Microproteomics: Quantitative proteomic profiling of small numbers of laser-captured cells

Cold Spring Harbor Protocols

Volumn 6, Issue 2, 2011, Pages

  Roulhac, Petra L ^a   Ward, James M ^a   Thompson, J Will ^a   Soderblom, Erik J ^a   Silva, Michael ^a   Moseley III, M Arthur ^a   Jarvis, Erich D ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALKYLATION; ARTICLE; IMMUNOBLOTTING; IMMUNOHISTOCHEMISTRY; LASER CAPTURE MICRODISSECTION; LIQUID CHROMATOGRAPHY; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEOMICS; QUANTITATIVE ANALYSIS; TANDEM MASS SPECTROMETRY;

EID: 79751480146     PISSN: None     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.prot5573     Document Type: Article

References (48)

1. Anderson CNG, Grant SGN. 2006. High throughput protein expression screening in the nervous system: Needs and limitations. J Physiol 575: 367-372. [Abstract/Free Full Text]
2. Asomugha CO, Gupta R, Srivastava OP. 2010. Identification of crystallin modifications in the human lens cortex and nucleus using laser capture microdissection and CyDye labeling. Mol Vis 16: 476-494. [Medline]
3. Bagnato C, Thumar J, Mayya V, Hwang S-I, Zebroski H, Claffey KP, Haudenschild C, Eng JK, Lundgren DH, Han DK. 2007. Proteomics analysis of human coronary atherosclerotic plaque: A feasibility study of direct tissue proteomics by liquid chromatography and tandem mass spectrometry. Mol Cell Proteomics 6: 1088-1102. [Abstract/Free Full Text]
4. Carducci C, Birarelli M, Santagata P, Leuzzi V, Carducci C, Antonozzi I. 2001. Automated high-performance liquid chromatographic method for the determination of guanidinoacetic acid in dried blood spots: A tool for early diagnosis of guanidinoacetate methyltransferase deficiency. J Chromatogr B Biomed Sci Appl 755: 343-348. [Medline]
5. Cox J, Mann M. 2008. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26: 1367-1372. [Medline]
6. Cui DP, Dougherty KJ, Machacek DW, Sawchuk M, Hochman S, Baro DJ. 2006. Divergence between motoneurons: Gene expression profiling provides a molecular characterization of functionally discrete somatic and autonomic motoneurons. Physiol Genomics 24: 276-289. [Abstract/Free Full Text]
7. Espina V, Wulfkuhle JD, Calvert VS, VanMeter A, Zhou W, Coukos G, Geho DH, Petricoin EF III, Liotta LA. 2006. Laser-capture microdissection. Nat Protoc 1: 586-603. [Medline]
8. Folli F, Guzzi V, Perego L, Coletta DK, Finzi G, Placidi C, La Rosa S, Capella C, Socci C, Lauro D et al. 2010. Proteomics reveals novel oxidative and glycolytic mechanisms in type 1 diabetic patients' skin which are normalized by kidney-pancreas transplantation. PLoS One 5: e9923. doi:10.1371/journal.pone.0009923. [Medline]
9. Geromanos SJ, Vissers JPC, Silva JC, Dorschel CA, Li G-Z, Gorenstein MV, Bateman RH, Langridge JI. 2009. The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependent LC-MS/MS. Proteomics 9: 1683-1695. [Medline]
10. Gutstein HB, Morris JS. 2007. Laser capture sampling and analytical issues in proteomics. Expert Rev Proteomics 4: 627-637. [Medline]
11. Gutstein HB, Morris JS, Annangudi SP, Sweedler JV. 2008. Microproteomics: Analysis of protein diversity in small samples. Mass Spectrom Rev 27: 316-330. [Medline]
12. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. 1999. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17: 994-999. [Medline]
13. Haqqani AS, Nesic M, Preston E, Baumann E, Kelly J, Stanimirovic D. 2005. Characterization of vascular protein expression patterns in cerebral ischemia/reperfusion using laser capture microdissection and ICAT-nanoLC-MS/MS. FASEB J 19: 1809-1821. [Abstract/Free Full Text]
