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Published in: Clinical and Translational Medicine 1/2014

Open Access 01-12-2014 | Review

Application of clinical proteomics in acute respiratory distress syndrome

Authors: Maneesh Bhargava, LeeAnn Higgins, Christine H Wendt, David H Ingbar

Published in: Clinical and Translational Medicine | Issue 1/2014

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Abstract

Acute Respiratory Distress Syndrome (ARDS) is a devastating cause of hypoxic respiratory failure, which continues to have high mortality. It is expected that a comprehensive systems- level approach will identify global and complex changes that contribute to the development of ARDS and subsequent repair of the damaged lung. In the last decade, powerful genome-wide analytical and informatics tools have been developed, that have provided valuable insights into the mechanisms of complex diseases such as ARDS. These tools include the rapid and precise measure of gene expression at the proteomic level. This article reviews the contemporary proteomics platforms that are available for comprehensive studies in ARDS. The challenges of various biofluids that could be investigated and some of the studies performed are also discussed.
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Literature
1.
go back to reference James P: Protein identification in the post-genome era: the rapid rise of proteomics. Q Rev Biophys 1997, 30: 279–331. 10.1017/S0033583597003399CrossRefPubMed James P: Protein identification in the post-genome era: the rapid rise of proteomics. Q Rev Biophys 1997, 30: 279–331. 10.1017/S0033583597003399CrossRefPubMed
2.
go back to reference Rottoli P, Bargagli E, Landi C, Magi B: Proteomic analysis in interstitial lung diseases: a review. Curr Opin Pulm Med 2009, 15: 470–478. 10.1097/MCP.0b013e32832ea4f2CrossRefPubMed Rottoli P, Bargagli E, Landi C, Magi B: Proteomic analysis in interstitial lung diseases: a review. Curr Opin Pulm Med 2009, 15: 470–478. 10.1097/MCP.0b013e32832ea4f2CrossRefPubMed
3.
go back to reference Bons JA, Drent M, Bouwman FG, Mariman EC, van Dieijen-Visser MP, Wodzig WK: Potential biomarkers for diagnosis of sarcoidosis using proteomics in serum. Respir Med 2007, 101: 1687–1695. 10.1016/j.rmed.2007.03.002CrossRefPubMed Bons JA, Drent M, Bouwman FG, Mariman EC, van Dieijen-Visser MP, Wodzig WK: Potential biomarkers for diagnosis of sarcoidosis using proteomics in serum. Respir Med 2007, 101: 1687–1695. 10.1016/j.rmed.2007.03.002CrossRefPubMed
4.
go back to reference Lehtio J, De Petris L: Lung cancer proteomics, clinical and technological considerations. J Proteomics 2010, 73: 1851–1863. 10.1016/j.jprot.2010.05.015CrossRefPubMed Lehtio J, De Petris L: Lung cancer proteomics, clinical and technological considerations. J Proteomics 2010, 73: 1851–1863. 10.1016/j.jprot.2010.05.015CrossRefPubMed
5.
go back to reference Cho WC: Proteome profiling for the identification of lung cancer signatures. Expert Rev Proteomics 2011, 8: 689–692. 10.1586/epr.11.65CrossRefPubMed Cho WC: Proteome profiling for the identification of lung cancer signatures. Expert Rev Proteomics 2011, 8: 689–692. 10.1586/epr.11.65CrossRefPubMed
6.
go back to reference Ostroff RM, Bigbee WL, Franklin W, Gold L, Mehan M, Miller YE, Pass HI, Rom WN, Siegfried JM, Stewart A, Walker JJ, Weissfeld JL, Williams S, Zichi D, Brody EN: Unlocking biomarker discovery: large scale application of aptamer proteomic technology for early detection of lung cancer. PLoS One 2010, 5: e15003. 10.1371/journal.pone.0015003PubMedCentralCrossRefPubMed Ostroff RM, Bigbee WL, Franklin W, Gold L, Mehan M, Miller YE, Pass HI, Rom WN, Siegfried JM, Stewart A, Walker JJ, Weissfeld JL, Williams S, Zichi D, Brody EN: Unlocking biomarker discovery: large scale application of aptamer proteomic technology for early detection of lung cancer. PLoS One 2010, 5: e15003. 10.1371/journal.pone.0015003PubMedCentralCrossRefPubMed
7.
go back to reference Hirsch J, Hansen KC, Burlingame AL, Matthay MA: Proteomics: current techniques and potential applications to lung disease. Am J Physiol Lung Cell Mol Physiol 2004, 287: L1-L23. 10.1152/ajplung.00301.2003CrossRefPubMed Hirsch J, Hansen KC, Burlingame AL, Matthay MA: Proteomics: current techniques and potential applications to lung disease. Am J Physiol Lung Cell Mol Physiol 2004, 287: L1-L23. 10.1152/ajplung.00301.2003CrossRefPubMed
8.
go back to reference Miller I, Eberini I, Gianazza E: Proteomics of lung physiopathology. Proteomics 2008, 8: 5053–5073. 10.1002/pmic.200800315CrossRefPubMed Miller I, Eberini I, Gianazza E: Proteomics of lung physiopathology. Proteomics 2008, 8: 5053–5073. 10.1002/pmic.200800315CrossRefPubMed
9.
go back to reference Magi B, Bini L, Perari MG, Fossi A, Sanchez JC, Hochstrasser D, Paesano S, Raggiaschi R, Santucci A, Pallini V, Rottoli P: Bronchoalveolar lavage fluid protein composition in patients with sarcoidosis and idiopathic pulmonary fibrosis: a two-dimensional electrophoretic study. Electrophoresis 2002, 23: 3434–3444. 10.1002/1522-2683(200210)23:19<3434::AID-ELPS3434>3.0.CO;2-RCrossRefPubMed Magi B, Bini L, Perari MG, Fossi A, Sanchez JC, Hochstrasser D, Paesano S, Raggiaschi R, Santucci A, Pallini V, Rottoli P: Bronchoalveolar lavage fluid protein composition in patients with sarcoidosis and idiopathic pulmonary fibrosis: a two-dimensional electrophoretic study. Electrophoresis 2002, 23: 3434–3444. 10.1002/1522-2683(200210)23:19<3434::AID-ELPS3434>3.0.CO;2-RCrossRefPubMed
10.
