Abstract
Proteomic study of clinical samples aims at the better understanding of physiological and pathological conditions, as well as the discovery of diagnostic and prognostic markers for the latter. Quantitative and/or qualitative variations of body fluid proteome may reflect health- or disease-associated events connected to the adjacent or distant body regions of the fluid production/secretion/excretion and/or systemic reactions to the presence of disease. Sample collection and preparation is a critical step in order to obtain useful and valid information in clinical proteomics analysis. In this chapter, we present the current protocols and guidelines for human body fluid collection and storage, prior to proteomic analysis. A variety of body fluids that are currently being used in proteomic analysis and have potential interest in clinical practice are presented including blood plasma and serum, urine, cerebrospinal fluid, cerumen, nasal secretions, saliva, tears, breast milk, bronchoalveolar fluid, nipple aspirate fluid, amniotic fluid, bile, cervico-vaginal fluid, and seminal plasma. With no doubt these body fluids differ in the extent of their application in clinical proteomics investigations, hence in some cases the presented SOPs are established following more extensive testing (e.g., plasma, serum, urine, CSF) than others (nasal secretions, saliva, tears, breast milk, bronchoalveolar fluid, nipple aspirate fluid, amniotic fluid, bile, cervico-vaginal fluid, and seminal plasma). However, even in these latter cases, the presented protocols were reported by at least two independent groups according to the literature. We hope they can thus serve as a reliable guide for sample collection based on our current knowledge in the field and excellent starting points for proteomics investigators. It should also be pointed that variations to these protocols exist and their further refinement in the future is foreseen following the evolution of the proteomics technologies.
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References
American Red Cross. Plasma. Available from http://www.redcrossblood.org/learn-about-blood/blood-components/plasma
Omenn GS, Menon R, Adamski M, Blackwell T, Haab BB, Gao W, States DJ (2007) The human plasma and serum proteome. In: Thongboonkerd V (ed) Proteomics of human body fluids. Humana, Totowa
Schulte I, Tammen H, Selle H et al (2005) Peptides in body fluids and tissues as markers of disease. Expert Rev Mol Diagn 5:145–157
Granger J, Siddiqui J, Copeland S et al (2005) Albumin depletion of human plasma also removes low abundance proteins including the cytokines. Proteomics 5:4713–4718
Guerrier L, Righetti PG, Boschetti E (2008) Reduction of dynamic protein concentration range of biological extracts for the discovery of low-abundance proteins by means of hexapeptide ligand library. Nat Protoc 3:883–890
Bodzon-Kulakowska A, Bierczynska-Krzysik A, Dylag T et al (2007) Methods for samples preparation in proteomic research. J Chromatogr B Analyt Technol Biomed Life Sci 849:1–31
Omenn GS (2007) THE HUPO human plasma proteome project. Proteomics Clin Appl 1:769–779
Muthusamy B, Hanumanthu G, Suresh S et al (2005) Plasma Proteome Database as a resource for proteomics research. Proteomics 5:3531–3536
Plasma Proteome Database. Available from http://www.plasmaproteomedatabase.org/index.html
Rai AJ, Gelfand CA, Haywood BC et al (2005) HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 5:3262–3277
Kim MR, Kim CW (2007) Human blood plasma preparation for two-dimensional gel electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 849:203–210
Di Domenico M, Scumaci D, Grasso S et al (2013) Biomarker discovery by plasma proteomics in familial Brugada Syndrome. Front Biosci (Landmark Ed) 18:564–571
Tammen H (2008) Specimen collection and handling: standardization of blood sample collection. Methods Mol Biol 428:35–42
Issaq HJ, Xiao Z, Veenstra TD (2007) Serum and plasma proteomics. Chem Rev 107:3601–3620
Adkins JN, Varnum SM, Auberry KJ et al (2002) Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol Cell Proteomics 1:947–955