14. Haqqani AS, Kelly J, Baumann E, Haseloff RF, Blasig IE, Stanimirovic DB. 2007. Protein markers of ischemic insult in brain endothelial cells identified using 2D gel electrophoresis and ICAT-based quantitative proteomics. J Proteome Res 6: 226-239. [Medline]
15. Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA. 2006. PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics 5: 1927-1941. [Abstract/Free Full Text]
16. Jarvis ED. 2004. Learned birdsong and the neurobiology of human language. Ann N Y Acad Sci 1016: 749-777. [Medline]
17. Jürgens U. 2009. The neural control of vocalization in mammals: A review. J Voice 23: 1-10. [Medline]
18. Kiebel GR, Auberry KJ, Jaitly N, Clark DA, Monroe ME, Peterson ES, Toli N, Anderson GA, Smith RD. 2006. PRISM: A data management system for high-throughput proteomics. Proteomics 6: 1783-1790. [Medline]
19. Kislinger T, Rahman K, Radulovic D, Cox B, Rossant J, Emili A. 2003. PRISM, a generic large scale proteomic investigation strategy for mammals. Mol Cell Proteomics 2: 96-106. [Abstract/Free Full Text]
20. Li C, Hong Y, Tan Y-X, Zhou H, Ai J-H, Li S-J, Zhang L, Xia Q-C, Wu J-R, Wang H-Y et al. 2004. Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry. Mol Cell Proteomics 3: 399-409. [Abstract/Free Full Text]
21. Li G-Z, Vissers JPC, Silva JC, Golick D, Gorenstein MV, Geromanos SJ. 2009. Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures. Proteomics 9: 1696-1719. [Medline]
22. Melle C, Ernst G, Grosheva M, Angelov DN, Irintchev A, Guntinas-Lichius O, von Eggeling F. 2009. Proteomic analysis of microdissected facial nuclei of the rat following facial nerve injury. J Neurosci Methods 185: 23-28. [Medline]
23. Merkley MA, Weinberger PM, Jackson LL, Podolsky RH, Lee JR, Dynan WS. 2009. 2D-DIGE proteomic characterization of head and neck squamous cell carcinoma. Otolaryngol Head Neck Surg 141: 626-632. [Medline]
24. Mustafa D, Kros JM, Luider T. 2008. Combining laser capture microdissection and proteomics techniques.Methods Mol Biol 428: 159-178. [Medline]
25. Nan Y, Yang S, Tian Y, Zhang W, Zhou B, Bu L, Huo S. 2009. Analysis of the expression protein profiles of lung squamous carcinoma cell using shot-gun proteomics strategy. Med Oncol 26: 215-221. [Medline]
26. Neubert H, Bonnert TP, Rumpel K, Hunt BT, Henle ES, James IT. 2008. Label-free detection of differential protein expression by LC/MALDI mass spectrometry. J Proteome Res 7: 2270-2279. [Medline]
27. Olsen JV, Andersen JR, Nielsen PA, Nielsen ML, Figeys D, Mann M, Winiewski JR. 2004. HysTag-A novel proteomic quantification tool applied to differential display analysis of membrane proteins from distinct areas of mouse brain. Mol Cell Proteomics 3: 82-92. [Abstract/Free Full Text]
28. Paa-Toli L, Masselon C, Barry RC, Shen YF, Smith RD. 2004. Proteomic analyses using an accurate mass and time tag strategy. Biotechniques 37: 621-639. [Medline]
29. Patel V, Hood BL, Molinolo AA, Lee NH, Conrads TP, Braisted JC, Krizman DB, Veenstra TD, Gutkind JS. 2008. Proteomic analysis of laser-captured paraffin-embedded tissues: A molecular portrait of head and neck cancer progression. Clin Cancer Res 14: 1002-1014. [Abstract/Free Full Text]
30. Pinaud R, Osorio C, Alzate O, Jarvis ED. 2008. Profiling of experience-regulated proteins in the songbird auditory forebrain using quantitative proteomics. Eur J Neurosci 27: 1409-1422. [Medline]
31. Scicchitano MS, Dalmas DA, Boyce RW, Thomas HC, Frazier KS. 2009. Protein extraction of formalin-fixed, paraffin-embedded tissue enables robust proteomic profiles by mass spectrometry. J Histochem Cytochem 57: 849-860. [Abstract/Free Full Text]