11.
go back to reference Anderson L, Anderson NG: High resolution two-dimensional electrophoresis of human plasma proteins. Proc Natl Acad Sci U S A 1977, 74: 5421–5425. 10.1073/pnas.74.12.5421PubMedCentralCrossRefPubMed Anderson L, Anderson NG: High resolution two-dimensional electrophoresis of human plasma proteins. Proc Natl Acad Sci U S A 1977, 74: 5421–5425. 10.1073/pnas.74.12.5421PubMedCentralCrossRefPubMed
12.
go back to reference Tanaka K, Waki H, Ido Y, Akita S, Yoshida Y, Yoshida T: Protein and Polymer Analyses up to m/z 100 000 by Laser Ionization Time-of-Flight Mass Spectrometry. Rapid Commun Mass Spectrom 1988, 02: 151–153. 10.1002/rcm.1290020802CrossRef Tanaka K, Waki H, Ido Y, Akita S, Yoshida Y, Yoshida T: Protein and Polymer Analyses up to m/z 100 000 by Laser Ionization Time-of-Flight Mass Spectrometry. Rapid Commun Mass Spectrom 1988, 02: 151–153. 10.1002/rcm.1290020802CrossRef
13.
go back to reference Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM: Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246: 64–71. 10.1126/science.2675315CrossRefPubMed Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM: Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246: 64–71. 10.1126/science.2675315CrossRefPubMed
14.
go back to reference Shevchenko A, Wilm M, Vorm O, Mann M: Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 1996, 68: 850–858. 10.1021/ac950914hCrossRefPubMed Shevchenko A, Wilm M, Vorm O, Mann M: Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 1996, 68: 850–858. 10.1021/ac950914hCrossRefPubMed
15.
go back to reference Vestling MM, Fenselau C: Polyvinylidene difluoride (PVDF): an interface for gel electrophoresis and matrix-assisted laser desorption/ionization mass spectrometry. Biochem Soc Trans 1994, 22: 547–551.CrossRefPubMed Vestling MM, Fenselau C: Polyvinylidene difluoride (PVDF): an interface for gel electrophoresis and matrix-assisted laser desorption/ionization mass spectrometry. Biochem Soc Trans 1994, 22: 547–551.CrossRefPubMed
16.
go back to reference Wilm M, Mann M: Analytical properties of the nanoelectrospray ion source. Anal Chem 1996, 68: 1–8. 10.1021/ac9509519CrossRefPubMed Wilm M, Mann M: Analytical properties of the nanoelectrospray ion source. Anal Chem 1996, 68: 1–8. 10.1021/ac9509519CrossRefPubMed
17.
go back to reference West-Nielsen M, Hogdall EV, Marchiori E, Hogdall CK, Schou C, Heegaard NH: Sample handling for mass spectrometric proteomic investigations of human sera. Anal Chem 2005, 77: 5114–5123. 10.1021/ac050253gCrossRefPubMed West-Nielsen M, Hogdall EV, Marchiori E, Hogdall CK, Schou C, Heegaard NH: Sample handling for mass spectrometric proteomic investigations of human sera. Anal Chem 2005, 77: 5114–5123. 10.1021/ac050253gCrossRefPubMed
18.
go back to reference Hubel A, Spindler R, Skubitz AP: Storage of human biospecimens: selection of the optimal storage temperature. Biopreserv Biobank 2014, 12: 165–175. 10.1089/bio.2013.0084CrossRefPubMed Hubel A, Spindler R, Skubitz AP: Storage of human biospecimens: selection of the optimal storage temperature. Biopreserv Biobank 2014, 12: 165–175. 10.1089/bio.2013.0084CrossRefPubMed
19.
go back to reference Landi MT, Caporaso N: Sample collection, processing and storage. IARC Sci Publ 1997, 142: 223–236.PubMed Landi MT, Caporaso N: Sample collection, processing and storage. IARC Sci Publ 1997, 142: 223–236.PubMed
20.
go back to reference Prieto DA, Johann DJ Jr, Wei BR, Ye X, Chan KC, Nissley DV, Simpson RM, Citrin DE, Mackall CL, Linehan WM, Blonder J: Mass spectrometry in cancer biomarker research: a case for immunodepletion of abundant blood-derived proteins from clinical tissue specimens. Biomark Med 2014, 8: 269–286. 10.2217/bmm.13.101PubMedCentralCrossRefPubMed Prieto DA, Johann DJ Jr, Wei BR, Ye X, Chan KC, Nissley DV, Simpson RM, Citrin DE, Mackall CL, Linehan WM, Blonder J: Mass spectrometry in cancer biomarker research: a case for immunodepletion of abundant blood-derived proteins from clinical tissue specimens. Biomark Med 2014, 8: 269–286. 10.2217/bmm.13.101PubMedCentralCrossRefPubMed
21.
go back to reference Corthals GL, Wasinger VC, Hochstrasser DF, Sanchez JC: The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 2000, 21: 1104–1115. 10.1002/(SICI)1522-2683(20000401)21:6<1104::AID-ELPS1104>3.0.CO;2-CCrossRefPubMed Corthals GL, Wasinger VC, Hochstrasser DF, Sanchez JC: The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 2000, 21: 1104–1115. 10.1002/(SICI)1522-2683(20000401)21:6<1104::AID-ELPS1104>3.0.CO;2-CCrossRefPubMed
22.
go back to reference Gundry RL, White MY, Nogee J, Tchernyshyov I, Van Eyk JE: Assessment of albumin removal from an immunoaffinity spin column: critical implications for proteomic examination of the albuminome and albumin-depleted samples. Proteomics 2009, 9: 2021–2028. 10.1002/pmic.200800686PubMedCentralCrossRefPubMed Gundry RL, White MY, Nogee J, Tchernyshyov I, Van Eyk JE: Assessment of albumin removal from an immunoaffinity spin column: critical implications for proteomic examination of the albuminome and albumin-depleted samples. Proteomics 2009, 9: 2021–2028. 10.1002/pmic.200800686PubMedCentralCrossRefPubMed
23.
go back to reference Han X, Jin M, Breuker K, McLafferty FW: Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons. Science 2006, 314: 109–112. 10.1126/science.1128868CrossRefPubMed Han X, Jin M, Breuker K, McLafferty FW: Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons. Science 2006, 314: 109–112. 10.1126/science.1128868CrossRefPubMed
24.
go back to reference Thomas CE, Kelleher NL, Mizzen CA: Mass spectrometric characterization of human histone H3: a bird’s eye view. J Proteome Res 2006, 5: 240–247. 10.1021/pr050266aCrossRefPubMed Thomas CE, Kelleher NL, Mizzen CA: Mass spectrometric characterization of human histone H3: a bird’s eye view. J Proteome Res 2006, 5: 240–247. 10.1021/pr050266aCrossRefPubMed
25.
go back to reference Nelsestuen GL, Harvey SB, Zhang Y, Kasthuri RS, Sinaiko AR, Ely EW, Bernard GR, Homoncik M, Jilma B: Top-down proteomic analysis by MALDI-TOF profiling: Concentration-independent biomarkers. Proteomics Clin Appl 2008, 2: 158–166. 10.1002/prca.200780107CrossRefPubMed Nelsestuen GL, Harvey SB, Zhang Y, Kasthuri RS, Sinaiko AR, Ely EW, Bernard GR, Homoncik M, Jilma B: Top-down proteomic analysis by MALDI-TOF profiling: Concentration-independent biomarkers. Proteomics Clin Appl 2008, 2: 158–166. 10.1002/prca.200780107CrossRefPubMed
26.
go back to reference Kasthuri RS, Wroblewski M, Jilma B, Key NS, Nelsestuen GL: Potential biomarkers of an exaggerated response to endotoxemia. Biomarkers 2007, 12: 287–302. 10.1080/13547500601160536CrossRefPubMed Kasthuri RS, Wroblewski M, Jilma B, Key NS, Nelsestuen GL: Potential biomarkers of an exaggerated response to endotoxemia. Biomarkers 2007, 12: 287–302. 10.1080/13547500601160536CrossRefPubMed
27.