Putnam DF (1971) Composition and concentrative properties of human urine. National Aeronautics and Space Administration, Washington
Rodriguez-Suarez E, Siwy J, Zurbig P et al (2013) Urine as a source for clinical proteome analysis: from discovery to clinical application. Biochim Biophys Acta 1844(5):884–898
Mischak H, Kolch W, Aivaliotis M et al (2010) Comprehensive human urine standards for comparability and standardization in clinical proteome analysis. Proteomics Clin Appl 4:464–478
Yamamoto T (2010) The 4th Human Kidney and Urine Proteome Project (HKUPP) workshop. 26 September 2009, Toronto, Canada. Proteomics 10:2069–2070
Yamamoto T, Langham RG, Ronco P et al (2008) Towards standard protocols and guidelines for urine proteomics: a report on the Human Kidney and Urine Proteome Project (HKUPP) symposium and workshop, 6 October 2007, Seoul, Korea and 1 November 2007, San Francisco, CA, USA. Proteomics 8:2156–2159
Zurbig P, Dihazi H, Metzger J et al (2011) Urine proteomics in kidney and urogenital diseases: moving towards clinical applications. Proteomics Clin Appl 5:256–268
van Gool AJ, Hendrickson RC (2012) The proteomic toolbox for studying cerebrospinal fluid. Expert Rev Proteomics 9:165–179
Ramström M, Bergquist J (2007) The human plasma and serum proteome. In: Thongboonkerd V (ed) Proteomics of human body fluids. Humana, Totowa
Kroksveen AC, Opsahl JA, Aye TT et al (2011) Proteomics of human cerebrospinal fluid: discovery and verification of biomarker candidates in neurodegenerative diseases using quantitative proteomics. J Proteomics 74:371–388
Teunissen CE, Petzold A, Bennett JL et al (2009) A consensus protocol for the standardization of cerebrospinal fluid collection and biobanking. Neurology 73:1914–1922
Casado B, Pannell LK, Iadarola P et al (2005) Identification of human nasal mucous proteins using proteomics. Proteomics 5:2949–2959
Casado B, Viglio S, Baraniuk JN (2007) Proteomics of sinusitis nasal lavage fluid. In: Thongboonkerd V (ed) Proteomics of human body fluids. Humana, Totowa
Casado B, Iadarola P, Pannell L (2008) Preparation of nasal secretions for proteome analysis. In: Posch A (ed) 2D PAGE: sample preparation and fractionation. Humana, Totowa, pp 77–87
Caseiro A, Ferreira R, Padrao A et al (2013) Salivary proteome and peptidome profiling in type 1 diabetes mellitus using a quantitative approach. J Proteome Res 12(4):1700–1709
Casado B, Iadarola P, Pannell LK (2008) Preparation of nasal secretions for proteome analysis. Methods Mol Biol 425:77–87
Lamy E, Mau M (2012) Saliva proteomics as an emerging, non-invasive tool to study livestock physiology, nutrition and diseases. J Proteomics 75:4251–4258
Vitorino R, Guedes S, Manadas B et al (2012) Toward a standardized saliva proteome analysis methodology. J Proteomics 75:5140–5165
He H, Sun G, Ping F et al (2011) A new and preliminary three-dimensional perspective: proteomes of optimization between OSCC and OLK. Artif Cells Blood Substit Immobil Biotechnol 39:26–30
Goncalves Lda R, Soares MR, Nogueira FC et al (2010) Comparative proteomic analysis of whole saliva from chronic periodontitis patients. J Proteomics 73:1334–1341
Rudney JD, Staikov RK, Johnson JD (2009) Potential biomarkers of human salivary function: a modified proteomic approach. Arch Oral Biol 54:91–100
Vitorino R, de Morais Guedes S, Ferreira R et al (2006) Two-dimensional electrophoresis study of in vitro pellicle formation and dental caries susceptibility. Eur J Oral Sci 114:147–153
Cabras T, Pisano E, Mastinu A et al (2010) Alterations of the salivary secretory peptidome profile in children affected by type 1 diabetes. Mol Cell Proteomics 9:2099–2108
Hu S, Wang J, Meijer J et al (2007) Salivary proteomic and genomic biomarkers for primary Sjogren’s syndrome. Arthritis Rheum 56:3588–3600
Ambatipudi KS, Swatkoski S, Moresco JJ et al (2012) Quantitative proteomics of parotid saliva in primary Sjogren’s syndrome. Proteomics 12:3113–3120
Wu ZZ, Wang JG, Zhang XL (2009) Diagnostic model of saliva protein finger print analysis of patients with gastric cancer. World J Gastroenterol 15:865–870
