Bottlenecks in proteomics

Advances in Experimental Medicine and Biology

Volumn 806, Issue , 2014, Pages 581-593

  Wetie, Arm G Ngounou ^a   Shipp, Devon A ^a   Darie, Costel C ^a  

^a CLARKSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DATA ANALYSIS; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; GEL ELECTROPHORESIS; HUMAN; IONIZATION; MASS SPECTROMETER; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ISOLATION; PROTEIN MODIFICATION; PROTEIN PURIFICATION; PROTEOMICS; METHODOLOGY; REVIEW;

MASS SPECTROMETRY; PROTEOMICS;

EID: 84907424136     PISSN: 00652598     EISSN: 22148019     Source Type: Book Series    
DOI: 10.1007/978-3-319-06068-2_29     Document Type: Article

References (52)

1. Darie CC, Shetty V, Spellman DS, Zhang G, Xu C, Cardasis HL, Blais S, Fenyo D, Neubert TA (2008) Blue native PAGE and mass spectrometry analysis of the ephrin stimulationdependent protein-protein interactions in NG108-EphB2 cells. Applications of Mass Spectrometry in Life Safety, NATO Science for Peace and Security Series. Springer, Düsseldorf, Germany
2. Ngounou Wetie AG et al (2012) Investigation of stable and transient protein-protein interactions: past, present, and future. Proteomics 13(3-4):538-557
3. Darie CC (2013) Mass spectrometry and its application in life sciences. Aust J Chem 66:1-2
4. Ngounou Wetie AG et al (2013) Identification of post-translational modifications by mass spectrometry. Aust J Chem 66:734-748
5. Ngounou Wetie AG et al (2014) Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. Cell Mol Life Sci 71:205-228
6. Petrareanu C et al (2013) Comparative proteomics reveals novel components at the plasma membrane of differentiated HepaRG cells and different distribution in hepatocyte-and biliarylike cells. PLoS One 8(8):e71859
7. Sokolowska I et al (2012) Proteomic analysis of plasma membranes isolated from undifferentiated and differentiated HepaRG cells. Proteome Sci 10(1):47
8. Sokolowska I et al (2013) Applications of mass spectrometry in proteomics. Aust J Chem 66:721-733
9. James P (1997) Protein identification in the post-genome era: the rapid rise of proteomics. Q Rev Biophys 30(4):279-331
10. Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422(6928):198-207
11. Ngounou Wetie AG et al (2013) Automated mass spectrometry-based functional assay for the routine analysis of the secretome. J Lab Autom 18(1):19-29
12. Sokolowska I et al (2012) Disulfide proteomics for identification of extracellular or secreted proteins. Electrophoresis 33(16):2527-2536
13. Sokolowska I et al (2013) Mass spectrometry investigation of glycosylation on the NXS/T sites in recombinant glycoproteins. Biochim Biophys Acta 1834(8):1474-1483
14. Sokolowska I et al (2012) Automatic determination of disulfide bridges in proteins. J Lab Autom 17(6):408-416
15. Sokolowska I et al (2011) Mass spectrometry for proteomics-based investigation of oxidative stress and heat shock proteins. In: Andreescu S, Hepel M (eds) Oxidative stress: diagnostics, prevention, and therapy. American Chemical Society, Washington, DC
16. Woods AG et al (2012) Potential biomarkers in psychiatry: focus on the cholesterol system. J Cell Mol Med 16(6):1184-1195
17. Woods AG et al (2011) Blue native page and mass spectrometry as an approach for the investigation of stable and transient protein-protein interactions. In: Andreescu S, Hepel M (eds) Oxidative stress: diagnostics, prevention, and therapy. American Chemical Society, Washington, DC
18. Viswanathan S, Unlu M, Minden JS (2006) Two-dimensional difference gel electrophoresis. Nat Protoc 1(3):1351-1358
19. Gygi SP et al (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17(10):994-999
20. Ong SE et al (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1(5):376-386
21. Stemmann O et al (2001) Dual inhibition of sister chromatid separation at metaphase. Cell 107(6):715-726
