Plasma/serum proteomics: Pre-analytical issues

Expert Review of Proteomics

Volumn 4, Issue 3, 2007, Pages 363-370

  Barelli, Stefano ^a   Crettaz, David ^a   Thadikkaran, Lynne ^a   Rubin, Olivier ^a   Tissot, Jean Daniel ^a  

^a Service Regional Vaudois de Transfusion Sanguine   (Switzerland)

Author keywords

Anticoagulant; Electrophoresis; Mass spectrometry; Peptidome; Plasma; Pre analytics; Proteome; Serum

Indexed keywords

PLASMA PROTEIN;

DNA SEQUENCE; HUMAN; MASS SPECTROMETRY; PLASMA; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN SECRETION; PROTEOMICS; RELIABILITY; REVIEW; SERUM; TWO DIMENSIONAL GEL ELECTROPHORESIS;

BLOOD PROTEIN ELECTROPHORESIS; BLOOD PROTEINS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; PLASMA; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SERUM;

EID: 34249998316     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.4.3.363     Document Type: Review

References (75)

1. Bodovitz S, Joos T, Bachmann J. Protein biochips: the calm before the storm. Drug Discov. Today 10(4), 283-287 (2005).
2. Hood L, Heath JR, Phelps ME, Lin B. Systems biology and new technologies enable predictive and preventative medicine. Science 306(5696), 640-643 (2004).
3. Kumar S, Mohan A, Guleria R. Biomarkers in cancer screening, research and detection: present and future: a review. Biomarkers 11(5), 385-405 (2006).
4. Sidransky D. Emerging molecular markers of cancer. Nat. Rev. Cancer 2(3), 210-219 (2002).
5. Tyers M, Mann M. From genomics to proteomics. Nature 422(6928), 193-197 (2003).
6. Tissot JD, Hohlfeld P, Layer A, Forestier F, Schneider P, Henry H. Clinical application. Gel electrophoresis. In: Encyclopedia of Separation Science. Wilson ID, Adlar ER, Cook M, Poole CF (Eds). Academic Press, London, UK 2468-2475 (2006).
7. Holland NT, Smith MT, Eskenazi B, Bastaki M. Biological sample collection and processing for molecular epidemiological studies. Mutat. Res. 543(3), 217-234 (2003).
8. Holland NT, Pfleger L, Berger E, Ho A, Bastaki M. Molecular epidemiology biomarkers - sample collection and processing considerations. Toxicol. Appl. Pharmacol. 206(2), 261-268 (2005).
9. Zolg W. The proteomic search for diagnostic biomarkers: lost in translation? Mol. Cell. Proteomics 5(10), 1720-1726 (2006).
10. Check E. Proteomics and cancer: running before we can walk? Nature 429(6991), 496-497 (2004).
11. Petricoin EF, Ardekani AM, Hitt BA et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359(9306), 572-577 (2002).
12. Ransohoff DF. Lessons from controversy: ovarian cancer screening and serum proteomics. J. Natl Cancer Inst. 97(4), 315-319 (2005).
13. US FDA. Patients will benefit from rapid development and delivery of new cancer treatments. In: New Federal Health Initiative to Improve Cancer Therapy. FDA Press release, USA (2006).
14. Rai AJ, Gelfand CA, Haywood BC et al. HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 5(13), 3262-3277 (2005). • Good overview of pre-analytical variables and their effects on plasma samples, illustrated by different proteomic techniques, in the frame of the Human Proteome Organisation's project.
15. Mischak H, Apweiler R, Banks RE et al. Clinical proteomics: a need to define the field and to begin to set adequate standards. Proteomics Clin. Appl. 1 148-156 (2007).
16. Rai AJ, Vitzthum F. Effects of preanalytical variables on peptide and protein measurements in human serum and plasma: implications for clinical proteomics. Expert Rev. Proteomics 3(4), 409-426 (2006).
17. Guder G, Narayanan S, Wisser H, Zawta B. Samples: From the Patient to the Laboratory. Weinheim D (Ed.) John Wiley & Sons Ltd., NJ, USA (2003).