Jarai T, Maasz G, Burian A et al (2012) Mass spectrometry-based salivary proteomics for the discovery of head and neck squamous cell carcinoma. Pathol Oncol Res 18:623–628
Dowling P, Wormald R, Meleady P et al (2008) Analysis of the saliva proteome from patients with head and neck squamous cell carcinoma reveals differences in abundance levels of proteins associated with tumour progression and metastasis. J Proteomics 71:168–175
Xiao H, Zhang L, Zhou H et al (2012) Proteomic analysis of human saliva from lung cancer patients using two-dimensional difference gel electrophoresis and mass spectrometry. Mol Cell Proteomics 11(M111):012112
WHO (2007) Common minimum technical standards and protocols for biological resource centres dedicated to cancer research. International Agency for Research on Cancer, Working Group Reports. vol. 2
Vitorino R, Barros AS, Caseiro A et al (2012) Evaluation of different extraction procedures for salivary peptide analysis. Talanta 94:209–215
Ananthi S, Santhosh RS, Nila MV et al (2011) Comparative proteomics of human male and female tears by two-dimensional electrophoresis. Exp Eye Res 92:454–463
Saijyothi AV, Angayarkanni N, Syama C et al (2010) Two dimensional electrophoretic analysis of human tears: collection method in dry eye syndrome. Electrophoresis 31:3420–3427
Zhou L, Beuerman RW, Chan CM et al (2009) Identification of tear fluid biomarkers in dry eye syndrome using iTRAQ quantitative proteomics. J Proteome Res 8:4889–4905
Acera A, Rocha G, Vecino E et al (2008) Inflammatory markers in the tears of patients with ocular surface disease. Ophthalmic Res 40:315–321
Argueso P, Balaram M, Spurr-Michaud S et al (2002) Decreased levels of the goblet cell mucin MUC5AC in tears of patients with Sjogren syndrome. Invest Ophthalmol Vis Sci 43:1004–1011
Saghizadeh M, Brown DJ, Castellon R et al (2001) Overexpression of matrix metalloproteinase-10 and matrix metalloproteinase-3 in human diabetic corneas: a possible mechanism of basement membrane and integrin alterations. Am J Pathol 158:723–734
Wong TT, Zhou L, Li J et al (2011) Proteomic profiling of inflammatory signaling molecules in the tears of patients on chronic glaucoma medication. Invest Ophthalmol Vis Sci 52:7385–7391
Liao Y, Alvarado R, Phinney B et al (2011) Proteomic characterization of human milk whey proteins during a twelve-month lactation period. J Proteome Res 10:1746–1754
Conti A, Giuffrida MG, Cavaletto M (2007) Proteomics of human milk. In: Thongboonkerd V (ed) Proteomics of human body fluids. Humana, Totowa
Gao X, McMahon RJ, Woo JG et al (2012) Temporal changes in milk proteomes reveal developing milk functions. J Proteome Res 11:3897–3907
Dallas DC, Guerrero A, Khaldi N et al (2013) Extensive in vivo human milk peptidomics reveals specific proteolysis yielding protective antimicrobial peptides. J Proteome Res 12:2295–2304
Govender P, Dunn MJ, Donnelly SC (2009) Proteomics and the lung: analysis of bronchoalveolar lavage fluid. Proteomics Clin Appl 3:1044–1051
Foster MW, Thompson JW, Que LG et al (2013) Proteomic analysis of human bronchoalveolar lavage fluid after subsgemental exposure. J Proteome Res 12:2194–2205
Lee AS (2004) American Thoracic Society. Bronchoalveolar Lavage. Available from http://www.thoracic.org/clinical/critical-care/critical-care-procedures/bronchoalveolar-lavage.php
Pastor MD, Nogal A, Molina-Pinelo S et al (2013) Identification of proteomic signatures associated with lung cancer and COPD. J Proteomics 89:227–237
Kosanam H, Sato M, Batruch I et al (2012) Differential proteomic analysis of bronchoalveolar lavage fluid from lung transplant patients with and without chronic graft dysfunction. Clin Biochem 45:223–230
Cederfur C, Malmstrom J, Nihlberg K et al (2012) Glycoproteomic identification of galectin-3 and -8 ligands in bronchoalveolar lavage of mild asthmatics and healthy subjects. Biochim Biophys Acta 1820:1429–1436
Ruhlen RL, Sauter ER (2007) Proteomics of nipple aspirate fluid, breast cyst fluid, milk, and colostrum. Proteomics Clin Appl 1:845–852
Ruhlen RL, Sauter ER (2007) Proteomic analysis of breast tissue and nipple aspirate fluid for breast cancer detection. Biomark Med 1:251–260
