• 1
    Andersen JS & Mann M (2000) Functional genomics by mass spectrometry. FEBS Lett 480, 2531.
  • 2
    Ryu DD & Nam DH (2000) Recent progress in biomolecular engineering. Biotechnol Prog 16, 216.
  • 3
    Marincola FM (2003) Translational medicine: a two-way road. J Transl Med 1, 1.
  • 4
    De Wit M, Fijneman RJ, Verheul HM, Meijer GA & Jimenez CR (2013) Proteomics in colorectal cancer translational research: biomarker discovery for clinical applications. Clin Biochem 46, 466479.
  • 5
    Lin LL, Huang HC & Juan HF (2012) Discovery of biomarkers for gastric cancer: a proteomics approach. J Proteomics 75, 30813097.
  • 6
    Ho L, Sharma N, Blackman L, Festa E, Reddy G & Pasinetti GM (2005) From proteomics to biomarker discovery in Alzheimer's disease. Brain Res Brain Res Rev 48, 360369.
  • 7
    Khan AR & Awan FR (2012) Mining of protein based biomarkers for type 2 diabetes mellitus. Pak J Pharm Sci 25, 889901.
  • 8
    Shaw JE, Sicree RA & Zimmet PZ (2010) Global estimates of the prevalence of diabetes for 2010 and 2030. Diabetes Res Clin Pract 87, 414.
  • 9
    American Diabetes Association (2012) Standards of medical care in diabetes – 2012. Diabetes Care 35, S11S63.
  • 10
    Wiśniewski JR, Zougman A, Nagaraj N & Mann M (2009) Universal sample preparation method for proteome analysis. Nat Methods 6, 359362.
  • 11
    Wiśniewski JR, Zougman A & Mann M (2009) Combination of FASP and Stage Tip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J Proteome Res 8, 56745678.
  • 12
    Ostasiewicz P, Zielinska DF, Mann M & Wiśniewski JR (2010) Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. J Proteome Res 9, 36883700.
  • 13
    Ethier M, Hou W, Duewel HS & Figeys D (2006) The proteomic reactor: a microfluidic device for processing minute amounts of protein prior to mass spectrometry analysis. J Proteome Res 5, 27542759.
  • 14
    Zhou H, Wang F, Wang Y, Ning Z, Hou W, Wright TG, Sundaram M, Zhong S, Yao Z & Figeys D (2011) Improved recovery and identification of membrane proteins from rat hepatic cells using a centrifugal proteomic reactor. Mol Cell Proteomics 10, O111.008425.
  • 15
    Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A & Mann M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1, 376386.
  • 16
    De Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Fröhlich F, Walther TC & Mann M (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 12511254.
  • 17
    Marimuthu A, Subbannayya Y, Sahasrabuddhe NA, Balakrishnan L, Syed N, Sekhar NR, Katte TV, Pinto SM, Srikanth SM, Kumar P et al. (2012) SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics Clin Appl doi:10.1002/prca.201200069.
  • 18
    Geiger T, Cox J, Ostasiewicz P, Wisniewski JR & Mann M (2010) Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods 7, 383385.
  • 19
    Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S et al. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3, 11541169.
  • 20
    Zieske LR (2006) A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies. J Exp Bot 57, 15011508.
  • 21
    Han X, Aslanian A & Yates JR 3rd (2008) Mass spectrometry for proteomics. Curr Opin Chem Biol 12, 483490.
  • 22
    Paulo JA, Kadiyala V, Banks PA, Steen H & Conwell DL (2012) Mass spectrometry-based proteomics for translational research: a technical overview. Yale J Biol Med 85, 5973.
  • 23
    Holman SW, Sims PF & Eyers CE (2012) The use of selected reaction monitoring in quantitative proteomics. Bioanalysis 4, 17631786.