18. Thomas L. Clinical Laboratory Diagnostics: Use and Assessment of Clinical Laboratory Results. AACC Press, Washington, USA (1998).
19. Miyazaki Y, Nomura S, Miyake T et al. High shear stress can initiate both platelet aggregation and shedding of procoagulant containing microparticles. Blood 88(9), 3456-3464 (1996).
20. Tammen H, Schulte I, Hess R et al. Peptidomic analysis of human blood specimens: comparison between plasma specimens and serum by differential peptide display. Proteomics 5(13), 3414-3422 (2005).
21. Hsieh SY, Chen RK, Pan YH, Lee HL. Systematical evaluation of the effects of sample collection procedures on low-molecular-weight serum/plasma proteome profiling. Proteomics 6(10), 3189-3198 (2006).
22. White JG. EDTA-induced changes in platelet structure and function: clot retraction. Platelets 11(1), 49-55 (2000).
23. Baumann S, Ceglarek U, Fiedler GM, Lembcke J, Leichtle A, Thiery J. Standardized approach to proteome profiling of human serum based on magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin. Chem. 51(6), 973-980 (2005). • Clear and precise representation of a serum peptide mass fingerprint. Three sections depict the influence of anticoagulant, freeze/thaw cycles and storage on proteome.
24. Huber-Lang M, Sarma JV, Zetoune FS et al. Generation of C5a in the absence of C3: a new complement activation pathway. Nat. Med. 12(6), 682-687 (2006).
25. Boyanton BL Jr, Blick KE. Stability studies of twenty-four analytes in human plasma and serum. Clin. Chem. 48(12), 2242-2247 (2002).
26. Laessig RH, Indriksons AA, Hassemer DJ, Paskey TA, Schwartz TH. Changes in serum chemical values as a result of prolonged contact with the clot. Am. J. Clin. Pathol. 66(3), 598-604 (1976).
27. Faurschou M, Borregaard N. Neutrophil granules and secretory vesicles in inflammation. Microbes Infect. 5(14), 1317-1327 (2003).
28. Ayache S, Panelli M, Marincola FM, Stroncek DF. Effects of storage time and exogenous protease inhibitors on plasma protein levels. Am. J. Clin. Pathol. 126(2), 174-184 (2006).
29. Findeisen P, Sismanidis D, Riedl M, Costina V, Neumaier M. Preanalytical impact of sample handling on proteome profiling experiments with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin. Chem. 51(12), 2409-2411 (2005). • Practical demonstration of refining quality assessment of sample handling while profiling plasma proteome.
30. House RV. Cytokine measurement techniques for assessing hypersensitivity. Toxicology 158(1-2), 51-58 (2001).
31. Engstad CS, Gutteberg TJ, Osterud B. Modulation of blood cell activation by four commonly used anticoagulants. Thromb. Haemost. 77(4), 690-696 (1997).
32. Thavasu PW, Longhurst S, Joel SP, Slevin ML, Balkwill FR. Measuring cytokine levels in blood. Importance of anticoagulants, processing, and storage conditions. J. Immunol. Methods 153(1-2), 115-124 (1992).
33. Muller-Steinhardt M, Kirchner H, Kluter H. Impact of storage at 22°C and citrate anticoagulation on the cytokine secretion of mononuclear leukocytes. Vox Sang. 75(1), 12-17 (1998).
34. Lambert-Messerlian GM, Eklund EE, Malone FD, Palomaki GE, Canick JA, D'Alton ME. Stability of first- and second-trimester serum markers after storage and shipment. Prenat. Diagn. 26(1), 17-21 (2006).
35. Appenzeller BM, Wennig R. Altered distribution of transferrin isoforms according to serum storage conditions. Clin. Chem. 51(11), 2159-2162 (2005).
36. Favaloro EJ, Soltani S, McDonald J. Potential laboratory misdiagnosis of hemophilia and von Willebrand disorder owing to cold activation of blood samples for testing. Am. J. Clin. Pathol. 122(5), 686-692 (2004).
