With or without you - Proteomics with or without major plasma/serum proteins

Journal of Proteomics

Volumn 140, Issue , 2016, Pages 62-80

  Gianazza, Elisabetta ^a   Miller, Ingrid ^b   Palazzolo, Luca ^a   Parravicini, Chiara ^a   Eberini, Ivano ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b UNIVERSITY OF VETERINARY MEDICINE   (Austria)

Author keywords

Depletion; Enrichment; Immunodepletion; Protein species; Serum proteins

Indexed keywords

ALBUMIN; APOLIPOPROTEIN; APOLIPOPROTEIN F; ARYLDIALKYLPHOSPHATASE; C REACTIVE PROTEIN; CHYMASE; CLUSTERIN; GLYCOPROTEIN; HUMAN SERUM ALBUMIN; IMMUNOGLOBULIN; INTERLEUKIN 1; INTERLEUKIN 6; PLASMA PROTEIN; SERUM AMYLOID A; THYROXINE BINDING GLOBULIN; TRANSFORMING GROWTH FACTOR BETA; TUMOR NECROSIS FACTOR ALPHA; ULINASTATIN; UNCLASSIFIED DRUG; BIOLOGICAL MARKER; PROTEOME;

IONIC STRENGTH; PH; PRECIPITATION; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN FUNCTION; PROTEIN GLYCOSYLATION; PROTEIN POLYMERIZATION; PROTEIN STRUCTURE; PROTEOMICS; REVIEW; ANIMAL; BLOOD; METABOLISM; PROCEDURES;

ANIMALS; BIOMARKERS; BLOOD PROTEINS; PROTEOME; PROTEOMICS;

EID: 84963820653     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2016.04.002     Document Type: Review

References (185)

1. Anderson N.L., Anderson N.G. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 2002, 1:845-867.
2. Subramanian S. Dye-ligand affinity chromatography: the interaction of Cibacron blue F3GA with proteins and enzymes. CRC Crit. Rev. Bioeng. 1984, 16:169-205.
3. Denizli A., Piskin E. Dye-ligand affinity systems. J. Biochem. Biophys. Methods 2001, 49:391-416.
4. Gianazza E., Arnaud P. A general method for the fractionation of plasma proteins: Pseudo-ligand affinity chromatography on immobilized Cibacron blue F3-G. Biochem. J. 1982, 201:129-136.
5. Gianazza E., Arnaud P. Chromatography of plasma proteins on immobilized Cibacron blue F3-GA. Mechanism of the molecular interaction. Biochem. J. 1982, 203:637-641.
6. Miller I., Gemeiner M. An electrophoretic study on interactions of albumins of different species with immobilized Cibacron blue F3G A. Electrophoresis 1998, 19:2506-2514.
7. Di Girolamo F., Righetti P.G. Plasma proteomics for biomarker discovery: a study in blue. Electrophoresis 2011, 32:3638-3644.
8. Andacht T.M., Pantazides B.G., Crow B.S., Fidder A., Noort D., Thomas J.D., et al. An enhanced throughput method for quantification of sulfur mustard adducts to human serum albumin via isotope dilution tandem mass spectrometry. J. Anal. Toxicol. 2014, 38:8-15.
9. Hebert G.A., Pelham P.L., Pittman B. Determination of the optimal ammonium sulfate concentration for the fractionation of rabbit, sheep, horse, and goat antisera. Appl. Microbiol. 1973, 25:26-36.
10. Mahn A., Ismail M. Depletion of highly abundant proteins in blood plasma by ammonium sulfate precipitation for 2D-PAGE analysis. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 2011, 879:3645-3648.
11. Saha S., Halder S., Bhattacharya D., Banerjee D., Chakrabarti A. Fractional precipitation of plasma proteome by ammonium sulfate: case studies in Leukemia and Thalassemia. J. Proteomics Bioinform. 2012, 5:163-171.
12. Fernandez-Costa C., Calamia V., Fernandez-Puente P., Capelo-Martinez J.L., Ruiz-Romero C., Blanco F.J. Sequential depletion of human serum for the search of osteoarthritis biomarkers. Proteome Sci. 2012, 10:55.
13. Henning A.K., Albrecht D., Riedel K., Mettenleiter T.C., Karger A. An alternative method for serum protein depletion/enrichment by precipitation at mildly acidic pH values and low ionic strength. Proteomics 2015, 15:1935-1940.
14. Gianazza E., Wait R., Begum S., Eberini I., Campagnoli M., Labò S., et al. Mapping the 5-50 kDa fraction of human amniotic fluid proteins by 2DE and ESI-MS. Proteomics Clin. Appl. 2007, 1:167-175.
15. Gianazza E., Guerini Rocco A., Marchetto A., Vergani L. Immobilized pH gradients with electrodic plateaus (and other unusual procedures for 2DE). Electrophoresis 2007, 28:2953-2956.
16. Tirumalai R.S., Chan K.C., Prieto D.A., Issaq H.J., Conrads T.P., Veenstra T.D. Characterization of the low molecular weight human serum proteome. Mol. Cell. Proteomics 2003, 2:1096-1103.
17. Gundry R.L., Fu Q., Jelinek C.A., Van Eyk J.E., Cotter R.J. Investigation of an albumin-enriched fraction of human serum and its albuminome. Proteomics Clin. Appl. 2007, 1:73-88.
18. Holewinski R.J., Jin Z., Powell M.J., Maust M.D., Van Eyk J.E. A fast and reproducible method for albumin isolation and depletion from serum and cerebrospinal fluid. Proteomics 2013, 13:743-750.