  • 24
    Van Riper SK, De Jong EP, Carlis JV & Griffin TJ (2013) Mass spectrometry-based proteomics: basic principles and emerging technologies and directions. Adv Exp Med Biol 990, 1.35
  • 25
    Wiśniewski JR, Ostasiewicz P, Duś K, Zielińska DF, Gnad F & Mann M (2012) Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol Syst Biol 8, 611.
  • 26
    Karas M & Hillenkamp F (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60, 22992301.
  • 27
    Fenn JB, Mann M, Meng CK, Wong SF & Whitehouse CM (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 6471.
  • 28
    Franck J, Arafah K, Elayed M, Bonnel D, Vergara D, Jacquet A, Vinatier D, Wisztorski M, Day R, Fournier I et al. (2009) MALDI imaging mass spectrometry: state of the art technology in clinical proteomics. Mol Cell Proteomics 8, 20232033.
  • 29
    Yanagisawa K, Shyr Y, Xu BJ, Massion PP, Larsen PH, White BC, Roberts JR, Edgerton M, Gonzalez A, Nadaf S et al. (2003) Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 362, 433439.
  • 30
    Groseclose MR, Massion PP, Chaurand P & Caprioli RM (2008) High-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue microarrays using MALDI imaging mass spectrometry. Proteomics 8, 37153724.
  • 31
    Michalski A, Damoc E, Lange O, Denisov E, Nolting D, Müller M, Viner R, Schwartz J, Remes P, Belford M et al. (2012) Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes. Mol Cell Proteomics 11, O111.013698.
  • 32
    Michalski A, Damoc E, Hauschild JP, Lange O, Wieghaus A, Makarov A, Nagaraj N, Cox J, Mann M & Horning S (2011) Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics 10, M111.011015.
  • 33
    Lamond AI, Uhlen M, Horning S, Makarov A, Robinson CV, Serrano L, Hartl FU, Baumeister W, Werenskiold AK, Andersen JS et al. (2012) Advancing cell biology through proteomics in space and time (PROSPECTS). Mol Cell Proteomics 11, O112.017731.
  • 34
    Ahlf DR, Compton PD, Tran JC, Early BP, Thomas PM & Kelleher NL (2012) Evaluation of the compact high-field orbitrap for top-down proteomics of human cells. J Proteome Res 11, 43084314.
  • 35
    Nagaraj N, Kulak NA, Cox J, Neuhauser N, Mayr K, Hoerning O, Vorm O & Mann M (2012) System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap. Mol Cell Proteomics 11, M111.013722.
  • 36
    Andrews GL, Simons BL, Young JB, Hawkridge AM & Muddiman DC (2011) Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). Anal Chem 83, 54425446.
  • 37
    Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R & Aebersold R (2012) Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 11, O111.016717.
  • 38
    Kowluru RA & Chan PS (2007) Oxidative stress and diabetic retinopathy. Exp Diabetes Res 2007, 43603.
  • 39
    Takada M, Ban Y, Yamamoto G, Ueda T, Saito Y, Nishimura E, Fujisawa K, Koide R, Mizutani M, Kozawa T et al. (2010) Periostin, discovered by nano-flow liquid chromatography and mass spectrometry, is a novel marker of diabetic retinopathy. Biochem Biophys Res Commun 399, 221226.
  • 40
    Li M, Ma YB, Gao HQ, Li BY, Cheng M, Xu L, Li XL & Li XH (2008) A novel approach of proteomics to study the mechanism of action of grape seed proanthocyanidin extracts on diabetic retinopathy in rats. Chin Med J (Engl) 121, 25442552.
  • 41
    Fort PE, Freeman WM, Losiewicz MK, Singh RS & Gardner TW (2009) The retinal proteome in experimental diabetic retinopathy: up-regulation of crystallins and reversal by systemic and periocular insulin. Mol Cell Proteomics 8, 767779.
  • 42
    Simó-Servat O, Hernández C & Simó R (2012) Usefulness of the vitreous fluid analysis in the translational research of diabetic retinopathy. Mediators Inflamm 2012, 872978.