37. Bohm M, Taschner S, Kretzschmar E, Gerlach R, Favaloro EJ, Scharrer I. Cold storage of citrated whole blood induces drastic time-dependent losses in factor VIII and von Willebrand factor: potential for misdiagnosis of haemophilia and von Willebrand disease. Blood Coagul. Fibrinolysis 17(1), 39-45 (2006).
38. Hoffmeister KM, Felbinger TW, Falet H et al. The clearance mechanism of chilled blood platelets. Cell 112(1), 87-97 (2003).
39. Rock G, Yousef H, Neurath D, Lu M. ADAMTS-13 in fresh, stored, and solvent/detergent-treated plasma. Transfusion 46(7), 1261-1262 (2006).
40. Cardigan R, Lawrie AS, Mackie IJ, Williamson LM. The quality of fresh-frozen plasma produced from whole blood stored at 4°C overnight. Transfusion 45(8), 1342-1348 (2005).
41. Baggerly KA, Morris JS, Coombes KR. Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics 20(5), 777-785 (2004).
42. Drake SK, Bowen RA, Remaley AT, Hortin GL. Potential interferences from blood collection tubes in mass spectrometric analyses of serum polypeptides. Clin. Chem. 50(12), 2398-2401 (2004).
43. Villanueva J, Philip J, Entenberg D et al. Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal. Chem. 76(6), 1560-1570 (2004). • Detailed description of automated technology applied to peptide profiling of serum sample from brain tumor patients.
44. Villanueva J, Philip J, Chaparro CA et al. Correcting common errors in identifying cancer-specific serum peptide signatures. J. Proteome Res. 4(4), 1060-1072 (2005).
45. Jiang X, Feng S, Tian R et al. Automation of nanoflow liquid chromatographytandem mass spectrometry for proteome analysis by using a strong cation exchange trap column. Proteomics 7(4), 528-539 (2007).
46. Lopez MF. Better approaches to finding the needle in a haystack: optimizing proteome analysis through automation. Electrophoresis 21(6), 1082-1093 (2000).
47. Pieper R, Gatlin CL, Makusky AJ 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 3(7), 1345-1364 (2003).
48. Righetti PG, Castagna A, Antonioli P, Boschetti E. Prefractionation techniques in proteome analysis: the mining tools of the third millennium. Electrophoresis 26(2), 297-319 (2005).
49. Righetti PG, Castagna A, Herbert B, Candiano G. How to bring the 'unseen' proteome to the limelight via electrophoretic pre-fractionation techniques. Biosci. Rep. 25(1-2), 3-17 (2005).
50. Baussant T, Bougueleret L, Johnson A et al. Effective depletion of albumin using a new peptide-based affinity medium. Proteomics 5(4), 973-977 (2005).
51. Bjorhall K, Miliotis T, Davidsson P. Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics 5(1), 307-317 (2005).
52. Chen YY, Lin SY, Yeh YY et al. A modified protein precipitation procedure for efficient removal of albumin from serum. Electrophoresis 26(11), 2117-2127 (2005).
53. Chromy BA, Gonzales AD, Perkins J et al. Proteomic analysis of human serum by two-dimensional differential gel electrophoresis after depletion of high-abundant proteins. J. Proteome Res. 3(6), 1120-1127 (2004).
54. Echan LA, Tang HY, Ali-Khan N, Lee K, Speicher DW. Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics 5(13), 3292-3303 (2005).
55. Fountoulakis M, Juranville JF, Jiang L et al. Depletion of the high-abundance plasma proteins. Amino Acids 27(3-4), 249-259 (2004).
56. Fu Q, Garnham CP, Elliott ST, Bovenkamp DE, Van Eyk JE. A robust, streamlined, and reproducible method for proteomic analysis of serum by delipidation, albumin and IgG depletion, and two-dimensional gel electrophoresis. Proteomics 5(10), 2656-2664 (2005).
57. Huang HL, Stasyk T, Morandell S et al. Enrichment of low-abundant serum proteins by albumin/immunoglobulin G immunoaffinity depletion under partly denaturing conditions. Electrophoresis 26(14), 2843-2849 (2005).