go back to reference Zhang Y, Wroblewski M, Hertz MI, Wendt CH, Cervenka TM, Nelsestuen GL: Analysis of chronic lung transplant rejection by MALDI-TOF profiles of bronchoalveolar lavage fluid. Proteomics 2006, 6: 1001–1010. 10.1002/pmic.200500105CrossRefPubMed Zhang Y, Wroblewski M, Hertz MI, Wendt CH, Cervenka TM, Nelsestuen GL: Analysis of chronic lung transplant rejection by MALDI-TOF profiles of bronchoalveolar lavage fluid. Proteomics 2006, 6: 1001–1010. 10.1002/pmic.200500105CrossRefPubMed
28.
go back to reference Jr GW, Cazares LH, Leung SM, Nasim S, Adam BL, Yip TT, Schellhammer PF, Gong L, Vlahou A: Proteinchip(R) surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures. Prostate Cancer Prostatic Dis 1999, 2: 264–276. 10.1038/sj.pcan.4500384CrossRefPubMed Jr GW, Cazares LH, Leung SM, Nasim S, Adam BL, Yip TT, Schellhammer PF, Gong L, Vlahou A: Proteinchip(R) surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures. Prostate Cancer Prostatic Dis 1999, 2: 264–276. 10.1038/sj.pcan.4500384CrossRefPubMed
29.
go back to reference Washburn MP, Wolters D, Yates JR 3rd: Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19: 242–247. 10.1038/85686CrossRefPubMed Washburn MP, Wolters D, Yates JR 3rd: Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19: 242–247. 10.1038/85686CrossRefPubMed
30.
go back to reference Yates JR 3rd: Mass spectrometry and the age of the proteome. J Mass Spectrom 1998, 33: 1–19. 10.1002/(SICI)1096-9888(199801)33:1<1::AID-JMS624>3.0.CO;2-9CrossRefPubMed Yates JR 3rd: Mass spectrometry and the age of the proteome. J Mass Spectrom 1998, 33: 1–19. 10.1002/(SICI)1096-9888(199801)33:1<1::AID-JMS624>3.0.CO;2-9CrossRefPubMed
31.
go back to reference Gundry RL, White MY, Murray CI, Kane LA, Fu Q, Stanley BA, Van Eyk JE, et al.: Preparation of Proteins and Peptides for Mass Spectrometry Analysis in A Bottom-Up Proteomics Workflow. In Current Protocols in Molecular Biology Edited by: Ausubel FM. 2009. Chapter 10:Unit10 25 Chapter 10:Unit10 25 Gundry RL, White MY, Murray CI, Kane LA, Fu Q, Stanley BA, Van Eyk JE, et al.: Preparation of Proteins and Peptides for Mass Spectrometry Analysis in A Bottom-Up Proteomics Workflow. In Current Protocols in Molecular Biology Edited by: Ausubel FM. 2009. Chapter 10:Unit10 25 Chapter 10:Unit10 25
32.
go back to reference Kim SC, Chen Y, Mirza S, Xu Y, Lee J, Liu P, Zhao Y: A clean, more efficient method for in-solution digestion of protein mixtures without detergent or urea. J Proteome Res 2006, 5: 3446–3452. 10.1021/pr0603396CrossRefPubMed Kim SC, Chen Y, Mirza S, Xu Y, Lee J, Liu P, Zhao Y: A clean, more efficient method for in-solution digestion of protein mixtures without detergent or urea. J Proteome Res 2006, 5: 3446–3452. 10.1021/pr0603396CrossRefPubMed
33.
go back to reference Wisniewski JR, Zougman A, Nagaraj N, Mann M: Universal sample preparation method for proteome analysis. Nat Methods 2009, 6: 359–362. 10.1038/nmeth.1322CrossRefPubMed Wisniewski JR, Zougman A, Nagaraj N, Mann M: Universal sample preparation method for proteome analysis. Nat Methods 2009, 6: 359–362. 10.1038/nmeth.1322CrossRefPubMed
34.
go back to reference Gharib SA, Nguyen E, Altemeier WA, Shaffer SA, Doneanu CE, Goodlett DR, Schnapp LM: Of mice and men: comparative proteomics of bronchoalveolar fluid. Eur Respir J 2010, 35: 1388–1395. 10.1183/09031936.00089409PubMedCentralCrossRefPubMed Gharib SA, Nguyen E, Altemeier WA, Shaffer SA, Doneanu CE, Goodlett DR, Schnapp LM: Of mice and men: comparative proteomics of bronchoalveolar fluid. Eur Respir J 2010, 35: 1388–1395. 10.1183/09031936.00089409PubMedCentralCrossRefPubMed
35.
go back to reference Schnapp LM, Donohoe S, Chen J, Sunde DA, Kelly PM, Ruzinski J, Martin T, Goodlett DR: Mining the acute respiratory distress syndrome proteome: identification of the insulin-like growth factor (IGF)/IGF-binding protein-3 pathway in acute lung injury. Am J Pathol 2006, 169: 86–95. 10.2353/ajpath.2006.050612PubMedCentralCrossRefPubMed Schnapp LM, Donohoe S, Chen J, Sunde DA, Kelly PM, Ruzinski J, Martin T, Goodlett DR: Mining the acute respiratory distress syndrome proteome: identification of the insulin-like growth factor (IGF)/IGF-binding protein-3 pathway in acute lung injury. Am J Pathol 2006, 169: 86–95. 10.2353/ajpath.2006.050612PubMedCentralCrossRefPubMed
36.
go back to reference Bhargava TB M, Viken KJ, Jagtap PD, Dey S, Steinbach MS, Wu B, Kumar V, Bitterman PB, Ingbar DH, Wendt CH: Proteomic profiles in acute respiratory distress syndrome differentiates survivors from non-survivors. PLoS One 2014. in press. Bhargava TB M, Viken KJ, Jagtap PD, Dey S, Steinbach MS, Wu B, Kumar V, Bitterman PB, Ingbar DH, Wendt CH: Proteomic profiles in acute respiratory distress syndrome differentiates survivors from non-survivors.PLoS One 2014. in press. Bhargava TB M, Viken KJ, Jagtap PD, Dey S, Steinbach MS, Wu B, Kumar V, Bitterman PB, Ingbar DH, Wendt CH: Proteomic profiles in acute respiratory distress syndrome differentiates survivors from non-survivors. PLoS One 2014. in press. Bhargava TB M, Viken KJ, Jagtap PD, Dey S, Steinbach MS, Wu B, Kumar V, Bitterman PB, Ingbar DH, Wendt CH: Proteomic profiles in acute respiratory distress syndrome differentiates survivors from non-survivors.PLoS One 2014. in press.
