, LIQUID; HUMANS; PROTEOME; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TANDEM MASS SPECTROMETRY;

EID: 65249161694     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr8005217     Document Type: Article

References (83)

1. Gao, J.; et al. Biomarker discovery in biological fluids. Methods 2005, 35, 291-302.
2. Issaq, H. J.; Conrads, T. P.; Janini, G. M.; Veenstra, T. D. Methods for fractionation, separation and profiling of proteins and peptides. Electrophoresis 2002, 23, 3048-61.
3. Luque-Garcia, J. L.; Neubert, T. A. Sample preparation for serum/ plasma profiling and biomarker identification by mass spectrometry. J. Chromatosr., A 2007, 1153, 259-76.
4. Koller, A.; et al. Proteomic survey of metabolic pathways in rice. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11969-74.
5. Marshall, J.; et al. Human serum proteins preseparated by electrophoresis or chromatography followed by tandem mass spectrometry. J. Proteome Res. 2004, 3, 364-82.
6. Putnam, F. The Plasma Proteins: Structure Function. and Genetic Control, 2nd ed.; Academic Press: New York, 1975.
7. Duckert, F.; Koller, F.; Matter, M. Purification and physiological properties of factor VII from plasma and serum; separation from prothrombin. Proc. Soc. Exp. Biol. Med. 1953, 82, 259-61.
8. Tollefsen, D. M.; Majerus, D. W.; Blank, M. K. Heparin cofactor II. Purification and properties of a heparin-dependent inhibitor of thrombin in human plasma. J. Biol. Chem. 1982, 257, 2162-9.
9. Kanai, M.; Raz, A.; Goodman, D. S. Retinol-binding protein: the transport protein for vitamin A in human plasma. J. Clin. Invest. 1968, 47, 2025-4.
10. McConnell, D. J.; Mason, B. The isolation of human plasma prekallikrein. Br. J. Pharmacol. 1970, 38, 490-502.
11. Vasileva, R.; Jakab, M.; Hasko, F. Application of ion-exchange chromatography for the production of human albumin. J. Chromatosr. 1981, 216, 279-84.
12. Poffenbarger, P. L. The purification and partial characterization of an insulin-like protein from human serum. J. Clin. Invest. 1975, 56, 1455-63.
13. Murthy, R. J.; Hercz, A. Purification of human alpha 1-antitrypsin by affinity chromatography on sepharose bound concanavalin A. FEBS Lett. 1973, 32, 243-6.
14. Zhu, P.; et al. Comparison of protein expression lists from mass spectrometry of human blood fluids using exact peptide sequences versus BLAST. Clin. Proteomics 2007, 2, 185.
15. Pieper, R.; et al. The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics 2003, 3, 1345-64.
16. Olsen, J. V.; Ong, S. E.; Mann, M. Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell. Proteomics 2004, 3, 608-14.
17. Adkins, J. N.; et al. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell. Proteomics 2002, 1, 947-55.
18. Tirumalai, R. S.; et al. Characterization of the low molecular weight human serum proteome. Mol. Cell. Proteomics 2003, 2, 1096-103.
19. Shen, Y.; et al. Ultra-high-efficiency strong cation exchange LC/ RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Anal. Chem. 2004, 76, 1134-44.
20. Shen, Y.; et al. Characterization of the human blood plasma proteome. Proteomics 2005.
21. Chan, K.; Lucas, D. A.; Hise, D.; Schaefer, C. F.; Xiao, Z.; Janini, G. M.; Beutow, K. H.; Issaq, H. J.; Veenstra, T. D.; Conrads, T. P. Analysis of the Human Serum Proteome. Clin. Proteomics 2004, 1, 101-225.
22. Moore, R. E.; Young, M. K.; Lee, T. D. Qscore: an algorithm for evaluating SEQUEST database search results. J. Am. Soc. Mass Spectrom. 2002, 13, 378-86.
23. Chelius, D.; et al. Analysis of the adenovirus type 5 proteome by liquid chromatography and tandem mass spectrometry methods. J. Proteome Res. 2002, 1, 501-13.
24. Zhu P-H, K. K.; Jankowski, A.; Marshall, J. Comparison of published human serum/plasma data. Mol. Cell. Proteomics 2004, 3, S235.
25. Jin, W. H.; et al. Human plasma proteome analysis by multidimensional chromatography prefractionation and linear ion trap mass spectrometry identification. J. Proteome Res. 2005, 4, 613-9.