58. Ramstrom M, Hagman C, Mitchell JK, Derrick PJ, Hakansson P, Bergquist J. Depletion of high-abundant proteins in body fluids prior to liquid chromatography fourier transform ion cyclotron resonance mass spectrometry. J. Proteome Res. 4(2), 410-416 (2005).
59. Gundry RL, Fu Q, Jelinek CA, Van Eyk JE, Cotter RJ. Investigation of an albumin-enriched fraction of human serum and its albuminome. Proteomics Clin. Appl. 1(1), 73-88 (2007).
60. Chromy BA, Gonzales AD, Perkins J et al. Proteomic analysis of human serum by two-dimensional differential gel electrophoresis after depletion of high-abundant proteins. J. Proteome Res. 3(6), 1120-1127 (2004).
61. Tirumalai RS, Chan KC, Prieto DA, Issaq HJ, Conrads TP, Veenstra TD. Characterization of the low molecular weight human serum proteome. Mol. Cell. Proteomics 2 1096-1103 (2003).
62. Tanaka Y, Akiyama H, Kuroda T et al. A novel approach and protocol for discovering extremely low-abundance proteins in serum. Proteomics 6(17), 4845-4855 (2006). • Clear demonstration of a low-molecularweight proteome. Lists of proteins are given, passing from crude serum analysis to hollow-fiber membrane-treated serum analysis.
63. Thulasiraman V, Lin S, Gheorghiu L et al. Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands. Electrophoresis 26(18), 3561-3571 (2005). • Methodological description of a fundamental approach with potential applications in biomarker discovery.
64. Righetti PG, Boschetti E. Sherlock Holmes and the proteome - a detective story. FEBS J. 274(4), 897-905 (2007). • How to capture the hidden proteome.
65. Liotta LA, Ferrari M, Petricoin E. Clinical proteomics: written in blood. Nature 425(6961), 905 (2003).
66. Villanueva J, Shaffer DR, Philip J et al. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J. Clin. Invest. 116(1), 271-284 (2006).
67. Liotta LA, Petricoin EF. Serum peptidome for cancer detection: spinning biologic trash into diagnostic gold. J. Clin. Invest. 116(1), 26-30 (2006).
68. Marshall J, Kupchak P, Zhu W et al. Processing of serum proteins underlies the mass spectral fingerprinting of myocardial infarction. J. Proteome Res. 2(4), 361-372 (2003).
69. Fliser D, Novak J, Thongboonkerd V et al. Advances in urinary proteome analysis and biomarker discovery. J. Am. Soc. Nephrol. 18(4), 1057-1071 (2007).
70. McCarthy J, Hopwood F, Oxley D et al. Carbamylation of proteins in 2-D electrophoresis - myth or reality? J. Proteome Res. 2(3), 239-242 (2003).
71. Righetti PG. Real and imaginary artefacts in proteome analysis via two-dimensional maps. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 841(1-2), 14-22 (2006).
72. Corzett TH, Fodor IK, Choi MW et al. Statistical analysis of the experimental variation in the proteomic characterization of human plasma by two-dimensional difference gel electrophoresis. J. Proteome Res. 5(10), 2611-2619 (2006).
73. Lee IN, Chen CH, Sheu JC et al. Identification of human hepatocellular carcinoma-related biomarkers by two-dimensional difference gel electrophoresis and mass spectrometry. J. Proteome Res. 4(6), 2062-2069 (2005).
74. Queloz PA, Crettaz D, Thadikkaran L, Sapin V, Tissot JD. Two-dimensional gel electrophoresis based technologies for potential biomarkers identification in amniotic fluid: a simple model. Protein Pept. Lett. 13(10), 959-963 (2006).
75. Queloz PA, Crettaz D, Thadikkaran L et al. Proteomic analyses of amniotic fluid: Potential applications in health and diseases. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 850(1-2), 336-342 (2007)