37.
go back to reference Piersma SR, Warmoes MO, de Wit M, de Reus I, Knol JC, Jimenez CR: Whole gel processing procedure for GeLC-MS/MS based proteomics. Proteome Sci 2013, 11: 17. 10.1186/1477-5956-11-17PubMedCentralCrossRefPubMed Piersma SR, Warmoes MO, de Wit M, de Reus I, Knol JC, Jimenez CR: Whole gel processing procedure for GeLC-MS/MS based proteomics. Proteome Sci 2013, 11: 17. 10.1186/1477-5956-11-17PubMedCentralCrossRefPubMed
38.
go back to reference Chang DW, Hayashi S, Gharib SA, Vaisar T, King ST, Tsuchiya M, Ruzinski JT, Park DR, Matute-Bello G, Wurfel MM, Bumgarner R, Heinecke JW, Martin TR: Proteomic and computational analysis of bronchoalveolar proteins during the course of the acute respiratory distress syndrome. Am J Respir Crit Care Med 2008, 178: 701–709. 10.1164/rccm.200712-1895OCPubMedCentralCrossRefPubMed Chang DW, Hayashi S, Gharib SA, Vaisar T, King ST, Tsuchiya M, Ruzinski JT, Park DR, Matute-Bello G, Wurfel MM, Bumgarner R, Heinecke JW, Martin TR: Proteomic and computational analysis of bronchoalveolar proteins during the course of the acute respiratory distress syndrome. Am J Respir Crit Care Med 2008, 178: 701–709. 10.1164/rccm.200712-1895OCPubMedCentralCrossRefPubMed
40.
go back to reference Yang F, Shen Y, Camp DG 2nd, Smith RD: High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis. Expert Rev Proteomics 2012, 9: 129–134. 10.1586/epr.12.15PubMedCentralCrossRefPubMed Yang F, Shen Y, Camp DG 2nd, Smith RD: High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis. Expert Rev Proteomics 2012, 9: 129–134. 10.1586/epr.12.15PubMedCentralCrossRefPubMed
41.
go back to reference Wang Y, Yang F, Gritsenko MA, Wang Y, Clauss T, Liu T, Shen Y, Monroe ME, Lopez-Ferrer D, Reno T, Moore RJ, Klemke RL, Camp DG 2nd, Smith RD: Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics 2011, 11: 2019–2026. 10.1002/pmic.201000722PubMedCentralCrossRefPubMed Wang Y, Yang F, Gritsenko MA, Wang Y, Clauss T, Liu T, Shen Y, Monroe ME, Lopez-Ferrer D, Reno T, Moore RJ, Klemke RL, Camp DG 2nd, Smith RD: Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics 2011, 11: 2019–2026. 10.1002/pmic.201000722PubMedCentralCrossRefPubMed
42.
go back to reference Mueller DR, Voshol H, Waldt A, Wiedmann B, Van Oostrum J: LC-MALDI MS and MS/MS-an efficient tool in proteome analysis. Subcell Biochem 2007, 43: 355–380. 10.1007/978-1-4020-5943-8_17CrossRefPubMed Mueller DR, Voshol H, Waldt A, Wiedmann B, Van Oostrum J: LC-MALDI MS and MS/MS-an efficient tool in proteome analysis. Subcell Biochem 2007, 43: 355–380. 10.1007/978-1-4020-5943-8_17CrossRefPubMed
43.
go back to reference Bhargava M, Dey S, Becker TL, Steinbach MS, Wu B, Lee SM, Higgins L, Kumar V, Bitterman PB, Ingbar DH, Wendt CH: Protein expression profile of rat type two alveolar epithelial cells during hyperoxic stress and recovery. Am J Physiol Lung Cell Mol Physiol 2013, 305(9):L604–614. 10.1152/ajplung.00079.2013PubMedCentralCrossRefPubMed Bhargava M, Dey S, Becker TL, Steinbach MS, Wu B, Lee SM, Higgins L, Kumar V, Bitterman PB, Ingbar DH, Wendt CH: Protein expression profile of rat type two alveolar epithelial cells during hyperoxic stress and recovery. Am J Physiol Lung Cell Mol Physiol 2013, 305(9):L604–614. 10.1152/ajplung.00079.2013PubMedCentralCrossRefPubMed
44.
go back to reference Eng JK, McCormack AL, Yates JR: An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 1994, 5: 976–989. 10.1016/1044-0305(94)80016-2CrossRefPubMed Eng JK, McCormack AL, Yates JR: An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 1994, 5: 976–989. 10.1016/1044-0305(94)80016-2CrossRefPubMed
45.
go back to reference Perkins DN, Pappin DJ, Creasy DM, Cottrell JS: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20: 3551–3567. 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2CrossRefPubMed Perkins DN, Pappin DJ, Creasy DM, Cottrell JS: Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20: 3551–3567. 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2CrossRefPubMed
46.
go back to reference Taylor JA, Johnson RS: Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom 1997, 11: 1067–1075. 10.1002/(SICI)1097-0231(19970615)11:9<1067::AID-RCM953>3.0.CO;2-LCrossRefPubMed Taylor JA, Johnson RS: Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom 1997, 11: 1067–1075. 10.1002/(SICI)1097-0231(19970615)11:9<1067::AID-RCM953>3.0.CO;2-LCrossRefPubMed
47.
go back to reference Zhang B, Chambers MC, Tabb DL: Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res 2007, 6: 3549–3557. 10.1021/pr070230dPubMedCentralCrossRefPubMed Zhang B, Chambers MC, Tabb DL: Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res 2007, 6: 3549–3557. 10.1021/pr070230dPubMedCentralCrossRefPubMed
48.
go back to reference Nesvizhskii AI, Aebersold R: Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics 2005, 4: 1419–1440. 10.1074/mcp.R500012-MCP200CrossRefPubMed Nesvizhskii AI, Aebersold R: Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics 2005, 4: 1419–1440. 10.1074/mcp.R500012-MCP200CrossRefPubMed
49.
go back to reference Gupta N, Pevzner PA: False discovery rates of protein identifications: a strike against the two-peptide rule. J Proteome Res 2009, 8: 4173–4181. 10.1021/pr9004794PubMedCentralCrossRefPubMed Gupta N, Pevzner PA: False discovery rates of protein identifications: a strike against the two-peptide rule. J Proteome Res 2009, 8: 4173–4181. 10.1021/pr9004794PubMedCentralCrossRefPubMed
50.
go back to reference Elias JE, Haas W, Faherty BK, Gygi SP: Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods 2005, 2: 667–675. 10.1038/nmeth785CrossRefPubMed Elias JE, Haas W, Faherty BK, Gygi SP: Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods 2005, 2: 667–675. 10.1038/nmeth785CrossRefPubMed
51.
go back to reference Kall L, Storey JD, MacCoss MJ, Noble WS: Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res 2008, 7: 29–34. 10.1021/pr700600nCrossRefPubMed Kall L, Storey JD, MacCoss MJ, Noble WS: Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res 2008, 7: 29–34. 10.1021/pr700600nCrossRefPubMed
52.
go back to reference Shen C, Sheng Q, Dai J, Li Y, Zeng R, Tang H: On the estimation of false positives in peptide identifications using decoy search strategy. Proteomics 2009, 9: 194–204. 10.1002/pmic.200800330PubMedCentralCrossRefPubMed Shen C, Sheng Q, Dai J, Li Y, Zeng R, Tang H: On the estimation of false positives in peptide identifications using decoy search strategy. Proteomics 2009, 9: 194–204. 10.1002/pmic.200800330PubMedCentralCrossRefPubMed
53.
go back to reference Chelius D, Bondarenko PV: Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res 2002, 1: 317–323. 10.1021/pr025517jCrossRefPubMed Chelius D, Bondarenko PV: Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res 2002, 1: 317–323. 10.1021/pr025517jCrossRefPubMed
54.
