Development of liquid microjunction extraction strategy for improving protein identification from tissue sections

Journal of Proteomics

Volumn 79, Issue , 2013, Pages 200-218

  Quanico, Jusal ^a,d   Franck, Julien ^a   Dauly, Claire ^b   Strupat, Kerstin ^c   Dupuy, Jocelyn ^b   Day, Robert ^d   Salzet, Michel ^a   Fournier, Isabelle ^a   Wisztorski, Maxence ^a  

^a UNIV LILLE   (France)

^b Thermo Fisher Scientific   (United States)

^c THERMO FISHER SCIENTIFIC   (Germany)

^d UNIVERSITÉ DE SHERBROOKE   (Canada)

Author keywords

Liquid extraction surface analysis (LESA); Liquid microjunction; MALDI MSI; Micro extraction; Protein identification; Shotgun proteomics

Indexed keywords

TRYPSIN;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CELL COUNT; CONTROLLED STUDY; LIQUID PHASE MICROEXTRACTION; MALE; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; RAT; REVERSED PHASE LIQUID CHROMATOGRAPHY; TISSUE SECTION;

ANIMALS; BRAIN CHEMISTRY; LIQUID PHASE MICROEXTRACTION; MALE; NERVE TISSUE PROTEINS; PROTEINS; PROTEOMICS; RATS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TANDEM MASS SPECTROMETRY;

EID: 84872865694     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2012.11.025     Document Type: Article

References (77)