  • 43
    Merchant ML & Klein JB (2009) Proteomics and diabetic retinopathy. Clin Lab Med 29, 139149.
  • 44
    Bishop PN (2000) Structural macromolecules and supramolecular organisation of the vitreous gel. Prog Retin Eye Res 19, 323344.
  • 45
    García-Ramírez M, Canals F, Hernández C, Colomé N, Ferrer C, Carrasco E, García-Arumí J & Simó R (2007) Proteomic analysis of human vitreous fluid by fluorescence-based difference gel electrophoresis (DIGE): a new strategy for identifying potential candidates in the pathogenesis of proliferative diabetic retinopathy. Diabetologia 50, 12941303.
  • 46
    Simó R, Higuera M, García-Ramírez M, Canals F, García-Arumí J & Hernández C (2008) Elevation of apolipoprotein A-I and apolipoprotein H levels in the vitreous fluid and overexpression in the retina of diabetic patients. Arch Ophthalmol 126, 10761081.
  • 47
    Kim T, Kim SJ, Kim K, Kang UB, Lee C, Park KS, Yu HG & Kim Y (2007) Profiling of vitreous proteomes from proliferative diabetic retinopathy and nondiabetic patients. Proteomics 7, 42034215.
  • 48
    Gao BB, Chen X, Timothy N, Aiello LP & Feener EP (2008) Characterization of the vitreous proteome in diabetes without diabetic retinopathy and diabetes with proliferative diabetic retinopathy. J Proteome Res 7, 25162525.
  • 49
    Grus FH, Joachim SC & Pfeiffer N (2007) Proteomics in ocular fluids. Proteomics Clin Appl 1, 876888.
  • 50
    Chiang SY, Tsai ML, Wang CY, Chen A, Chou YC, Hsia CW, Wu YF, Chen HM, Huang TH, Chen PH et al. (2012) Proteomic analysis and identification of aqueous humor proteins with a pathophysiological role in diabetic retinopathy. J Proteomics 75, 29502959.
  • 51
    Herber S, Grus FH, Sabuncuo P & Augustin AJ (2001) Two-dimensional analysis of tear protein patterns of diabetic patients. Electrophoresis 22, 18381844.
  • 52
    Kim HJ, Kim PK, Yoo HS & Kim CW (2012) Comparison of tear proteins between healthy and early diabetic retinopathy patients. Clin Biochem 45, 6067.
  • 53
    Csősz É, Boross P, Csutak A, Berta A, Tóth F, Póliska S, Török Z & Tőzsér J (2012) Quantitative analysis of proteins in the tear fluid of patients with diabetic retinopathy. J Proteomics 75, 21962204.
  • 54
    Caramori ML, Fioretto P & Mauer M (2000) The need for early predictors of diabetic nephropathy risk: is albumin excretion rate sufficient? Diabetes 49, 13991408.
  • 55
    Chavers BM, Bilous RW, Ellis EN, Steffes MW & Mauer SM (1989) Glomerular lesions and urinary albumin excretion in type I diabetes without overt proteinuria. N Engl J Med 320, 966970.
  • 56
    Sharma K, Lee S, Han S, Lee S, Francos B, McCue P, Wassell R, Shaw MA & RamachandraRao SP (2005) Two-dimensional fluorescence difference gel electrophoresis analysis of the urine proteome in human diabetic nephropathy. Proteomics 5, 26482655.
  • 57
    Jiang H, Guan G, Zhang R, Liu G, Cheng J, Hou X & Cui Y (2009) Identification of urinary soluble E-cadherin as a novel biomarker for diabetic nephropathy. Diabetes Metab Res Rev 25, 232241.
  • 58
    Dihazi H, Müller GA, Lindner S, Meyer M, Asif AR, Oellerich M & Strutz F (2007) Characterization of diabetic nephropathy by urinary proteomic analysis: identification of a processed ubiquitin form as a differentially excreted protein in diabetic nephropathy patients. Clin Chem 53, 16361645.