19. Scumaci D., Gaspari M., Saccomanno M., Argiro G., Quaresima B., Faniello C.M., et al. Assessment of an ad hoc procedure for isolation and characterization of human albuminome. Anal. Biochem. 2011, 418:161-163.
20. Camaggi C.M., Zavatto E., Gramantieri L., Camaggi V., Strocchi E., Righini R., et al. Serum albumin-bound proteomic signature for early detection and staging of hepatocarcinoma: sample variability and data classification. Clin. Chem. Lab. Med. 2010, 48:1319-1326.
21. Mahn A., Reyes A., Zamorano M., Cifuentes W., Ismail M. Depletion of highly abundant proteins in blood plasma by hydrophobic interaction chromatography for proteomic analysis. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 2010, 878:1038-1044.
22. Schade R., Calzado E.G., Sarmiento R., Chacana P.A., Porankiewicz-Asplund J., Terzolo H.R. Chicken egg yolk antibodies (IgY-technology): a review of progress in production and use in research and human and veterinary medicine. Altern. Lab. Anim 2005, 33:129-154.
23. Tan S.H., Mohamedali A., Kapur A., Baker M.S. Ultradepletion of human plasma using chicken antibodies: a proof of concept study. J. Proteome Res. 2013, 12:2399-2413.
24. Harmsen M.M., De Haard H.J. Properties, production, and applications of camelid single-domain antibody fragments. Appl. Microbiol. Biotechnol. 2007, 77:13-22.
25. Kullolli M., Warren J., Arampatzidou M., Pitteri S.J. Performance evaluation of affinity ligands for depletion of abundant plasma proteins. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 2013, 939:10-16.
26. Chromy B.A., Gonzales A.D., Perkins J., Choi M.W., Corzett M.H., Chang B.C., et al. Proteomic analysis of human serum by two-dimensional differential gel electrophoresis after depletion of high-abundant proteins. J. Proteome Res. 2004, 3:1120-1127.
27. Bjorhall K., Miliotis T., Davidsson P. Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics 2005, 5:307-317.
28. Roche S., Tiers L., Provansal M., Seveno M., Piva M.T., Jouin P., et al. Depletion of one, six, twelve or twenty major blood proteins before proteomic analysis: the more the better?. J. Proteome 2009, 72:945-951.
29. Smith M.P., Wood S.L., Zougman A., Ho J.T., Peng J., Jackson D., et al. A systematic analysis of the effects of increasing degrees of serum immunodepletion in terms of depth of coverage and other key aspects in top-down and bottom-up proteomic analyses. Proteomics 2011, 11:2222-2235.
30. Macdonald N., Cumberbatch M., Singh M., Moggs J.G., Orphanides G., Dearman R.J., et al. Proteomic analysis of suction blister fluid isolated from human skin. Clin. Exp. Dermatol. 2006, 31:445-448.
31. Muller A.C., Breitwieser F.P., Fischer H., Schuster C., Brandt O., Colinge J., et al. A comparative proteomic study of human skin suction blister fluid from healthy individuals using immunodepletion and iTRAQ labeling. J. Proteome Res. 2012, 11:3715-3727.
32. Patel B.B., Barrero C.A., Braverman A., Kim P.D., Jones K.A., Chen D.E., et al. Assessment of two immunodepletion methods: off-target effects and variations in immunodepletion efficiency may confound plasma proteomics. J. Proteome Res. 2012, 11:5947-5958.
33. Righetti P.G., Boschetti E., Lomas L., Citterio A. Protein equalizer technology: the quest for a "democratic proteome". Proteomics 2006, 6:3980-3992.
34. Righetti P.G., Boschetti E., Candiano G. Mark Twain: how to fathom the depth of your pet proteome. J. Proteome 2012, 75:4783-4791.
35. Righetti P.G., Candiano G., Citterio A., Boschetti E. Combinatorial peptide ligand libraries as a "Trojan horse" in deep discovery proteomics. Anal. Chem. 2015, 87:293-305.
36. Fasoli E., Farinazzo A., Sun C.J., Kravchuk A.V., Guerrier L., Fortis F., et al. Interaction among proteins and peptide libraries in proteome analysis: pH involvement for a larger capture of species. J. Proteome 2010, 73:733-742.
37. Candiano G., Santucci L., Bruschi M., Petretto A., D'Ambrosio C., Scaloni A., et al. "Cheek-to-cheek" urinary proteome profiling via combinatorial peptide ligand libraries: A novel, unexpected elution system. J. Proteome 2012, 75:796-805.
38. Candiano G., Dimuccio V., Bruschi M., Santucci L., Gusmano R., Boschetti E., et al. Combinatorial peptide ligand libraries for urine proteome analysis: investigation of different elution systems. Electrophoresis 2009, 30:2405-2411.
39. Di Girolamo F., Boschetti E., Chung M.C., Guadagni F., Righetti P.G. "Proteomineering" or not? The debate on biomarker discovery in sera continues. J. Proteome 2011, 74:589-594.
40. Bellei E., Monari E., Bergamini S., Ozben T., Tomasi A. Optimizing protein recovery yield from serum samples treated with beads technology. Electrophoresis 2011, 32:1414-1421.
41. Sennels L., Salek M., Lomas L., Boschetti E., Righetti P.G., Rappsilber J. Proteomic analysis of human blood serum using peptide library beads. J. Proteome Res. 2007, 6:4055-4062.
42. Simo C., Bachi A., Cattaneo A., Guerrier L., Fortis F., Boschetti E., et al. Performance of combinatorial peptide libraries in capturing the low-abundance proteome of red blood cells. 1. Behavior of mono- to hexapeptides. Anal. Chem. 2008, 80:3547-3556.
