Sample collection in clinical proteomics-Proteolytic activity profile of serum and plasma

Proteomics - Clinical Applications

Volumn 8, Issue 5-6, 2014, Pages 299-307

  Jambunathan, Kalyani ^a   Galande, Amit K ^a  

^a SRI INTERNATIONAL   (United States)

Author keywords

Anticoagulants; Combinatorial library; Fluorogenic probes; Plasma; Proteases; Serum

Indexed keywords

AMINO ACID; EDETIC ACID; HEPARIN; ISOLEUCINE; LEUCINE; PHENYLALANINE; PROTEINASE; SERINE; THREONINE; TYROSINE; BIOLOGICAL MARKER; CITRIC ACID;

ARTICLE; BLOOD ANALYSIS; BODY FLUID; CLINICAL RESEARCH; COMBINATORIAL LIBRARY; DIAGNOSTIC TEST; DISEASE MARKER; HUMAN; PEPTIDOMICS; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN DEGRADATION; PROTEIN MOTIF; PROTEOMICS; ADULT; BLOOD; BLOOD SAMPLING; MALE; METABOLISM; PLASMA; PROCEDURES; SERUM;

ADULT; AMINO ACID MOTIFS; BIOLOGICAL MARKERS; BLOOD SPECIMEN COLLECTION; CITRATES; EDETIC ACID; HEPARIN; HUMANS; MALE; PLASMA; PROTEOLYSIS; PROTEOMICS; SERUM;

EID: 84902003718     PISSN: 18628346     EISSN: 18628354     Source Type: Journal    
DOI: 10.1002/prca.201300037     Document Type: Article

References (36)