26. Omenn, G. S.; et al. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005, 5, 3226-45.
27. States, D. J.; et al. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol. 2006, 24, 333-8.
28. Liu, T.; et al. Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry. Mol. Cell. Proteomics 2006, 5, 2167-74.
29. Whiteaker, J. R.; et al. Head-to-head comparison of serum fractionation techniques. J. Proteome Res. 2007, 6, 828-36.
30. Faca, V.; et al. Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J. Proteome Res. 2007, 6, 3558-65.
31. Sennels, L.; et al. Proteomic analysis of human blood serum using peptide library beads. J. Proteome Res. 2007, 6, 4055-62.
32. Richter, R.; et al. Composition of the peptide fraction in human blood plasma: database of circulating human peptides. J. Chromatosr., B: Biomed. Sci. Appl. 1999, 726, 25-35.
33. Tanaka, Y.; et al. A novel approach and protocol for discovering extremely low-abundance proteins in serum. Proteomics 2006, 6, 4845-55.
34. Qian, W. J.; Jacobs, J. M.; Liu, T.; Camp, D. G., II.; Smith, R. D. Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol. Cell. Proteomics 2006, 5, 1727-44.
35. Guzzetta, A. W.; Thakur, R. A.; Mylchreest, I. C. A robust microelectrospray ionization technique for high-throughput liquid chromatography/mass spectrometry proteomics using a sanded metal needle as an emitter. Rapid Commun. Mass Spectrom. 2002, 16,2067-72.
36. Tietz. Tietz Fundamentals of Clinical Chemistry; W. B. Saunders: Philadelphia, PA, 2001; p 1091.
37. Marshall, J.; et al. Involvement of cytosolic phospholipase A2 and secretory phospholipase A2 in arachidonic acid release from human neutrophils. J. Immunol. 2000, 164, 2084-91.
38. Marshall, J.; et al. Processing of serum proteins underlies the mass spectral fingerprinting of myocardial infarction. J. Proteome Res. 2003, 2, 361-72.
39. Sviridov, D.; Meilinger, B.; Drake, S. K.; Hoehn, G. T.; Hortin, G. L. Coelution of other proteins with albumin during size-exclusion HPLC: Implications for analysis of urinary albumin. Clin. Chem. 2006, 52, 389-97.
40. Craig, R.; Cortens, J. P.; Beavis, R. C. Open source system for analyzing, validating, and storing protein identification data. J Proteome Res. 2004, 3, 1234-2.
41. Codd, E. F. A relational model of data for large shared data banks. 1970. MD Comput. 1998, 15, 162-6.
42. Field, H. I.; Fenyo, D.; Beavis, R. C. RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics 2002, 2, 36-47.
43. Altschul, S. F.; et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25, 3389-402.
44. Anderson, L.; Hunter, C. L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 2006, 5, 573-88.
45. Zhang, R.; et al. Mining biomarkers in human sera using proteomic tools. Proteomics 2004, 4, 244-56.
46. Whiteaker, J. R.; et al. Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers. Anal. Biochem. 2007, 362, 44-54.
47. Ghosh, S.; Gepstein, S.; Heikkila, J. J.; Dumbroff, E. B. Use of a scanning densitometer or an ELISA plate reader for measurement of nanogram amounts of protein in crude extracts from biological tissues. Anal. Biochem. 1988, 169, 227-33.
48. Schagger, H.; von Jagow, G. Tricine-sodium dodecyl sulfatepolyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal. Biochem. 1987, 166, 368-79.
49. Schagger, H.; Aquila, H.; Von Jagow, G. Coomassie blue-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for direct visualization of polypeptides during electrophoresis. Anal. Biochem. 1988, 173, 201-5.
50. Dionne, R.; Forest, J. C.; Moutquin, J. M.; De Grandpre, P.; Masse, J. Electrophoretic method for separating small peptides in serum without extraction of macromolecules: application to the detection of preeclampsia. Clin. Biochem. 1994, 27, 99-103.
51. Laemmli, U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970, 227, 680-5.
52. Jin, X.; Chen, Y.; Lubman, D. M.; Misek, D.; Hanash, S. M. Capillary electrophoresis/tandem mass spectrometry for analysis of proteins from two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis. Rapid Commun. Mass Spectrom. 1999, 13, 232734.
53. Wheeler, D. L.; et al. Database resources of the National Center for Biotechnology. Nucleic Acids Res. 2003, 31, 28-33.
54. Pruitt, K. D.; Tatusova, T.; Maglott, D. R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007, 35, D61-5.
55. aglott, D. R.; Katz, K. S.; Sicotte, H.; Pruitt, K. D. NCBI's LocusLink nd RefSeq. Nucleic Acids Res. 2000, 28, 126-8.