43. Di Girolamo F., Righetti P.G., Soste M., Feng Y., Picotti P. Reproducibility of combinatorial peptide ligand libraries for proteome capture evaluated by selected reaction monitoring. J. Proteome 2013, 89:215-226.
44. Sihlbom C., Kanmert I., Bahr H., Davidsson P. Evaluation of the combination of bead technology with SELDI-TOF-MS and 2-D DIGE for detection of plasma proteins. J. Proteome Res. 2008, 7:4191-4198.
45. Fernandez C., Santos H.M., Ruiz-Romero C., Blanco F.J., Capelo-Martinez J.L. A comparison of depletion versus equalization for reducing high-abundance proteins in human serum. Electrophoresis 2011, 32:2966-2974.
46. Selvaraju S., El Rassi Z. Reduction of protein concentration range difference followed by multicolumn fractionation prior to 2-DE and LC-MS/MS profiling of serum proteins. Electrophoresis 2011, 32:674-685.
47. Zhu G., Zhao P., Deng N., Tao D., Sun L., Liang Z., et al. Single chain variable fragment displaying M13 phage library functionalized magnetic microsphere-based protein equalizer for human serum protein analysis. Anal. Chem. 2012, 84:7633-7637.
48. Mouton-Barbosa E., Roux-Dalvai F., Bouyssie D., Berger F., Schmidt E., Righetti P.G., et al. In-depth exploration of cerebrospinal fluid by combining peptide ligand library treatment and label-free protein quantification. Mol. Cell. Proteomics 2010, 9:1006-1021.
49. Liao Y., Alvarado R., Phinney B., Lonnerdal B. Proteomic characterization of human milk whey proteins during a twelve-month lactation period. J. Proteome Res. 2011, 10:1746-1754.
50. Molinari C.E., Casadio Y.S., Hartmann B.T., Livk A., Bringans S., Arthur P.G., et al. Proteome mapping of human skim milk proteins in term and preterm milk. J. Proteome Res. 2012, 11:1696-1714.
51. Jagtap P., Bandhakavi S., Higgins L., McGowan T., Sa R., Stone M.D., et al. Workflow for analysis of high mass accuracy salivary data set using MaxQuant and ProteinPilot search algorithm. Proteomics 2012, 12:1726-1730.
52. Rolland A.D., Lavigne R., Dauly C., Calvel P., Kervarrec C., Freour T., et al. Identification of genital tract markers in the human seminal plasma using an integrative genomics approach. Hum. Reprod. 2013, 28:199-209.
53. Lichtenauer A.M., Herzog R., Tarantino S., Aufricht C., Kratochwill K. Equalizer technology followed by DIGE-based proteomics for detection of cellular proteins in artificial peritoneal dialysis effluents. Electrophoresis 2014, 35:1387-1394.
54. Peffers M.J., McDermott B., Clegg P.D., Riggs C.M. Comprehensive Protein Profiling of Synovial Fluid in Osteoarthritis Following Protein Equalization. Osteoarthr. Cartil. 2015, Vol. 23:1204-1213. Osteoarthritis Research Society.
55. Fakelman F., Felix K., Buchler M.W., Werner J. New pre-analytical approach for the deep proteome analysis of sera from pancreatitis and pancreas cancer patients. Arch. Physiol. Biochem. 2010, 116:208-217.
56. Au J.S., Cho W.C., Yip T.T., Yip C., Zhu H., Leung W.W., et al. Deep proteome profiling of sera from never-smoked lung cancer patients. Biochem. Pharmacol. 2007, 61:570-577.
57. Monari E., Casali C., Cuoghi A., Nesci J., Bellei E., Bergamini S., et al. Enriched sera protein profiling for detection of non-small cell lung cancer biomarkers. Protein Sci. 2011, 9:55.
58. Milan E., Lazzari C., Anand S., Floriani I., Torri V., Sorlini C., et al. SAA1 is over-expressed in plasma of non small cell lung cancer patients with poor outcome after treatment with epidermal growth factor receptor tyrosine-kinase inhibitors. J. Proteome 2012, 76:91-101. Spec No.
59. Marrocco C., Rinalducci S., Mohamadkhani A., D'Amici G.M., Zolla L. Plasma gelsolin protein: a candidate biomarker for hepatitis B-associated liver cirrhosis identified by proteomic approach. Blood Transfus. 2010, 8 Suppl. 3:s105-s112.
60. Shetty V., Jain P., Nickens Z., Sinnathamby G., Mehta A., Philip R. Investigation of plasma biomarkers in HIV-1/HCV mono- and coinfected individuals by multiplex iTRAQ quantitative proteomics. OMICS 2011, 15:705-717.
61. Fekkar A., Pionneau C., Brossas J.Y., Marinach-Patrice C., Snounou G., Brock M., et al. DIGE enables the detection of a putative serum biomarker of fungal origin in a mouse model of invasive aspergillosis. J. Proteome 2012, 75:2536-2549.
62. Ruis-Gonzalez M.D., Canete M.D., Gomez-Chaparro J.L., Abril N., Canete R., Lopez-Barea J. Alterations of protein expression in serum of infants with intrauterine growth restriction and different gestational ages. J. Proteome 2015, 119:169-182.
63. Balfoussia E., Skenderi K., Tsironi M., Anagnostopoulos A.K., Parthimos N., Vougas K., et al. A proteomic study of plasma protein changes under extreme physical stress. J. Proteome 2014, 98:1-14.