1. Craven R.A., Banks R.E. Laser capture microdissection and proteomics: possibilities and limitation. Proteomics 2001, 1:1200-1204.
2. Mustafa D., Kros J.M., Luider T. Combining laser capture microdissection and proteomics techniques. Methods Mol Biol 2008, 428:159-178.
3. Rodriguez A.S., Espina B.H., Espina V., Liotta L.A. Automated laser capture microdissection for tissue proteomics. Methods Mol Biol 2008, 441:71-90.
4. Craven R.A., Banks R.E. Laser capture microdissection for proteome analysis. Curr Protoc Protein Sci 2003, 22.3.1-22.3.27. [Chapter 22:Unit 22 3].
5. Cha S., Imielinski M.B., Rejtar T., Richardson E.A., Thakur D., Sgroi D.C., et al. In situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection: annotation by protein set enrichment analysis and gene ontology. Mol Cell Proteomics 2010, 9:2529-2544.
6. Wang N., Xu M., Wang P., Li L. Development of mass spectrometry-based shotgun method for proteome analysis of 500 to 5000 cancer cells. Anal Chem 2010, 82:2262-2271.
7. Stingl C., van Vilsteren F.G., Guzel C., Ten Kate F.J., Visser M., Krishnadath K.K., et al. Reproducibility of protein identification of selected cell types in Barrett's esophagus analyzed by combining laser-capture microdissection and mass spectrometry. J Proteome Res 2011, 10:288-298.
8. Thakur D., Rejtar T., Wang D., Bones J., Cha S., Clodfelder-Miller B., et al. Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry. J Chromatogr A 2011, 1218:8168-8174.
9. Wisniewski J.R., Ostasiewicz P., Mann M. High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J Proteome Res 2011, 10:3040-3049.
10. Castellino S., Groseclose M.R., Wagner D. MALDI imaging mass spectrometry: bridging biology and chemistry in drug development. Bioanalysis 2011, 3:2427-2441.
11. Prideaux B., Dartois V., Staab D., Weiner D.M., Goh A., Via L.E., et al. High-sensitivity MALDI-MRM-MS imaging of moxifloxacin distribution in tuberculosis-infected rabbit lungs and granulomatous lesions. Anal Chem 2011, 83:2112-2118.
12. Goodwin R.J., Mackay C.L., Nilsson A., Harrison D.J., Farde L., Andren P.E., et al. Qualitative and quantitative MALDI imaging of the positron emission tomography ligands raclopride (a D2 dopamine antagonist) and SCH 23390 (a D1 dopamine antagonist) in rat brain tissue sections using a solvent-free dry matrix application method. Anal Chem 2011, 83:9694-9701.
13. Goodwin R.J., Macintyre L., Watson D.G., Scullion S.P., Pitt A.R. A solvent-free matrix application method for matrix-assisted laser desorption/ionization imaging of small molecules. Rapid Commun Mass Spectrom 2010, 24:1682-1686.
14. Goodwin R.J., Scullion P., Macintyre L., Watson D.G., Pitt A.R. Use of a solvent-free dry matrix coating for quantitative matrix-assisted laser desorption ionization imaging of 4-bromophenyl-1,4-diazabicyclo(3.2.2)nonane-4-carboxylate in rat brain and quantitative analysis of the drug from laser microdissected tissue regions. Anal Chem 2010, 82:3868-3873.
15. Khatib-Shahidi S., Andersson M., Herman J.L., Gillespie T.A., Caprioli R.M. Direct molecular analysis of whole-body animal tissue sections by imaging MALDI mass spectrometry. Anal Chem 2006, 78:6448-6456.
16. Bouslimani A., Bec N., Glueckmann M., Hirtz C., Larroque C. Matrix-assisted laser desorption/ionization imaging mass spectrometry of oxaliplatin derivatives in heated intraoperative chemotherapy (HIPEC)-like treated rat kidney. Rapid Commun Mass Spectrom 2010, 24:415-421.
17. Solon E.G., Schweitzer A., Stoeckli M., Prideaux B. Autoradiography, MALDI-MS, and SIMS-MS imaging in pharmaceutical discovery and development. AAPS J 2010, 12:11-26.
18. Lee Y.J., Perdian D.C., Song Z., Yeung E.S., Nikolau B.J. Use of mass spectrometry for imaging metabolites in plants. Plant J 2012, 70:81-95.
19. Sarsby J., Towers M.W., Stain C., Cramer R., Koroleva O.A. Mass spectrometry imaging of glucosinolates in Arabidopsis flowers and siliques. Phytochemistry 2012, 77:110-118.
20. Yoshimura Y., Zaima N., Moriyama T., Kawamura Y. Different localization patterns of anthocyanin species in the pericarp of black rice revealed by imaging mass spectrometry. PLoS One 2012, 7:e31285.
21. Porta T., Grivet C., Kraemer T., Varesio E., Hopfgartner G. Single hair cocaine consumption monitoring by mass spectrometric imaging. Anal Chem 2011, 83:4266-4272.
22. Van Dyck S., Flammang P., Meriaux C., Bonnel D., Salzet M., Fournier I., et al. Localization of secondary metabolites in marine invertebrates: contribution of MALDI MSI for the study of saponins in Cuvierian tubules of H. forskali. PLoS One 2010, 5:e13923.
23. Miura D., Fujimura Y., Yamato M., Hyodo F., Utsumi H., Tachibana H., et al. Ultrahighly sensitive in situ metabolomic imaging for visualizing spatiotemporal metabolic behaviors. Anal Chem 2010, 82:9789-9796.
24. Esquenazi E., Coates C., Simmons L., Gonzalez D., Gerwick W.H., Dorrestein P.C. Visualizing the spatial distribution of secondary metabolites produced by marine cyanobacteria and sponges via MALDI-TOF imaging. Mol Biosyst 2008, 4:562-570.
25. Veloso A., Astigarraga E., Barreda-Gomez G., Manuel I., Ferrer I., Giralt M.T., et al. Anatomical distribution of lipids in human brain cortex by imaging mass spectrometry. J Am Soc Mass Spectrom 2011, 22:329-338.