32. Shekouh AR, Thompson CC, Prime W, Campbell F, Hamlett J, Herrington CS, Lemoine NR, Crnogorac-Jurcevic T, Buechler MW, Friess H et al. 2003. Application of laser capture microdissection combined with two-dimensional electrophoresis for the discovery of differentially regulated proteins in pancreatic ductal adenocarcinoma. Proteomics 3: 1988-2001. [Medline]
33. Silva JC, Denny R, Dorschel CA, Gorenstein M, Kass IJ, Li G-Z, McKenna T, Nold MJ, Richardson K, Young P et al. 2005. Quantitative proteomic analysis by accurate mass retention time pairs. Anal Chem 77: 2187-2200. [Medline]
34. Silva JC, Denny R, Dorschel C, Gorenstein MV, Li G-Z, Richardson K, Wall D, Geromanos SJ. 2006. Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: A sweet tale. Mol Cell Proteomics 5:589-607. [Abstract/Free Full Text]
35. Sloley S, Smith S, Gandhi S, Busby JAC, London S, Luksch H, Clayton DF, Bhattacharya SK. 2007. Proteomic analyses of zebra finch optic tectum and comparative histochemistry. J Proteome Res 6: 2341-2350. [Medline]
36. Smith RD, Anderson GA, Lipton MS, Paa-Toli L, Shen YF, Conrads TP, Veenstra TD, Udseth HR. 2002. An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics 2: 513-523. [Medline]
37. Stephens AN, Hannan NJ, Rainczuk A, Meehan KL, Chen J, Nicholls PK, Rombauts LJF, Stanton PG, Robertson DM, Salamonsen LA. 2010. Post-translational modifications and protein-specific isoforms in endometriosis revealed by 2D DIGE. J Proteome Res 9: 2438-2449. [Medline]
38. Tolmachev AV, Monroe ME, Purvine SO, Moore RJ, Jaitly N, Adkins JN, Anderson GA, Smith RD. 2008. Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments. Anal Chem 80: 8514-8525. [Medline]
39. Tumani H, Lehmensiek V, Lehnert S, Otto M, Brettschneider J. 2010. 2D DIGE of the cerebrospinal fluid proteome in neurological diseases. Expert Rev Proteomics 7: 29-38. [Medline]
40. Waanders LF, Chwalek K, Monetti M, Kumar C, Lammert E, Mann M. 2009. Quantitative proteomic analysis of single pancreatic islets. Proc Natl Acad Sci 106: 18902-18907. [Abstract/Free Full Text]
41. Wada K, Howard JT, McConnell P, Whitney O, Lints T, Rivas MV, Horita H, Patterson MA, White SA, Scharff C et al. 2006. A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Proc Natl Acad Sci 103: 15212-15217. [Abstract/Free Full Text]
42. Wang Z, Han J, Schey KL. 2008. Spatial differences in an integral membrane proteome detected in laser capture microdissected samples. J Proteome Res 7: 2696-2702. [Medline]
43. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S et al. 2010. The genome of a songbird. Nature 464: 757-762. [Medline]
44. Yao H, Zhang Z, Xiao Z, Chen Y, Li C, Zhang P, Li M, Liu Y, Guan Y, Yu Y et al. 2009. Identification of metastasis associated proteins in human lung squamous carcinoma using two-dimensional difference gel electrophoresis and laser capture microdissection. Lung Cancer 65: 41-48. [Medline]
45. Zang L, Palmer-Toy D, Hancock WS, Sgroi DC, Karger BL. 2004. Proteomic analysis of ductal carcinoma of the breast using laser capture microdissection, LC-MS, and 16O/18O isotopic labeling. J Proteome Res 3: 604-612. [Medline]
46. Zhang D, Koay ES. 2008. Analysis of laser capture microdissected cells by 2-dimensional gel electrophoresis.Methods Mol Biol 428: 77-91. [Medline]
47. Zhang H, Lin Q, Ponnusamy S, Kothandaraman N, Lim TK, Zhao C, Kit HS, Arijit B, Rauff M, Hew C-L et al. 2007. Differential recovery of membrane proteins after extraction by aqueous methanol and trifluoroethanol.Proteomics 7: 1654-1663. [Medline]
48. Zhang Y, Ye Y, Shen D, Jiang K, Zhang H, Sun W, Zhang J, Xu F, Cui Z, Wang S. 2010. Identification of transgelin-2 as a biomarker of colorectal cancer by laser capture microdissection and quantitative proteome analysis. Cancer Sci 101: 523-529. [Medline]