64. Soler L., Miller I., Hummel K., Razzazi-Fazeli E., Jessen F., Escribano D., et al. Growth promotion in pigs by oxytetracycline coincides with down regulation of serum inflammatory parameters and of hibernation-associated protein HP-27. Electrophoresis 2016.
65. Drabovich A.P., Martinez-Morillo E., Diamandis E.P. Toward an integrated pipeline for protein biomarker development. Biochim. Biophys. Acta 1854, 2015:677-686.
66. Hanash S. HUPO initiatives relevant to clinical proteomics. Mol. Cell. Proteomics 2004, 3:298-301.
67. Uhlen M., Bjorling E., Agaton C., Szigyarto C.A., Amini B., Andersen E., et al. A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell. Proteomics 2005, 4:1920-1932.
68. Uhlen M., Oksvold P., Fagerberg L., Lundberg E., Jonasson K., Forsberg M., et al. Towards a knowledge-based human protein atlas. Nat. Biotechnol. 2010, 28:1248-1250.
69. Uhlen M., Fagerberg L., Hallstrom B.M., Lindskog C., Oksvold P., Mardinoglu A., et al. Proteomics. Tissue-based map of the human proteome. Science 2015, 347:1260419.
70. van den Bemd G.J., Krijgsveld J., Luider T.M., van Rijswijk A.L., Demmers J.A., Jenster G. Mass spectrometric identification of human prostate cancer-derived proteins in serum of xenograft-bearing mice. Mol. Cell. Proteomics 2006, 5:1830-1839.
71. Li Y., Tang Z.Y., Tian B., Ye S.L., Qin L.X., Xue Q., et al. Serum CYFRA 21-1 level reflects hepatocellular carcinoma metastasis: study in nude mice model and clinical patients. J. Cancer Res. Clin. Oncol. 2006, 132:515-520.
72. Cervi D., Yip T.T., Bhattacharya N., Podust V.N., Peterson J., Abou-Slaybi A., et al. Platelet-associated PF-4 as a biomarker of early tumor growth. Blood 2008, 111:1201-1207.
73. Chong P.K., Lee H., Zhou J., Liu S.C., Loh M.C., So J.B., et al. Reduced plasma APOA1 level is associated with gastric tumor growth in MKN45 mouse xenograft model. J. Proteome 2010, 73:1632-1640.
74. Balys R., Alaoui-Jamali M., Hier M., Black M., Domanowski G., Rochon L., et al. Clinically relevant oral cancer model for serum proteomic eavesdropping on the tumour microenvironment. J. Otolaryngol. 2006, 35:157-166.
75. Bijian K., Mlynarek A.M., Balys R.L., Jie S., Xu Y., Hier M.P., et al. Serum proteomic approach for the identification of serum biomarkers contributed by oral squamous cell carcinoma and host tissue microenvironment. J. Proteome Res. 2009, 8:2173-2185.
76. Wu C.C., Peng P.H., Chang Y.T., Huang Y.S., Chang K.P., Hao S.P., et al. Identification of potential serum markers for nasopharyngeal carcinoma from a xenografted mouse model using Cy-dye labeling combined with three-dimensional fractionation. Proteomics 2008, 8:3605-3620.
77. He Y., Wu X., Liu X., Yan G., Xu C. LC-MS/MS analysis of ovarian cancer metastasis-related proteins using a nude mouse model: 14-3-3 zeta as a candidate biomarker. J. Proteome Res. 2010, 9:6180-6190.
78. Tang H.Y., Beer L.A., Chang-Wong T., Hammond R., Gimotty P., Coukos G., et al. A xenograft mouse model coupled with in-depth plasma proteome analysis facilitates identification of novel serum biomarkers for human ovarian cancer. J. Proteome Res. 2012, 11:678-691.
79. Faca V.M., Song K.S., Wang H., Zhang Q., Krasnoselsky A.L., Newcomb L.F., et al. A mouse to human search for plasma proteome changes associated with pancreatic tumor development. PLoS Med. 2008, 5.
80. Pitteri S.J., JeBailey L., Faca V.M., Thorpe J.D., Silva M.A., Ireton R.C., et al. Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery. PLoS One 2009, 4.
81. Tang H.Y., Beer L.A., Tanyi J.L., Zhang R., Liu Q., Speicher D.W. Protein isoform-specific validation defines multiple chloride intracellular channel and tropomyosin isoforms as serological biomarkers of ovarian cancer. J. Proteome 2013, 89:165-178.
82. Bjellqvist B., Ek K., Righetti P.G., Gianazza E., Görg A., Westermeier R., et al. Isoelectric focusing in immobilized pH gradients: Principles, methodology and some applications. J. Biochem. Biophys. Methods 1982, 6:317-339.
83. Gianazza E., Astrua-Testori S., Giacon P., Righetti P.G. An improved protocol for 2D maps of serum proteins with immobilized pH gradients in the first dimension. Electrophoresis 1985, 6:332-339.
84. Wait R., Begum S., Brambilla D., Carabelli A.M., Conserva F., Rocco Guerini A., et al. Redox options in two-dimensional electrophoresis. Amino Acids 2005, 28:239-272.
85. Tsuji S., Kato H., Matsuoka Y., Fukushima T., Nanjoh I., Amano T., et al. Phylogenetical and ontogenetical studies on the molecular weight heterogeneity of bovine serum transferrin. Biochem. Genet. 1984, 22:1127-1143.
86. Evans R.W., Williams J. The electrophoresis of transferrins in urea/polyacrylamide gels. Biochem. J. 1980, 189:541-546.