56. ink, A. J.; et al. Direct analysis of protein complexes using mass pectrometry. Nat. Biotechnol. 1999, 17, 676-82.
57. raig, R.; Beavis, R. C. TANDEM: matching proteins with tandem ass spectra. Bioinformatics 2004, 20, 1466-7.
58. hang, H.; Li, X. J.; Martin, D. B.; Aebersold, R. Identification and uantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol. 2003, 21, 660-6.
59. argile, B. J.; Bundy, J. L.; Stephenson, J. L., Jr. Potential for false ositive identifications from large databases through tandem mass pectrometry. J. Proteome Res. 2004, 3, 1082-5.
60. app, E. A.; et al. An evaluation, comparison, and accurate enchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics 2005, 5, 3475-90.
61. Brosch, M.; Swamy, S.; Hubbard, T.; Choudhary, J. Comparison of mascot and X!tandem performance for low and high accuracy mass spectrometry and the development of an adjusted mascot threshold. Mol. Cell. Proteomics 2008.
62. Anderson, N. L.; Anderson, N. G. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 2003, 2, 50.
63. Wait, R. Proteins of rat serum, urine, and cerebrospinal fluid: VI. Further protein identifications and interstrain comparison. Electrophoresis 2001, 22, 3043-52.
64. Bergquist, J.; Palmblad, M.; Wetterhall, M.; Hakansson, P.; Markides, K. E. Peptide mapping of proteins in human body fluids using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Mass Spectrom. Rev. 2002, 21, 2-15.
65. 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. GenomeBiolosy2006, 7, R80.
66. Hortin, G. L. The MALDI-TOF mass spectrometric view of the plasma proteome and peptidome. Clin. Chem. 2006, 52, 1223-37.
67. Kulasingam, V.; et al. "Product ion monitoring" assay for prostate specific antigen in serum using a linear ion-trap. J. Proteome Res. 2008, 7, 640-647.
68. Keshishian, H.; Addona, T.; Burgess, M.; Kuhn, E.; Carr, S. A. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 2007, 6, 2212-29.
69. Hager, J. W.; Yves Le Blanc, J. C. Product ion scanning using a Q-q-Qlinear ion trap (Q TRAPTM) mass spectrometer. Rapid Commun. Mass Spectrom. 2003, 17, 1056-64.
70. Brenner, S.; et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 2000, 18, 630-4.
71. Cohen, S. N.; Chang, A. C. A method for selective cloning of eukaryotic DNA fragments in Escherichia coli by repeated transformation. Mol. Gen. Genet. 1974, 134, 133-41.
72. Istrail, S.; et al. Whole-genome shotgun assembly and comparison of human genome assemblies. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 1916-21.
73. Sanger, F.; Nicklen, S.; Coulson, A. R. DNA sequencing with chainterminating nhibitors. Proc. Natl. Acad. Sci. U.S.A. 1977, 74, 54637.
74. Schena, M. Genome analysis with gene expression microarrays. BioEssays 1996, 18, 427-31.
75. Smith, L. M.; et al. Fluorescence detection in automated DNA sequence analysis. Nature 1986, 321, 674-9.
76. Mullis, K. B. Target amplification for DNA analysis by the poly merase chain reaction. Ann. Biol. Clin. 1990, 48, 579-82.
77. Zhang, S.; Zhang, J.; Horvath, C. Rapid separation of peptides and proteins by isocratic capillary electrochromatography at elevated temperature. J. Chromatogr., A 2001, 914, 189-200.
78. Nissum, M.; et al. Two-dimensional separation of human plasma proteins using iterative free-flow electrophoresis. Proteomics 2007, 7, 4218-27.
79. Corr, J. J.; et al. Design considerations for high speed quantitative mass spectrometry with MALDI ionization. J. Am. Soc. Mass Spectrom. 2006, 17, 1129-41.
80. Shilov, I. V.; et al. The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol. Cell. Proteomics 2007, 6, 1638-55.
81. Tucholska, M.; et al. Endogenous peptides from biophysical and biochemical fractionation of serum analyzed by matrix-assisted laser desorption/ionization and electrospray ionization hybrid quadrupole time-of-flight. Anal. Biochem. 2007, 370, 228-45.
82. Ping, P.; et al. A functional annotation of subproteomes in human plasma. Proteomics 2005, 5, 3506-19.
83. Bjorhall, K.; Miliotis, T.; Davidsson, P. Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics 2005, 5, 307-17.