  • 59
    Papale M, Di Paolo S, Magistroni R, Lamacchia O, Di Palma AM, De Mattia A, Rocchetti MT, Furci L, Pasquali S, De Cosmo S et al. (2010) Urine proteome analysis may allow noninvasive differential diagnosis of diabetic nephropathy. Diabetes Care 33, 24092415.
  • 60
    Theodorescu D, Wittke S, Ross MM, Walden M, Conaway M, Just I, Mischak H & Frierson HF (2006) Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis. Lancet Oncol 7, 230240.
  • 61
    Mischak H, Julian BA & Novak J (2007) High-resolution proteome/peptidome analysis of peptides and low-molecular-weight proteins in urine. Proteomics Clin Appl 1, 792.
  • 62
    Rossing K, Mischak H, Dakna M, Zürbig P, Novak J, Julian BA, Good DM, Coon JJ, Tarnow L, & Rossing P, Network Predictions (2008) Urinary proteomics in diabetes and CKD. J Am Soc Nephrol 19, 12831290.
  • 63
    Alkhalaf A, Zürbig P, Bakker SJ, Bilo HJ, Cerna M, Fischer C, Fuchs S, Janssen B, Medek K, Mischak H, Group Predictions et al. (2010) Multicentric validation of proteomic biomarkers in urine specific for diabetic nephropathy. PLoS ONE 5, e13421.
  • 64
    Zürbig P, Jerums G, Hovind P, Macisaac RJ, Mischak H, Nielsen SE, Panagiotopoulos S, Persson F & Rossing P (2012) Urinary proteomics for early diagnosis in diabetic nephropathy. Diabetes 61, 33043313.
  • 65
    Otu HH, Can H, Spentzos D, Nelson RG, Hanson RL, Looker HC, Knowler WC, Monroy M, Libermann TA, Karumanchi SA et al. (2007) Prediction of diabetic nephropathy using urine proteomic profiling 10 years prior to development of nephropathy. Diabetes Care 30, 638643.
  • 66
    Overgaard AJ, Hansen HG, Lajer M, Pedersen L, Tarnow L, Rossing P, McGuire JN & Pociot F (2010) Plasma proteome analysis of patients with type 1 diabetes with diabetic nephropathy. Proteome Sci 8, 4.
  • 67
    Hotta O, Yusa N, Mukaiyama I & Taguma Y (1999) Usefulness of serum cystatin-C as a marker of the renal function: a comparative evaluation with beta 2-microglobulin, alpha 1-microglobulin and creatinine. Nihon Jinzo Gakkai Shi 41, 797803.
  • 68
    Jenkins AJ, Lyons TJ, Zheng D, Otvos JD, Lackland DT, McGee D, Garvey WT & Klein RL & DCCT/EDIC Research Group (2003) Lipoproteins in the DCCT/EDIC cohort: associations with diabetic nephropathy. Kidney Int 64, 817828.
  • 69
    Overgaard AJ, Thingholm TE, Larsen MR, Tarnow L, Rossing P, McGuire JN & Pociot F (2010) Quantitative iTRAQ-based proteomic identification of candidate biomarkers for diabetic nephropathy in plasma of type 1 diabetic patients. Clin Proteomics 6, 105114.
  • 70
    Tilton RG, Haidacher SJ, Lejeune WS, Zhang X, Zhao Y, Kurosky A, Brasier AR & Denner L (2007) Diabetes-induced changes in the renal cortical proteome assessed with two-dimensional gel electrophoresis and mass spectrometry. Proteomics 7, 17291742.
  • 71
    Li BY, Cheng M, Gao HQ, Ma YB, Xu L, Li XH, Li XL & You BA (2008) Back-regulation of six oxidative stress proteins with grape seed proanthocyanidin extracts in rat diabetic nephropathy. J Cell Biochem 104, 668679.