go back to reference Barr JR, Maggio VL, Patterson DG Jr, Cooper GR, Henderson LO, Turner WE, Smith SJ, Hannon WH, Needham LL, Sampson EJ: Isotope dilution-mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I. Clin Chem 1996, 42: 1676–1682.PubMed Barr JR, Maggio VL, Patterson DG Jr, Cooper GR, Henderson LO, Turner WE, Smith SJ, Hannon WH, Needham LL, Sampson EJ: Isotope dilution-mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I. Clin Chem 1996, 42: 1676–1682.PubMed
55.
go back to reference Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R: Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17: 994–999. 10.1038/13690CrossRefPubMed Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R: Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17: 994–999. 10.1038/13690CrossRefPubMed
56.
go back to reference Liu H, Sadygov RG, Yates JR 3rd: A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004, 76: 4193–4201. 10.1021/ac0498563CrossRefPubMed Liu H, Sadygov RG, Yates JR 3rd: A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004, 76: 4193–4201. 10.1021/ac0498563CrossRefPubMed
57.
go back to reference Zhou W, Liotta LA, Petricoin EF: The spectra count label-free quantitation in cancer proteomics. Cancer Genomics Proteomics 2012, 9: 135–142.PubMedCentralPubMed Zhou W, Liotta LA, Petricoin EF: The spectra count label-free quantitation in cancer proteomics. Cancer Genomics Proteomics 2012, 9: 135–142.PubMedCentralPubMed
58.
go back to reference Tabb DL, MacCoss MJ, Wu CC, Anderson SD, Yates JR 3rd: Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal Chem 2003, 75: 2470–2477. 10.1021/ac026424oCrossRefPubMed Tabb DL, MacCoss MJ, Wu CC, Anderson SD, Yates JR 3rd: Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal Chem 2003, 75: 2470–2477. 10.1021/ac026424oCrossRefPubMed
59.
go back to reference Xie F, Liu T, Qian WJ, Petyuk VA, Smith RD: Liquid chromatography-mass spectrometry-based quantitative proteomics. J Biol Chem 2011, 286: 25443–25449. 10.1074/jbc.R110.199703PubMedCentralCrossRefPubMed Xie F, Liu T, Qian WJ, Petyuk VA, Smith RD: Liquid chromatography-mass spectrometry-based quantitative proteomics. J Biol Chem 2011, 286: 25443–25449. 10.1074/jbc.R110.199703PubMedCentralCrossRefPubMed
60.
go back to reference Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M: Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1: 376–386. 10.1074/mcp.M200025-MCP200CrossRefPubMed Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M: Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1: 376–386. 10.1074/mcp.M200025-MCP200CrossRefPubMed
61.
go back to reference Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ: Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3: 1154–1169. 10.1074/mcp.M400129-MCP200CrossRefPubMed Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ: Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3: 1154–1169. 10.1074/mcp.M400129-MCP200CrossRefPubMed
62.
go back to reference Pierce A, Unwin RD, Evans CA, Griffiths S, Carney L, Zhang L, Jaworska E, Lee CF, Blinco D, Okoniewski MJ, Miller CJ, Bitton DA, Spooncer E, Whetton AD: Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases. Mol Cell Proteomics 2008, 7: 853–863. 10.1074/mcp.M700251-MCP200CrossRefPubMed Pierce A, Unwin RD, Evans CA, Griffiths S, Carney L, Zhang L, Jaworska E, Lee CF, Blinco D, Okoniewski MJ, Miller CJ, Bitton DA, Spooncer E, Whetton AD: Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases. Mol Cell Proteomics 2008, 7: 853–863. 10.1074/mcp.M700251-MCP200CrossRefPubMed
63.
go back to reference Dayon L, Hainard A, Licker V, Turck N, Kuhn K, Hochstrasser DF, Burkhard PR, Sanchez JC: Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal Chem 2008, 80: 2921–2931. 10.1021/ac702422xCrossRefPubMed Dayon L, Hainard A, Licker V, Turck N, Kuhn K, Hochstrasser DF, Burkhard PR, Sanchez JC: Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal Chem 2008, 80: 2921–2931. 10.1021/ac702422xCrossRefPubMed
64.
go back to reference Guo Y, Singleton PA, Rowshan A, Gucek M, Cole RN, Graham DR, Van Eyk JE, Garcia JG: Quantitative proteomics analysis of human endothelial cell membrane rafts: evidence of MARCKS and MRP regulation in the sphingosine 1-phosphate-induced barrier enhancement. Mol Cell Proteomics 2007, 6: 689–696. 10.1074/mcp.M600398-MCP200PubMedCentralCrossRefPubMed Guo Y, Singleton PA, Rowshan A, Gucek M, Cole RN, Graham DR, Van Eyk JE, Garcia JG: Quantitative proteomics analysis of human endothelial cell membrane rafts: evidence of MARCKS and MRP regulation in the sphingosine 1-phosphate-induced barrier enhancement. Mol Cell Proteomics 2007, 6: 689–696. 10.1074/mcp.M600398-MCP200PubMedCentralCrossRefPubMed
65.
go back to reference Bhargava M, Dey S, Becker T, Steinbach M, Wu B, Lee SM, Higgins L, Kumar V, Bitterman PB, Ingbar DH, Wendt CH: Protein expression profile of rat type two alveolar epithelial cells during hyperoxic stress and recovery. Am J Physiol Lung Cell Mol Physiol 2013, 305: L604-L614. 10.1152/ajplung.00079.2013PubMedCentralCrossRefPubMed Bhargava M, Dey S, Becker T, Steinbach M, Wu B, Lee SM, Higgins L, Kumar V, Bitterman PB, Ingbar DH, Wendt CH: Protein expression profile of rat type two alveolar epithelial cells during hyperoxic stress and recovery. Am J Physiol Lung Cell Mol Physiol 2013, 305: L604-L614. 10.1152/ajplung.00079.2013PubMedCentralCrossRefPubMed
66.
go back to reference Kuhn E, Wu J, Karl J, Liao H, Zolg W, Guild B: Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards. Proteomics 2004, 4: 1175–1186. 10.1002/pmic.200300670CrossRefPubMed Kuhn E, Wu J, Karl J, Liao H, Zolg W, Guild B: Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards. Proteomics 2004, 4: 1175–1186. 10.1002/pmic.200300670CrossRefPubMed
67.
go back to reference Tai SS, Bunk DM, White E, Welch MJ: Development and evaluation of a reference measurement procedure for the determination of total 3,3’,5-triiodothyronine in human serum using isotope-dilution liquid chromatography-tandem mass spectrometry. Anal Chem 2004, 76: 5092–5096. 10.1021/ac049516hCrossRefPubMed Tai SS, Bunk DM, White E, Welch MJ: Development and evaluation of a reference measurement procedure for the determination of total 3,3’,5-triiodothyronine in human serum using isotope-dilution liquid chromatography-tandem mass spectrometry. Anal Chem 2004, 76: 5092–5096. 10.1021/ac049516hCrossRefPubMed
68.
go back to reference JW H: A new linear ion trap mass spectrometer. Rapid Commun Mass Spectrom 2002, 16: 512–526. 10.1002/rcm.607CrossRef JW H: A new linear ion trap mass spectrometer. Rapid Commun Mass Spectrom 2002, 16: 512–526. 10.1002/rcm.607CrossRef
69.