87. Yamashita H., Nakatsuka T., Hirose M. Structural and functional characteristics of partially disulfide-reduced intermediates of ovotransferrin N lobe: Cystine localization by indirect end-labeling approach and implications for the reduction pathway. J. Biol. Chem. 1995, 270:29806-29812.
88. Miller I., Haynes P., Gemeiner M., Aebersold R., Manzoni C., Lovati M.R., et al. Proteins of rat serum: II. Influence of some biological parameters on the 2-DE pattern. Electrophoresis 1998, 19:1493-1500.
89. Wait R., Miller I., Eberini I., Cairoli F., Veronesi C., Battocchio M., et al. Strategies for proteomics with incompletely characterised genomes: the proteome of Bos taurus serum. Electrophoresis 2002, 23:3418-3427.
90. Meier F., Seidel B., Geserick G., Luther P., Patzelt D. Haptoglobintypisierung von Serumproben ausgewählter Säugetiere mittels Stärkegelelektrophorese. Mh Vet-Med. 1980, 35:617-620.
91. Jungblut P.R., Holzhutter H.G., Apweiler R., Schluter H. The speciation of the proteome. Chem. Cent. J. 2008, 2:16.
92. Mastrangelo A., Colasanti T., Barbati C., Pecani A., Sabatinelli D., Pendolino M., et al. The role of Posttranslational protein modifications in Rheumatological diseases: focus on Rheumatoid Arthritis. J. Immunol. Res. 2015, 2015:712490.
93. Ren R.J., Dammer E.B., Wang G., Seyfried N.T., Levey A.I. Proteomics of protein post-translational modifications implicated in neurodegeneration. Transl. Neurosci. 2014, 3:23.
94. Fukami H., Okunishi H., Miyazaki M. Chymase: its pathophysiological roles and inhibitors. Curr. Pharm. Des. 1998, 4:439-453.
95. Caughey G.H. Mast cell proteases as protective and inflammatory mediators. Adv. Exp. Med. Biol. 2011, 716:212-234.
96. Raymond W.W., Ruggles S.W., Craik C.S., Caughey G.H. Albumin is a substrate of human chymase. Prediction by combinatorial peptide screening and development of a selective inhibitor based on the albumin cleavage site. J. Biol. Chem. 2003, 278:34517-34524.
97. Galanakis D.K. Anticoagulant albumin fragments that bind to fibrinogen/fibrin: possible implications. Semin. Thromb. Hemost. 1992, 18:44-52.
98. Huntington J.A., Read R.J., Carrell R.W. Structure of a serpin-protease complex shows inhibition by deformation. Nature 2000, 407:923-926.
99. Gooptu B., Dickens J.A., Lomas D.A. The molecular and cellular pathology of alpha(1)-antitrypsin deficiency. Trends Mol. Med. 2014, 20:116-127.
100. Speer C.P., Ninjo A., Gahr M. Elastase-alpha 1-proteinase inhibitor in early diagnosis of neonatal septicemia. J. Pediatr. 1986, 108:987-990.
101. Harm K., Bartfeld K.P., Mathew T. Plasma concentrations of granulocytic elastase-alpha 1-proteinase inhibitor complex in patients with severe head injury, multiple trauma or cerebral bleeding. Clin. Biochem. 1989, 22:149-153.
102. Tegtmeyer F.K., Moller J., Richter A., Wilken B., Fischer T. Plasma concentration of elastase-alpha 1-proteinase inhibitor complex in surfactant-treated preterm neonates with respiratory distress syndrome. Eur. Respir. J. 1994, 7:260-264.
103. Ishikawa N., Kamitsuji H., Murakami T., Nakayama A., Umeki Y. Plasma levels of granulocyte elastase-alpha1-proteinase inhibitor complex in children with hemolytic uremic syndrome caused by verotoxin-producing Escherichia coli. Pediatr. Int. 2000, 42:637-641.
104. Jirasakuldech B., Schussler G.C., Yap M.G., Drew H., Josephson A., Michl J. A characteristic serpin cleavage product of thyroxine-binding globulin appears in sepsis sera. J. Clin. Endocrinol. Metab. 2000, 85:3996-3999.
105. Afandi B., Schussler G.C., Arafeh A.H., Boutros A., Yap M.G., Finkelstein A. Selective consumption of thyroxine-binding globulin during cardiac bypass surgery. Metabolism 2000, 49:270-274.
106. Eberini I., Calabresi L., Wait R., Tedeschi G., Pirillo A., Puglisi L., et al. Macrophage metalloproteinases degrade HDL-associated apoA-I at both the N- and the C-terminus. Biochem. J. 2002, 362:627-634.
107. Eberini I., Gianazza E., Breghi L., Klugmann S., Calabresi L., Gomaraschi M., et al. Apolipoprotein A-I breakdown is induced by thrombolysis in coronary patients. Ann. Med. 2007, 39:306-311.
108. Mizon C., Piva F., Queyrel V., Balduyck M., Hachulla E., Mizon J. Urinary bikunin determination provides insight into proteinase/proteinase inhibitor imbalance in patients with inflammatory diseases. Clin. Chemistry Lab. Med. 2002, 40:579-586.
109. Robey F.A., Ohura K., Futaki S., Fujii N., Yajima H., Goldman N., et al. Proteolysis of human C-reactive protein produces peptides with potent immunomodulating activity. J. Biol. Chem. 1987, 262:7053-7057.
110. Yavin E.J., Fridkin M. Peptides derived from human C-reactive protein inhibit the enzymatic activities of human leukocyte elastase and cathepsin G: use of overlapping peptide sequences to identify a unique inhibitor. J. Pept. Res. 1998, 51:282-289.