Pavlou MP, Kulasingam V, Sauter ER et al (2010) Nipple aspirate fluid proteome of healthy females and patients with breast cancer. Clin Chem 56:848–855
Pawlik TM, Hawke DH, Liu Y et al (2006) Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein. BMC Cancer 6:68
Alexander H, Stegner AL, Wagner-Mann C et al (2004) Proteomic analysis to identify breast cancer biomarkers in nipple aspirate fluid. Clin Cancer Res 10:7500–7510
Noble J, Dua RS, Locke I et al (2007) Proteomic analysis of nipple aspirate fluid throughout the menstrual cycle in healthy pre-menopausal women. Breast Cancer Res Treat 104:191–196
Cho CK, Smith CR, Diamandis EP (2010) Amniotic fluid proteome analysis from Down syndrome pregnancies for biomarker discovery. J Proteome Res 9:3574–3582
Kolialexi A, Tounta G, Mavrou A et al (2011) Proteomic analysis of amniotic fluid for the diagnosis of fetal aneuploidies. Expert Rev Proteomics 8:175–185
Amniocentesis protocol (2011) Available from http://hsc.unm.edu/som/obgyn/docs/protocols/20.pdf
Tsangaris GT, Kolialexi A, Karamessinis PM et al (2006) The normal human amniotic fluid supernatant proteome. In Vivo 20:479–490
Cho CK, Shan SJ, Winsor EJ et al (2007) Proteomics analysis of human amniotic fluid. Mol Cell Proteomics 6:1406–1415
Barbhuiya MA, Sahasrabuddhe NA, Pinto SM et al (2011) Comprehensive proteomic analysis of human bile. Proteomics 11:4443–4453
Farina A, Dumonceau JM, Lescuyer P (2009) Proteomic analysis of human bile and potential applications for cancer diagnosis. Expert Rev Proteomics 6:285–301
Farina A, Dumonceau JM, Frossard JL et al (2009) Proteomic analysis of human bile from malignant biliary stenosis induced by pancreatic cancer. J Proteome Res 8:159–169
Tang LJ, De Seta F, Odreman F et al (2007) Proteomic analysis of human cervical-vaginal fluids. J Proteome Res 6:2874–2883
Shaw JL, Smith CR, Diamandis EP (2007) Proteomic analysis of human cervico-vaginal fluid. J Proteome Res 6:2859–2865
Lockwood CJ, Senyei AE, Dische MR et al (1991) Fetal fibronectin in cervical and vaginal secretions as a predictor of preterm delivery. N Engl J Med 325:669–674
Kalinka J, Sobala W, Wasiela M et al (2005) Decreased proinflammatory cytokines in cervicovaginal fluid, as measured in midgestation, are associated with preterm delivery. Am J Reprod Immunol 54:70–76
Dasari S, Pereira L, Reddy AP et al (2007) Comprehensive proteomic analysis of human cervical-vaginal fluid. J Proteome Res 6:1258–1268
Di Quinzio MK, Oliva K, Holdsworth SJ et al (2007) Proteomic analysis and characterisation of human cervico-vaginal fluid proteins. Aust N Z J Obstet Gynaecol 47:9–15
Pereira L, Reddy AP, Jacob T et al (2007) Identification of novel protein biomarkers of preterm birth in human cervical-vaginal fluid. J Proteome Res 6:1269–1276
Davalieva K, Kiprijanovska S, Noveski P et al (2012) Human seminal plasma proteome study: a search for male infertility biomarkers. Balkan J Med Genet 15:35–38
Milardi D, Grande G, Vincenzoni F et al (2012) Proteomic approach in the identification of fertility pattern in seminal plasma of fertile men. Fertil Steril 97:67–73 e61
Davalieva K, Kiprijanovska S, Noveski P et al (2012) Proteomic analysis of seminal plasma in men with different spermatogenic impairment. Andrologia 44:256–264
Hassan MI, Kumar V, Kashav T et al (2007) Proteomic approach for purification of seminal plasma proteins involved in tumor proliferation. J Sep Sci 30:1979–1988
WHO (2010) Laboratory manual for the examination and processing of human semen, 5th edn. WHO, Geneva
da Silva BF, Souza GH, lo Turco EG et al (2013) Differential seminal plasma proteome according to semen retrieval in men with spinal cord injury. Fertil Steril 100:959–969
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Lygirou, V., Makridakis, M., Vlahou, A. (2015). Biological Sample Collection for Clinical Proteomics: Existing SOPs. In: Vlahou, A., Makridakis, M. (eds) Clinical Proteomics. Methods in Molecular Biology, vol 1243. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1872-0_1
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DOI: https://doi.org/10.1007/978-1-4939-1872-0_1
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