1. Lopez-Otin, C., Bond, J. S., Proteases: multifunctional enzymes in life and disease. J. Biol. Chem. 2008, 283, 30433-30437.
2. Puente, X. S., Sanchez, L. M., Overall, C. M., Lopez-Otin, C., Human and mouse proteases: a comparative genomic approach. Nat. Rev. Genet. 2003, 4, 544-558.
3. Turk, B., Targeting proteases: successes, failures and future prospects. Nat. Rev. Drug Discov. 2006, 5, 785-799.
4. Lee, S., Kim, K., Protease activity: meeting its theranostic potential. Theranostics 2012, 2, 125-126.
5. Abbenante, G., Fairlie, D. P., Protease inhibitors in the clinic. Med. Chem. 2004, 1, 71-104.
6. Drag, M., Salvesen, G. S., Emerging principles in protease-based drug discovery. Nat. Rev. Drug Discov. 2010, 9, 690-701.
7. Lim, M. D., Dickherber, A., Compton, C. C., Before you analyze a human specimen think quality, variability and bias. Anal. Chem. 2011, 83, 8-13.
8. Chuang, C. K., Lin, S. P., Lin, Y. T., Huang, F. Y., Effects of anticoagulants in amino acid analysis: comparisons of heparin, EDTA and sodium citrate in vacutainer tubes for plasma preparation. Clin. Chem. 1198, 44, 1052-1056.
9. Luque-Garcia, J. L., Neubert, T. A., Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry. J. Chromatogr. A 2007, 1153, 259-276.
10. Garcia, M. E., Blanco, J. L., Caballero, J., Gargallo-Viola, D., Anticoagulants interfere with PCR used to diagnose invasive aspergillosis. J. Clin. Microbiol. 2002, 40, 1567-1568.
11. Hu, S., Loo, J. A., Wong, D. T., Human body fluid proteome analysis. Proteomics 2006, 6, 6326-6353.
12. Miles, R. R., Roberts, R. F., Putnam, A. R., Roberts, W. L., Comparison of serum and heparinized plasma samples for measurement of chemistry analytes. Clin. Chem. 2004, 50, 1704-1705.
13. Cherpes, T. L., Meyn, L. A., Hillier, S. L., Plasma versus serum for detection of herpes simplex virus type-2 specific immunoglobulin G antibodies with a glycoprotein G2-based enzyme immune assay. J. Clin. Microbiol. 2003, 41, 2758-2759.
14. Tworoger, S. S., Hankinson, S. E., Collection, processing and storage of biological samples in epidemiologic studies: sex hormones, carotenoids, inflammatory markers and proteomics as examples. Cancer Epidemiol. Biomarkers Prev. 2006, 15, 1578-1581.
15. Rai, A. J., Gelfand, C. A., Haywood, B. C., Warunek, D. J. et al., HUPO Plasma proteome project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 2005, 5, 3262-3277.
16. Tammen, H., Schulte, I., Hess, R., Menzel, C. et al., Peptidomic analysis of human blood specimens: comparison between plasma specimens and serum by differential peptide display. Proteomics 2005, 5, 3414-3422.
17. Westmark, C. J., Hervey, C. M., Berry-Kravisc, E. M., Maltera, J. S., Effects of anticoagulants on amyloid-protein precursor and amyloid beta levels in plasma. J. Alzheimers Dis. 2011, 1, 101, doi: 10.4172/2161-0460.1000101.
18. Lam, N. Y. L., Rainer, T. H., Chiu, R. W. K., Lo, Y. M. D., EDTA is a better anticoagulant than heparin or citrate for delayed blood processing for plasma DNA analysis. Clin. Chem. 2004, 50, 256-257.
19. Ferre, N., Camps, J., Marsillach, J., Mackness, B. et al., Comparison of paraoxanase 1 measurements in serum and in lithium heparin anticoagulated plasma samples. Clin. Chem. 2005, 51, 922-923.
20. Dong, N., Dong, J., Liu, P., Xu, L. et al., Effects of anticoagulants on human plasma soluble corin levels measured by ELISA. Clin. Chim. Acta 2010, 411, 1998-2003.
21. Gerlach, R. F., Demacq, C., Jung, K., Tanus-Santos, J. E., Rapid separation of serum does not avoid artificially higher matrix metalloproteinase (MMP)-9 levels in serum versus plasma. Clin. Biochem. 2007, 40, 119-123.
22. Manello, F., Jung, K., Tonti, G. A., Canestrari, F., Heparin affects matrix metalloproteinases and tissue inhibitors of metalloproteinases circulating in peripheral blood. Clin. Biochem. 2008, 41, 1466-1473.
23. Dowell, B., Egawa, S., Borden, K., Comparison of serum, EDTA- plasma and heparin-plasma results for the Abbott free PSA and total PSA assays. Tumor Biol. 2002, 23, S1(56).
24. Watson, D. S., Jambunathan, K., Askew, D. S., Kodukula, K., Galande, A. K., Robust substrate profiling method reveals striking differences in specificities of serum and lung fluid proteases. Biotechniques 2011, 51, 95-104.
25. Jambunathan, K., Watson, D. S., Kodukula, K., Galande, A. K., Proteolytic fingerprinting of complex biological samples using combinatorial libraries of fluorogenic probes. Curr. Protoc. Protein Sci. 2012, 70, 21.22.1-21.22.13.
26. Neefjes, J., Dantuma, N. P., Fluorescence probes for proteolysis: tools for drug discovery. Nat. Rev. Drug Discov. 2004, 3, 58-69.
27. Thomas, D. A., Francis, P., Smith, C., Ratcliffe, S. et al., A broad-spectrum fluorescence based peptide library for the rapid identification of protease substrates. Proteomics 2006, 6, 2112-2120.
28. Jambunathan, K., Watson, D. S., Endsley, A. N., Kodukula, K., Galande, A. K., Comparative analysis of substrate specificities of two post-proline cleaving endopeptidases, prolyl oligopeptidase and fibroblast activation protein α. FEBS Lett. 2012, 586, 2507-2512.
29. Jambunathan, K., Watson, D. S., Najvar, L. K., Wiederhold, N. P. et al., Prolyl endopeptidase activity in lung fluid: a novel diagnostic biomarker in a guinea pig model of invasive pulmonary aspergillosis. Med. Mycol. 2013, 51, 592-602.
30. Sennels, L., Salek, M., Lomas, L., Boschetti, E. et al., Proteomic analysis of human blood serum using peptide library beads. J. Prot. Res. 2007, 6, 4055-4062.
31. King, J. Y., Ferrara, R., Tabibiazar, R., Spin, J. M. et al., Pathway analysis of coronary atherosclerosis. Physiol. Genomics 2005, 23, 103-118.
32. Kirouac, M., Vachon, V., Quievy, D., Schwartz, J. L., Laprade, R., Protease inhibitors fail to prevent pore formation by the activated Bacillus thuringiensis toxin Cry1Aa in insect brush border membrane vesicles. Appl. Environ. Microbiol. 2006, 72, 506-515.
33. Pan, Z., Jeffery, D. A., Chehade, K., Beltman, J. et al., Development of activity-based probes for trypsin-family serine proteases. Bioorg. Med. Chem. Lett. 2006, 16, 2882-2885.
34. Jambunathan, K., Galande, A. K., Design of a serum stability tag for bioactive peptides. Pept. Protein Lett. 2013, 21, 32-38.
35. Walker, J. R., Altman, R. K., Warren, J. W., Altman, E., Using protein-based motifs to stabilize peptides. J. Pept. Res. 2003, 62, 214-226.
36. Yi, J., Kim, C., Gelfand, C. A., Inhibition of intrinsic proteolytic activities moderates preanalytical variability and instability of human plasma. J. Proteome Res. 2007, 6, 1768-1781.