111. El Kebir D., Zhang Y., Potempa L.A., Wu Y., Fournier A., Filep J.G. C-reactive protein-derived peptide 201-206 inhibits neutrophil adhesion to endothelial cells and platelets through CD32. J. Leukoc. Biol. 2011, 90:1167-1175.
112. Kshirsagar B., Wilson B., Wiggins R.C. Polymeric complexes and fragments of albumin in normal human plasma. Clin. Chim. Acta 1984, 143:265-273.
113. Bazzi C., Petrini C., Rizza V., Sabadini E., Arrigo G., Beltrame A., et al. SDS-PAGE patterns and polymeric albumin in proteinuria of lupus glomerulonephritis. Clin. Nephrol. 1995, 43:96-103.
114. Alberti A., Pontisso P., Realdi G. Virus receptors for polymerized human albumin: a prognostic marker in HBeAg-positive chronic hepatitis type B?. J. Med. Virol. 1982, 10:141-146.
115. Mora I., Porres J.C., Bartolome F.J., Hernandez Guio C., Gutiez J., Carreno V. Receptors for polymerized human serum albumin and other hepatitis B virus markers during acute hepatitis B-predictive value of the outcome of the disease. Hepato-Gastroenterology 1986, 33:250-254.
116. Lomas D.A., Mahadeva R. Alpha1-antitrypsin polymerization and the serpinopathies: pathobiology and prospects for therapy. J. Clin. Invest. 2002, 110:1585-1590.
117. Carrell R.W., Lomas D.A. Alpha1-antitrypsin deficiency-a model for conformational diseases. N. Engl. J. Med. 2002, 346:45-53.
118. DeMeo D.L., Banos M., Perez J., Tan L., Barker A.F., Campbell E., et al. Circulating polymers of alpha-1-antitrypsin in PiZZ subjects. Am. J. Respir. Crit. Care Med. 2012, 185:A4361.
119. Janciauskiene S., Dominaitiene R., Sternby N.H., Piitulainen E., Eriksson S. Detection of circulating and endothelial cell polymers of Z and wild type alpha 1-antitrypsin by a monoclonal antibody. J. Biol. Chem. 2002, 277:26540-26546.
120. de Jong G., van Eijk H.G. Microheterogeneity of human serum transferrin: A biological phenomenon studied by isoelectric focusing in immobilized pH gradients. Electrophoresis 1988, 9:589-598.
121. de Jong G., van Noort W.L., Feelders R.A., de Jeu-Jaspars C.M., van Eijk H.G. Adaptation of transferrin protein and glycan synthesis. Clin. Chim. Acta 1992, 212:27-45.
122. Grigorian A., Mkhikian H., Li C.F., Newton B.L., Zhou R.W., Demetriou M. Pathogenesis of multiple sclerosis via environmental and genetic dysregulation of N-glycosylation. Semin. Immunopathol. 2012, 34:415-424.
123. Schedin-Weiss S., Winblad B., Tjernberg L.O. The role of protein glycosylation in Alzheimer disease. FEBS J. 2014, 281:46-62.
124. Pu Q., Yu C. Glycosyltransferases, glycosylation and atherosclerosis. Glycoconj. J. 2014, 31:605-611.
125. Christiansen M.N., Chik J., Lee L., Anugraham M., Abrahams J.L., Packer N.H. Cell surface protein glycosylation in cancer. Proteomics 2014, 14:525-546.
126. Ma Z., Vosseller K. Cancer metabolism and elevated O-GlcNAc in oncogenic signaling. J. Biol. Chem. 2014, 289:34457-34465.
127. Drake R.R., Ball L. Glycosylation and Cancer. Advances in Cancer Research 2015, Elsevier.
128. Pinho S.S., Reis C.A. Glycosylation in cancer: mechanisms and clinical implications. Nat. Rev. Cancer 2015, 15:540-555.
129. Stowell S.R., Ju T., Cummings R.D. Protein glycosylation in cancer. Annu. Rev. Pathol. 2015, 10:473-510.
130. Saldova R., Wormald M.R., Dwek R.A., Rudd P.M. Glycosylation changes on serum glycoproteins in ovarian cancer may contribute to disease pathogenesis. Dis. Markers 2008, 25:219-232.
131. Hashimoto S., Asao T., Takahashi J., Yagihashi Y., Nishimura T., Saniabadi A.R., et al. Alpha1-acid glycoprotein fucosylation as a marker of carcinoma progression and prognosis. Cancer 2004, 101:2825-2836.
132. Lin S.Y., Chen Y.Y., Fan Y.Y., Lin C.W., Chen S.T., Wang A.H., et al. Precise mapping of increased sialylation pattern and the expression of acute phase proteins accompanying murine tumor progression in BALB/c mouse by integrated sera proteomics and glycomics. J. Proteome Res. 2008, 7:3293-3303.
133. Gornik O., Lauc G. Glycosylation of serum proteins in inflammatory diseases. Dis. Markers 2008, 25:267-278.
134. Shiyan S.D., Bovin N.V. Carbohydrate composition and immunomodulatory activity of different glycoforms of alpha1-acid glycoprotein. Glycoconj. J. 1997, 14:631-638.
135. Mackiewicz A., Mackiewicz K. Glycoforms of serum alpha 1-acid glycoprotein as markers of inflammation and cancer. Glycoconj. J. 1995, 12:241-247.
136. Ceciliani F., Pocacqua V. The acute phase protein alpha1-acid glycoprotein: a model for altered glycosylation during diseases. Curr. Protein Pept. Sci. 2007, 8:91-108.