go back to reference Yocum AK, Chinnaiyan AM: Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry. Brief Funct Genomic Proteomic 2009, 8: 145–157. 10.1093/bfgp/eln056PubMedCentralCrossRefPubMed Yocum AK, Chinnaiyan AM: Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry. Brief Funct Genomic Proteomic 2009, 8: 145–157. 10.1093/bfgp/eln056PubMedCentralCrossRefPubMed
70.
go back to reference Yocum AK, Khan AP, Zhao R, Chinnaiyan AM: Development of selected reaction monitoring-MS methodology to measure peptide biomarkers in prostate cancer. Proteomics 2010, 10: 3506–3514. 10.1002/pmic.201000023CrossRefPubMed Yocum AK, Khan AP, Zhao R, Chinnaiyan AM: Development of selected reaction monitoring-MS methodology to measure peptide biomarkers in prostate cancer. Proteomics 2010, 10: 3506–3514. 10.1002/pmic.201000023CrossRefPubMed
71.
go back to reference Bereman MS, MacLean B, Tomazela DM, Liebler DC, MacCoss MJ: The development of selected reaction monitoring methods for targeted proteomics via empirical refinement. Proteomics 2012, 12: 1134–1141. 10.1002/pmic.201200042PubMedCentralCrossRefPubMed Bereman MS, MacLean B, Tomazela DM, Liebler DC, MacCoss MJ: The development of selected reaction monitoring methods for targeted proteomics via empirical refinement. Proteomics 2012, 12: 1134–1141. 10.1002/pmic.201200042PubMedCentralCrossRefPubMed
72.
go back to reference Gray RD, MacGregor G, Noble D, Imrie M, Dewar M, Boyd AC, Innes JA, Porteous DJ, Greening AP: Sputum proteomics in inflammatory and suppurative respiratory diseases. Am J Respir Crit Care Med 2008, 178: 444–452. 10.1164/rccm.200703-409OCPubMedCentralCrossRefPubMed Gray RD, MacGregor G, Noble D, Imrie M, Dewar M, Boyd AC, Innes JA, Porteous DJ, Greening AP: Sputum proteomics in inflammatory and suppurative respiratory diseases. Am J Respir Crit Care Med 2008, 178: 444–452. 10.1164/rccm.200703-409OCPubMedCentralCrossRefPubMed
73.
go back to reference Kipnis E, Hansen K, Sawa T, Moriyama K, Zurawel A, Ishizaka A, Wiener-Kronish J: Proteomic analysis of undiluted lung epithelial lining fluid. Chest 2008, 134: 338–345. 10.1378/chest.07-1643CrossRefPubMed Kipnis E, Hansen K, Sawa T, Moriyama K, Zurawel A, Ishizaka A, Wiener-Kronish J: Proteomic analysis of undiluted lung epithelial lining fluid. Chest 2008, 134: 338–345. 10.1378/chest.07-1643CrossRefPubMed
74.
go back to reference Bowler RP, Duda B, Chan ED, Enghild JJ, Ware LB, Matthay MA, Duncan MW: Proteomic analysis of pulmonary edema fluid and plasma in patients with acute lung injury. Am J Physiol Lung Cell Mol Physiol 2004, 286: L1095-L1104. 10.1152/ajplung.00304.2003CrossRefPubMed Bowler RP, Duda B, Chan ED, Enghild JJ, Ware LB, Matthay MA, Duncan MW: Proteomic analysis of pulmonary edema fluid and plasma in patients with acute lung injury. Am J Physiol Lung Cell Mol Physiol 2004, 286: L1095-L1104. 10.1152/ajplung.00304.2003CrossRefPubMed
75.
go back to reference Griese M, Noss J, von Bredow C: Protein pattern of exhaled breath condensate and saliva. Proteomics 2002, 2: 690–696. 10.1002/1615-9861(200206)2:6<690::AID-PROT690>3.0.CO;2-6CrossRefPubMed Griese M, Noss J, von Bredow C: Protein pattern of exhaled breath condensate and saliva. Proteomics 2002, 2: 690–696. 10.1002/1615-9861(200206)2:6<690::AID-PROT690>3.0.CO;2-6CrossRefPubMed
76.
go back to reference Nicholas B, Skipp P, Mould R, Rennard S, Davies DE, O’Connor CD, Djukanovic R: Shotgun proteomic analysis of human-induced sputum. Proteomics 2006, 6: 4390–4401. 10.1002/pmic.200600011CrossRefPubMed Nicholas B, Skipp P, Mould R, Rennard S, Davies DE, O’Connor CD, Djukanovic R: Shotgun proteomic analysis of human-induced sputum. Proteomics 2006, 6: 4390–4401. 10.1002/pmic.200600011CrossRefPubMed
77.
go back to reference Wattiez R, Falmagne P: Proteomics of bronchoalveolar lavage fluid. J Chromatogr B Analyt Technol Biomed Life Sci 2005, 815: 169–178. 10.1016/j.jchromb.2004.10.029CrossRefPubMed Wattiez R, Falmagne P: Proteomics of bronchoalveolar lavage fluid. J Chromatogr B Analyt Technol Biomed Life Sci 2005, 815: 169–178. 10.1016/j.jchromb.2004.10.029CrossRefPubMed
78.
go back to reference Lenz AG, Meyer B, Weber H, Maier K: Two-dimensional electrophoresis of dog bronchoalveolar lavage fluid proteins. Electrophoresis 1990, 11: 510–513. 10.1002/elps.1150110616CrossRefPubMed Lenz AG, Meyer B, Weber H, Maier K: Two-dimensional electrophoresis of dog bronchoalveolar lavage fluid proteins. Electrophoresis 1990, 11: 510–513. 10.1002/elps.1150110616CrossRefPubMed
79.
go back to reference Lindahl M, Stahlbom B, Tagesson C: Two-dimensional gel electrophoresis of nasal and bronchoalveolar lavage fluids after occupational exposure. Electrophoresis 1995, 16: 1199–1204. 10.1002/elps.11501601200CrossRefPubMed Lindahl M, Stahlbom B, Tagesson C: Two-dimensional gel electrophoresis of nasal and bronchoalveolar lavage fluids after occupational exposure. Electrophoresis 1995, 16: 1199–1204. 10.1002/elps.11501601200CrossRefPubMed
80.
go back to reference Wattiez R, Hermans C, Bernard A, Lesur O, Falmagne P: Human bronchoalveolar lavage fluid: two-dimensional gel electrophoresis, amino acid microsequencing and identification of major proteins. Electrophoresis 1999, 20: 1634–1645. 10.1002/(SICI)1522-2683(19990601)20:7<1634::AID-ELPS1634>3.0.CO;2-JCrossRefPubMed Wattiez R, Hermans C, Bernard A, Lesur O, Falmagne P: Human bronchoalveolar lavage fluid: two-dimensional gel electrophoresis, amino acid microsequencing and identification of major proteins. Electrophoresis 1999, 20: 1634–1645. 10.1002/(SICI)1522-2683(19990601)20:7<1634::AID-ELPS1634>3.0.CO;2-JCrossRefPubMed
81.