22. Anderson L, Hunter CL (2006) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics 5(4):573-588
23. Liu H, Sadygov RG, Yates JR III (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76(14):4193-4201
24. Savitski MF, Savitski MM (2010) Unbiased detection of posttranslational modifications using mass spectrometry. Methods Mol Biol 673:203-210
25. Spiro RG (2002) Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. Glycobiology 12(4):43R-56R
26. Marino K et al (2010) A systematic approach to protein glycosylation analysis: a path through the maze. Nat Chem Biol 6(10):713-723
27. Tarrant MK, Cole PA (2009) The chemical biology of protein phosphorylation. Annu Rev Biochem 78:797-825
28. Gorman JJ, Wallis TP, Pitt JJ (2002) Protein disulfide bond determination by mass spectrometry. Mass Spectrom Rev 21(3):183-216
29. McAuley A et al (2008) Contributions of a disulfide bond to the structure, stability, and dimerization of human IgG1 antibody CH3 domain. Protein Sci 17(1):95-106
30. Koh GC et al (2012) Analyzing protein-protein interaction networks. J Proteome Res 11(4):2014-2031
31. De Las Rivas J, Fontanillo C (2010) Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PLoS Comput Biol 6(6):e1000807
32. Krause F (2006) Detection and analysis of protein-protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (membrane) protein complexes and supercomplexes. Electrophoresis 27(13):2759-2781
33. Schagger H, von Jagow G (1991) Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal Biochem 199(2):223-231
34. Anderson LE, McClure WO (1973) An improved scintillation cocktail of high-solubilizing power. Anal Biochem 51(1):173-179
35. O'Connell PB, Brady CJ (1976) Polyacrylamide gels with modified cross-linkages. Anal Biochem 76(l):63-73
36. Hansen JN (1976) Electrophoresis of ribonucleic acid on a polyacrylamide gel which contains disulfide cross-linkages. Anal Biochem 76(l):37-44
37. Bornemann S et al (2010) A novel polyacrylamide gel system for proteomic use offering controllable pore expansion by crosslinker cleavage. Electrophoresis 31(4):585-592
38. Wei J, Buriak JM, Siuzdak G (1999) Desorption-ionization mass spectrometry on porous silicon. Nature 399(6733):243-246
39. Yates JR, Ruse CI, Nakorchevsky A (2009) Proteomics by mass spectrometry: approaches, advances, and applications. Annu Rev Biomed Eng 11:49-79
40. Perkins DN et al (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20(18):3551-3567
41. Eng JK, McCormack AL, Yates JR (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5(11):976-989
42. Tabb DL, McDonald WH, Yates JR III (2002) DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res 1(1):21-26
43. Craig R, Beavis RC (2003) A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun Mass Spectrom 17(20):2310-2316
44. Pedrioli PG et al (2004) A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 22(11):1459-1466
45. Deutsch EW, Lam H, Aebersold R (2008) Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics 33(1):18-25
46. Deutsch E (2008) mzML: a single, unifying data format for mass spectrometer output. Proteomics 8(14):2776-2777
47. 1 H NMR spectroscopy and liquid chromatographymass spectrometry applied to the investigation of metabolic changes caused by gentamicininduced nephrotoxicity in the rat. Biomarkers 10(2-3):173-187
48. Kussmann M, Rezzi S, Daniel H (2008) Profiling techniques in nutrition and health research. Curr Opin Biotechnol 19(2):83-99
49. Lescuyer P, Hochstrasser D, Rabilloud T (2007) How shall we use the proteomics toolbox for biomarker discovery? J Proteome Res 6(9):3371-3376
50. Surinova S et al (2011) On the development of plasma protein biomarkers. J Proteome Res 10(1):5-16
51. Drake RR et al (2011) Challenges to developing proteomic-based breast cancer diagnostics. OMICS 15(5):251-259
52. Woods AG, Sokolowska I, Darie CC (2012) Identification of consistent alkylation of cysteine- less peptides in a proteomics experiment. Biochem Biophys Res Commun 419(2):305-308