137. McCarthy C., Saldova R., Wormald M.R., Rudd P.M., McElvaney N.G., Reeves E.P. The role and importance of glycosylation of acute phase proteins with focus on alpha-1 antitrypsin in acute and chronic inflammatory conditions. J. Proteome Res. 2014, 13:3131-3143.
138. Marklova E., Albahri Z. Screening and diagnosis of congenital disorders of glycosylation. Clin. Chim. Acta 2007, 385:6-20.
139. Van Molle W., Denecker G., Rodriguez I., Brouckaert P., Vandenabeele P., Libert C. Activation of caspases in lethal experimental hepatitis and prevention by acute phase proteins. J. Immunol. 1999, 163:5235-5241.
140. Eckersall P.D. Acute phase proteins as markers of inflammatory lesions. Comp. Haematol. Int. 1995, 5:93-97.
141. Gruys E., Toussaint M.J.M., Upragarin N., Van Ederen A.M., Adewuyi A., Candiani D., et al. Acute phase reactants, challenge in the future. 5th International Colloquium on Animal Acute Phase Proteins. Dublin, Ireland 2005, 60.
142. Juan H.F., Chen J.H., Hsu W.T., Huang S.C., Chen S.T., Yi-Chung Lin J., et al. Identification of tumor-associated plasma biomarkers using proteomic techniques: from mouse to human. Proteomics 2004, 4:2766-2775.
143. Penno M.A., Klingler-Hoffmann M., Brazzatti J.A., Boussioutas A., Putoczki T., Ernst M., et al. 2D-DIGE analysis of sera from transgenic mouse models reveals novel candidate protein biomarkers for human gastric cancer. J. Proteome 2012, 77:40-58.
144. Humphries J.M., Penno M.A., Weiland F., Klingler-Hoffmann M., Zuber A., Boussioutas A., et al. Identification and validation of novel candidate protein biomarkers for the detection of human gastric cancer. Biochim. Biophys. Acta 1844, 2014:1051-1058.
145. Jeffery C.J. An introduction to protein moonlighting. Biochem. Soc. Trans. 2014, 42:1679-1683.
146. Hernandez S., Ferragut G., Amela I., Perez-Pons J., Pinol J., Mozo-Villarias A., et al. MultitaskProtDB: a database of multitasking proteins. Nucleic Acids Res. 2014, 42:D517-D520.
147. Mani M., Chen C., Amblee V., Liu H., Mathur T., Zwicke G., et al. MoonProt: a database for proteins that are known to moonlight. Nucleic Acids Res. 2015, 43:D277-D282.
148. Khan I.K., Kihara D. Computational characterization of moonlighting proteins. Biochem. Soc. Trans. 2014, 42:1780-1785.
149. Hernandez S., Calvo A., Ferragut G., Franco L., Hermoso A., Amela I., et al. Can bioinformatics help in the identification of moonlighting proteins?. Biochem. Soc. Trans. 2014, 42:1692-1697.
150. Martin A.C. Structural biology of moonlighting: lessons from antibodies. Biochem. Soc. Trans. 2014, 42:1704-1708.
151. Bielli P., Calabrese L. Structure to function relationships in ceruloplasmin: a 'moonlighting' protein. Cell. Mol. Life Sci. 2002, 59:1413-1427.
152. Derebe M.G., Zlatkov C.M., Gattu S., Ruhn K.A., Vaishnava S., Diehl G.E., et al. Serum amyloid A is a retinol binding protein that transports retinol during bacterial infection. eLife 2014, 3.
153. Lapidot T., Petit I. Current understanding of stem cell mobilization: the roles of chemokines, proteolytic enzymes, adhesion molecules, cytokines, and stromal cells. Exp. Hematol. 2002, 30:973-981.
154. Bristow C.L., Babayeva M.A., LaBrunda M., Mullen M.P., Winston R. alpha1Proteinase inhibitor regulates CD4+ lymphocyte levels and is rate limiting in HIV-1 disease. PLoS One 2012, 7:e31383.
155. Wyatt A.R., Yerbury J.J., Ecroyd H., Wilson M.R. Extracellular chaperones and proteostasis. Annu. Rev. Biochem. 2013, 82:295-322.
156. Wyatt A.R., Yerbury J.J., Dabbs R.A., Wilson M.R. Roles of extracellular chaperones in amyloidosis. J. Mol. Biol. 2012, 421:499-516.
157. Maugeais C., Braschi S., Ouguerram K., Maugeais P., Mahot P., Jacotot B., et al. Lipoprotein kinetics in patients with analbuminemia. Evidence for the role of serum albumin in controlling lipoprotein metabolism. Arterioscler. Thromb. Vasc. Biol. 1997, 17:1369-1375.
158. Nagase S., Shimamune K., Shumiya S. Albumin-deficient rat mutant. Science 1979, 205:590-591.
159. Sugiyama K., Emori T., Nagase S. Synthesis and secretion of plasma proteins by isolated hepatocytes of analbuminemic rats. J. Biochem. 1982, 92:775-779.
160. Liang K., Vaziri N.D. HMG-CoA reductase, cholesterol 7alpha-hydroxylase, LCAT, ACAT, LDL receptor, and SRB-1 in hereditary analbuminemia. Kidney Int. 2003, 64:192-198.
161. Kang J., Holland M., Jones H., Kaysen G.A. Coordinate augmentation in expression of genes encoding transcription factors and liver secretory proteins in hypo-oncotic states. Kidney Int. 1999, 56:452-460.
162. Figueira T.R., Castilho R.F., Saito A., Oliveira H.C., Vercesi A.E. The higher susceptibility of congenital analbuminemic rats to Ca2 + -induced mitochondrial permeability transition is associated with the increased expression of cyclophilin D and nitrosothiol depletion. Mol. Genet. Metab. 2011, 104:521-528.