go back to reference Wattiez R, Hermans C, Cruyt C, Bernard A, Falmagne P: Human bronchoalveolar lavage fluid protein two-dimensional database: study of interstitial lung diseases. Electrophoresis 2000, 21: 2703–2712. 10.1002/1522-2683(20000701)21:13<2703::AID-ELPS2703>3.0.CO;2-WCrossRefPubMed Wattiez R, Hermans C, Cruyt C, Bernard A, Falmagne P: Human bronchoalveolar lavage fluid protein two-dimensional database: study of interstitial lung diseases. Electrophoresis 2000, 21: 2703–2712. 10.1002/1522-2683(20000701)21:13<2703::AID-ELPS2703>3.0.CO;2-WCrossRefPubMed
82.
go back to reference Bell DY, Hook GE: Pulmonary alveolar proteinosis: analysis of airway and alveolar proteins. Am Rev Respir Dis 1979, 119: 979–990.PubMed Bell DY, Hook GE: Pulmonary alveolar proteinosis: analysis of airway and alveolar proteins. Am Rev Respir Dis 1979, 119: 979–990.PubMed
83.
go back to reference Sabounchi-Schutt F, Astrom J, Eklund A, Grunewald J, Bjellqvist B: Detection and identification of human bronchoalveolar lavage proteins using narrow-range immobilized pH gradient DryStrip and the paper bridge sample application method. Electrophoresis 2001, 22: 1851–1860. 10.1002/1522-2683(200105)22:9<1851::AID-ELPS1851>3.0.CO;2-8CrossRefPubMed Sabounchi-Schutt F, Astrom J, Eklund A, Grunewald J, Bjellqvist B: Detection and identification of human bronchoalveolar lavage proteins using narrow-range immobilized pH gradient DryStrip and the paper bridge sample application method. Electrophoresis 2001, 22: 1851–1860. 10.1002/1522-2683(200105)22:9<1851::AID-ELPS1851>3.0.CO;2-8CrossRefPubMed
84.
go back to reference Noel-Georis I, Bernard A, Falmagne P, Wattiez R: Database of bronchoalveolar lavage fluid proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2002, 771: 221–236. 10.1016/S1570-0232(02)00114-9CrossRefPubMed Noel-Georis I, Bernard A, Falmagne P, Wattiez R: Database of bronchoalveolar lavage fluid proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2002, 771: 221–236. 10.1016/S1570-0232(02)00114-9CrossRefPubMed
85.
go back to reference Plymoth A, Lofdahl CG, Ekberg-Jansson A, Dahlback M, Lindberg H, Fehniger TE, Marko-Varga G: Human bronchoalveolar lavage: biofluid analysis with special emphasis on sample preparation. Proteomics 2003, 3: 962–972. 10.1002/pmic.200300387CrossRefPubMed Plymoth A, Lofdahl CG, Ekberg-Jansson A, Dahlback M, Lindberg H, Fehniger TE, Marko-Varga G: Human bronchoalveolar lavage: biofluid analysis with special emphasis on sample preparation. Proteomics 2003, 3: 962–972. 10.1002/pmic.200300387CrossRefPubMed
86.
go back to reference Li SQ, Qi HW, Wu CG, Zhang XJ, Yang SG, Zhao X, Wu Z, Wang Y, Que HP, Liu SJ: Comparative proteomic study of acute pulmonary embolism in a rat model. Proteomics 2007, 7: 2287–2299. 10.1002/pmic.200500665CrossRefPubMed Li SQ, Qi HW, Wu CG, Zhang XJ, Yang SG, Zhao X, Wu Z, Wang Y, Que HP, Liu SJ: Comparative proteomic study of acute pulmonary embolism in a rat model. Proteomics 2007, 7: 2287–2299. 10.1002/pmic.200500665CrossRefPubMed
87.
go back to reference Au JS, Cho WC, Yip TT, Yip C, Zhu H, Leung WW, Tsui PY, Kwok DL, Kwan SS, Cheng WW, Tzang LC, Yang M, Law SC: Deep proteome profiling of sera from never-smoked lung cancer patients. Biomed Pharmacother 2007, 61: 570–577. 10.1016/j.biopha.2007.08.017CrossRefPubMed Au JS, Cho WC, Yip TT, Yip C, Zhu H, Leung WW, Tsui PY, Kwok DL, Kwan SS, Cheng WW, Tzang LC, Yang M, Law SC: Deep proteome profiling of sera from never-smoked lung cancer patients. Biomed Pharmacother 2007, 61: 570–577. 10.1016/j.biopha.2007.08.017CrossRefPubMed
88.
go back to reference Nguyen EV, Gharib SA, Schnapp LM, Goodlett DR: Shotgun MS proteomic analysis of bronchoalveolar lavage fluid in normal subjects. Proteomics Clin Appl 2014, 8(10):737–747. 10.1002/prca.201300018PubMedCentralCrossRefPubMed Nguyen EV, Gharib SA, Schnapp LM, Goodlett DR: Shotgun MS proteomic analysis of bronchoalveolar lavage fluid in normal subjects. Proteomics Clin Appl 2014, 8(10):737–747. 10.1002/prca.201300018PubMedCentralCrossRefPubMed
89.
go back to reference Levitt JE, Gould MK, Ware LB, Matthay MA: The pathogenetic and prognostic value of biologic markers in acute lung injury. J Intensive Care Med 2009, 24: 151–167. 10.1177/0885066609332603CrossRefPubMed Levitt JE, Gould MK, Ware LB, Matthay MA: The pathogenetic and prognostic value of biologic markers in acute lung injury. J Intensive Care Med 2009, 24: 151–167. 10.1177/0885066609332603CrossRefPubMed
90.
go back to reference Chen X, Shan Q, Jiang L, Zhu B, Xi X: Quantitative proteomic analysis by iTRAQ for identification of candidate biomarkers in plasma from acute respiratory distress syndrome patients. Biochem Biophys Res Commun 2013, 441: 1–6. 10.1016/j.bbrc.2013.09.027CrossRefPubMed Chen X, Shan Q, Jiang L, Zhu B, Xi X: Quantitative proteomic analysis by iTRAQ for identification of candidate biomarkers in plasma from acute respiratory distress syndrome patients. Biochem Biophys Res Commun 2013, 441: 1–6. 10.1016/j.bbrc.2013.09.027CrossRefPubMed
91.
go back to reference Gerszten RE, Accurso F, Bernard GR, Caprioli RM, Klee EW, Klee GG, Kullo I, Laguna TA, Roth FP, Sabatine M, Srinivas P, Wang TJ, Ware LB: Challenges in translating plasma proteomics from bench to bedside: update from the NHLBI Clinical Proteomics Programs. Am J Physiol Lung Cell Mol Physiol 2008, 295: L16-L22. 10.1152/ajplung.00044.2008PubMedCentralCrossRefPubMed Gerszten RE, Accurso F, Bernard GR, Caprioli RM, Klee EW, Klee GG, Kullo I, Laguna TA, Roth FP, Sabatine M, Srinivas P, Wang TJ, Ware LB: Challenges in translating plasma proteomics from bench to bedside: update from the NHLBI Clinical Proteomics Programs. Am J Physiol Lung Cell Mol Physiol 2008, 295: L16-L22. 10.1152/ajplung.00044.2008PubMedCentralCrossRefPubMed
92.