163. Wait R., Chiesa G., Parolini C., Miller I., Begum S., Brambilla D., et al. Reference maps of mouse serum acute-phase proteins: changes with LPS-induced inflammation and apolipoprotein A-I and A-II transgenes. Proteomics 2005, 5:4245-4253.
164. Furlaneto C.J., Campa A. A novel function of serum amyloid A: A potent stimulus for the release of tumor necrosis factor-α, interleukin-1β, and interleukin-8 by human blood neutrophil. Biochem. Biophys. Res. Commun. 2000, 268:405-408.
165. Hyka N., Dayer J.M., Modoux C., Kohno T., Edwards C.K., Roux-Lombard P., et al. Apolipoprotein A-I inhibits the production of interleukin-1β and tumor necrosis factor-α by blocking contact-mediated activation of monocytes by T lymphocytes. Blood 2001, 97:2381-2389.
166. Furlaneto C.J., Ribeiro F.P., Hatanaka E., Souza G., Cassatella M.A., Campa A. Apolipoproteins A-I and A-II downregulate neutrophil functions. Lipids 2002, 37:925-928.
167. Hurn B.A.L., Chantler S.M. Production of reagent antibodies. Methods Enzymol. 1980, 70:104-141.
168. Tsolakos N., Brookes C., Taylor S., Gorringe A., Tang C.M., Feavers I.M., et al. Identification of vaccine antigens using integrated proteomic analyses of surface immunogens from serogroup B Neisseria meningitidis. J. Proteome 2014, 101:63-76.
169. Karunakaran K.P., Yu H., Jiang X., Chan Q., Moon K.M., Foster L.J., et al. Outer membrane proteins preferentially load MHC class II peptides: implications for a Chlamydia trachomatis T cell vaccine. Vaccine 2015, 33:2159-2166.
170. Virginio E.D., Kubitschek-Barreira P.H., Batista M.V., Schirmer M.R., Abdelhay E., Shikanai-Yasuda M.A., et al. Immunoproteome of Aspergillus fumigatus using sera of patients with invasive aspergillosis. Int. J. Mol. Sci. 2014, 15:14505-14530.
171. Radulovic Z.M., Kim T.K., Porter L.M., Sze S.H., Lewis L., Mulenga A. A 24-48 h fed Amblyomma americanum tick saliva immuno-proteome. BMC Genomics 2014, 15:518.
172. Alsoe L., Stacy J.E., Fossa A., Funderud S., Brekke O.H., Gaudernack G. Identification of prostate cancer antigens by automated high-throughput filter immunoscreening. J. Immunol. Methods 2008, 330:12-23.
173. Krah A., Jungblut P.R. Immunoproteomics. Methods Mol. Med. 2004, 94:19-32.
174. Ahn C.S., Han X., Bae Y.A., Ma X., Kim J.T., Cai H., et al. Alteration of immunoproteome profile of Echinococcus granulosus hydatid fluid with progression of cystic echinococcosis. Parasites Vectors 2015, 8:10.
175. Kunnath-Velayudhan S., Salamon H., Wang H.Y., Davidow A.L., Molina D.M., Huynh V.T., et al. Dynamic antibody responses to the Mycobacterium tuberculosis proteome. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:14703-14708.
176. Lin Y.F., Chen C.Y., Tsai M.H., Wu M.S., Wang Y.C., Chuang E.Y., et al. Duodenal ulcer-related antigens from Helicobacter pylori: immunoproteome and protein microarray approaches. Mol. Cell. Proteomics 2007, 6:1018-1026.
177. Lahner E., Bernardini G., Possenti S., Renzone G., Scaloni A., Santucci A., et al. Immunoproteomics of Helicobacter pylori infection in patients with atrophic body gastritis, a predisposing condition for gastric cancer. Int. J. Med. Microbiol. 2011, 301:125-132.
178. Vu D.H., Schneider P., Tissot J.D. Electrophoretic characteristics of monoclonal immunoglobulin G of different subclasses. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 2002, 771:355-368.
179. Stulik J., Tichy M., Kovarova H. Two-dimensional gel electrophoresis of four serum samples from patients with IgD myeloma. Clin. Chim. Acta 1993, 218:149-158.
180. Tissot J.D., Invernizzi F., Schifferli F., Spertini F., Schneider P. Two-dimensional electrophoretic analysis of cryoproteins: A report of 335 samples. Electrophoresis 1999, 20:606-613.
181. Krotkiewski H. Carbohydrate moiety of immunoglobulins in health and pathology. Acta Biochim. Pol. 1999, 46:341-350.
182. Rudd P.M., Elliott T., Cresswell P., Wilson I.A., Dwek R.A. Glycosylation and the immune system. Science 2001, 291:2370-2376.
183. Maverakis E., Kim K., Shimoda M., Gershwin M.E., Patel F., Wilken R., et al. Glycans in the immune system and the altered glycan theory of autoimmunity: a critical review. J. Autoimmun. 2015, 57:1-13.
184. Shade K.T., Platzer B., Washburn N., Mani V., Bartsch Y.C., Conroy M., et al. A single glycan on IgE is indispensable for initiation of anaphylaxis. J. Exp. Med. 2015, 212:457-467.
185. Reily C., Ueda H., Huang Z.Q., Mestecky J., Julian B.A., Willey C.D., et al. Cellular signaling and production of galactose-deficient IgA1 in IgA nephropathy, an autoimmune disease. Int. J. Immunol. Res. 2014, 2014:197548.