go back to reference Ranieri VM, Rubenfeld GD, Thompson BT, Ferguson ND, Caldwell E, Fan E, Camporota L, Slutsky AS: Acute respiratory distress syndrome: the Berlin Definition. JAMA 2012, 307: 2526–2533.PubMed Ranieri VM, Rubenfeld GD, Thompson BT, Ferguson ND, Caldwell E, Fan E, Camporota L, Slutsky AS: Acute respiratory distress syndrome: the Berlin Definition. JAMA 2012, 307: 2526–2533.PubMed
93.
go back to reference Ferguson ND, Fan E, Camporota L, Antonelli M, Anzueto A, Beale R, Brochard L, Brower R, Esteban A, Gattinoni L, Rhodes A, Slutsky AS, Vincent JL, Rubenfeld GD, Thompson BT, Ranieri VM: The Berlin definition of ARDS: an expanded rationale, justification, and supplementary material. Intensive Care Med 2012, 38: 1573–1582. 10.1007/s00134-012-2682-1CrossRefPubMed Ferguson ND, Fan E, Camporota L, Antonelli M, Anzueto A, Beale R, Brochard L, Brower R, Esteban A, Gattinoni L, Rhodes A, Slutsky AS, Vincent JL, Rubenfeld GD, Thompson BT, Ranieri VM: The Berlin definition of ARDS: an expanded rationale, justification, and supplementary material. Intensive Care Med 2012, 38: 1573–1582. 10.1007/s00134-012-2682-1CrossRefPubMed
94.
go back to reference Bernard GR, Artigas A, Brigham KL, Carlet J, Falke K, Hudson L, Lamy M, Legall JR, Morris A, Spragg R: The American-European Consensus Conference on ARDS. Definitions, mechanisms, relevant outcomes, and clinical trial coordination. Am J Respir Crit Care Med 1994, 149: 818–824. 10.1164/ajrccm.149.3.7509706CrossRefPubMed Bernard GR, Artigas A, Brigham KL, Carlet J, Falke K, Hudson L, Lamy M, Legall JR, Morris A, Spragg R: The American-European Consensus Conference on ARDS. Definitions, mechanisms, relevant outcomes, and clinical trial coordination. Am J Respir Crit Care Med 1994, 149: 818–824. 10.1164/ajrccm.149.3.7509706CrossRefPubMed
95.
go back to reference Rubenfeld GD, Caldwell E, Peabody E, Weaver J, Martin DP, Neff M, Stern EJ, Hudson LD: Incidence and outcomes of acute lung injury. N Engl J Med 2005, 353: 1685–1693. 10.1056/NEJMoa050333CrossRefPubMed Rubenfeld GD, Caldwell E, Peabody E, Weaver J, Martin DP, Neff M, Stern EJ, Hudson LD: Incidence and outcomes of acute lung injury. N Engl J Med 2005, 353: 1685–1693. 10.1056/NEJMoa050333CrossRefPubMed
96.
go back to reference Villar J, Blanco J, Anon JM, Santos-Bouza A, Blanch L, Ambros A, Gandia F, Carriedo D, Mosteiro F, Basaldua S, Fernandez RL, Kacmarek RM: The ALIEN study: incidence and outcome of acute respiratory distress syndrome in the era of lung protective ventilation. Intensive Care Med 2011, 37: 1932–1941. 10.1007/s00134-011-2380-4CrossRefPubMed Villar J, Blanco J, Anon JM, Santos-Bouza A, Blanch L, Ambros A, Gandia F, Carriedo D, Mosteiro F, Basaldua S, Fernandez RL, Kacmarek RM: The ALIEN study: incidence and outcome of acute respiratory distress syndrome in the era of lung protective ventilation. Intensive Care Med 2011, 37: 1932–1941. 10.1007/s00134-011-2380-4CrossRefPubMed
97.
go back to reference Force ADT, Ranieri VM, Rubenfeld GD, Thompson BT, Ferguson ND, Caldwell E, Fan E, Camporota L, Slutsky AS: Acute respiratory distress syndrome: the Berlin Definition. JAMA 2012, 307: 2526–2533. Force ADT, Ranieri VM, Rubenfeld GD, Thompson BT, Ferguson ND, Caldwell E, Fan E, Camporota L, Slutsky AS: Acute respiratory distress syndrome: the Berlin Definition. JAMA 2012, 307: 2526–2533.
98.
go back to reference de Torre C, Ying SX, Munson PJ, Meduri GU, Suffredini AF: Proteomic analysis of inflammatory biomarkers in bronchoalveolar lavage. Proteomics 2006, 6: 3949–3957. 10.1002/pmic.200500693CrossRefPubMed de Torre C, Ying SX, Munson PJ, Meduri GU, Suffredini AF: Proteomic analysis of inflammatory biomarkers in bronchoalveolar lavage. Proteomics 2006, 6: 3949–3957. 10.1002/pmic.200500693CrossRefPubMed
99.
go back to reference Gessner C, Dihazi H, Brettschneider S, Hammerschmidt S, Kuhn H, Eschrich K, Keller T, Engelmann L, Sack U, Wirtz H: Presence of cytokeratins in exhaled breath condensate of mechanical ventilated patients. Respir Med 2008, 102: 299–306. 10.1016/j.rmed.2007.08.012CrossRefPubMed Gessner C, Dihazi H, Brettschneider S, Hammerschmidt S, Kuhn H, Eschrich K, Keller T, Engelmann L, Sack U, Wirtz H: Presence of cytokeratins in exhaled breath condensate of mechanical ventilated patients. Respir Med 2008, 102: 299–306. 10.1016/j.rmed.2007.08.012CrossRefPubMed
100.
go back to reference Gillet LC, Navarro P, Tate S, Rost H, Selevsek N, Reiter L, Bonner R, Aebersold R: 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 2012, 11: O111. 10.1074/mcp.O111.016717PubMedCentralCrossRefPubMed Gillet LC, Navarro P, Tate S, Rost H, Selevsek N, Reiter L, Bonner R, Aebersold R: 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 2012, 11: O111. 10.1074/mcp.O111.016717PubMedCentralCrossRefPubMed
101.
go back to reference Bailey DJ, Rose CM, McAlister GC, Brumbaugh J, Yu P, Wenger CD, Westphall MS, Thomson JA, Coon JJ: Instant spectral assignment for advanced decision tree-driven mass spectrometry. Proc Natl Acad Sci U S A 2012, 109: 8411–8416. 10.1073/pnas.1205292109PubMedCentralCrossRefPubMed Bailey DJ, Rose CM, McAlister GC, Brumbaugh J, Yu P, Wenger CD, Westphall MS, Thomson JA, Coon JJ: Instant spectral assignment for advanced decision tree-driven mass spectrometry. Proc Natl Acad Sci U S A 2012, 109: 8411–8416. 10.1073/pnas.1205292109PubMedCentralCrossRefPubMed
Metadata
Title
Application of clinical proteomics in acute respiratory distress syndrome
Authors
Maneesh Bhargava
LeeAnn Higgins
Christine H Wendt
David H Ingbar
Publication date
01-12-2014
Publisher
Springer Berlin Heidelberg
Published in
Clinical and Translational Medicine / Issue 1/2014
Electronic ISSN: 2001-1326
DOI
https://doi.org/10.1186/s40169-014-0034-1

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