26. Rompp A., Guenther S., Schober Y., Schulz O., Takats Z., Kummer W., et al. Histology by mass spectrometry: label-free tissue characterization obtained from high-accuracy bioanalytical imaging. Angew Chem Int Ed Engl 2010, 49:3834-3838.
27. Chen R., Jiang X., Conaway M.C., Mohtashemi I., Hui L., Viner R., et al. Mass spectral analysis of neuropeptide expression and distribution in the nervous system of the lobster Homarus americanus. J Proteome Res 2010, 9:818-832.
28. Djidja M.C., Francese S., Loadman P.M., Sutton C.W., Scriven P., Claude E., et al. Detergent addition to tryptic digests and ion mobility separation prior to MS/MS improves peptide yield and protein identification for in situ proteomic investigation of frozen and formalin-fixed paraffin-embedded adenocarcinoma tissue sections. Proteomics 2009, 9:2750-2763.
29. Chen R., Hui L., Sturm R.M., Li L. Three dimensional mapping of neuropeptides and lipids in crustacean brain by mass spectral imaging. J Am Soc Mass Spectrom 2009, 20:1068-1077.
30. Colsch B., Jackson S.N., Dutta S., Woods A.S. Molecular microscopy of brain gangliosides: illustrating their distribution in hippocampal cell layers. ACS Chem Neurosci 2011, 2:213-222.
31. Delvolve A.M., Colsch B., Woods A.S. Highlighting anatomical sub-structures in rat brain tissue using lipid imaging. Anal Methods 2011, 3:1729-1736.
32. Hanrieder J., Ljungdahl A., Falth M., Mammo S.E., Bergquist J., Andersson M. l-DOPA-induced dyskinesia is associated with regional increase of striatal dynorphin peptides as elucidated by imaging mass spectrometry. Mol Cell Proteomics 2011, 10. [M111 009308].
33. Minerva L., Boonen K., Menschaert G., Landuyt B., Baggerman G., Arckens L. Linking mass spectrometric imaging and traditional peptidomics: a validation in the obese mouse model. Anal Chem 2011, 83:7682-7691.
34. Meriaux C., Arafah K., Tasiemski A., Wisztorski M., Bruand J., Boidin-Wichlacz C., et al. Multiple changes in peptide and lipid expression associated with regeneration in the nervous system of the medicinal leech. PLoS One 2011, 6:e18359.
35. Seeley E.H., Caprioli R.M. Molecular imaging of proteins in tissues by mass spectrometry. Proc Natl Acad Sci USA 2008, 105:18126-18131.
36. Grassl J., Taylor N.L., Millar A.H. Matrix-assisted laser desorption/ionisation mass spectrometry imaging and its development for plant protein imaging. Plant Methods 2011, 7:21.
37. Kaspar S., Peukert M., Svatos A., Matros A., Mock H.P. MALDI-imaging mass spectrometry - an emerging technique in plant biology. Proteomics 2011, 11:1840-1850.
38. Bonnel D., Legouffe R., Willand N., Baulard A., Hamm G., Deprez B., et al. MALDI imaging techniques dedicated to drug-distribution studies. Bioanalysis 2011, 3:1399-1406.
39. Stoeckli M., Staab D., Staufenbiel M., Wiederhold K.H., Signor L. Molecular imaging of amyloid beta peptides in mouse brain sections using mass spectrometry. Anal Biochem 2002, 311:33-39.
40. Stauber J., Lemaire R., Franck J., Bonnel D., Croix D., Day R., et al. MALDI imaging of formalin-fixed paraffin-embedded tissues: application to model animals of Parkinson disease for biomarker hunting. J Proteome Res 2008, 7:969-978.
41. Elsner M., Rauser S., Maier S., Schone C., Balluff B., Meding S., et al. MALDI imaging mass spectrometry reveals COX7A2, TAGLN2 and S100-A10 as novel prognostic markers in Barrett's adenocarcinoma. J Proteomics 2012, 75(15):4693-4704.
42. Meding S., Nitsche U., Balluff B., Elsner M., Rauser S., Schone C., et al. Tumor classification of six common cancer types based on proteomic profiling by MALDI imaging. J Proteome Res 2012, 11:1996-2003.
43. Nipp M., Elsner M., Balluff B., Meding S., Sarioglu H., Ueffing M., et al. S100-A10, thioredoxin, and S100-A6 as biomarkers of papillary thyroid carcinoma with lymph node metastasis identified by MALDI imaging. J Mol Med (Berl) 2012, 90:163-174.
44. Le Faouder J., Laouirem S., Chapelle M., Albuquerque M., Belghiti J., Degos F., et al. Imaging mass spectrometry provides fingerprints for distinguishing hepatocellular carcinoma from cirrhosis. J Proteome Res 2011, 10:3755-3765.
45. Rauser S., Marquardt C., Balluff B., Deininger S.O., Albers C., Belau E., et al. Classification of HER2 receptor status in breast cancer tissues by MALDI imaging mass spectrometry. J Proteome Res 2010, 9:1854-1863.
46. Balluff B., Rauser S., Meding S., Elsner M., Schone C., Feuchtinger A., et al. MALDI imaging identifies prognostic seven-protein signature of novel tissue markers in intestinal-type gastric cancer. Am J Pathol 2011, 179:2720-2729.
47. Willems S.M., van Remoortere A., van Zeijl R., Deelder A.M., McDonnell L.A., Hogendoorn P.C. Imaging mass spectrometry of myxoid sarcomas identifies proteins and lipids specific to tumour type and grade, and reveals biochemical intratumour heterogeneity. J Pathol 2010, 222:400-409.
48. Lemaire R., Menguellet S.A., Stauber J., Marchaudon V., Lucot J.P., Collinet P., et al. Specific MALDI imaging and profiling for biomarker hunting and validation: fragment of the 11S proteasome activator complex, Reg alpha fragment, is a new potential ovary cancer biomarker. J Proteome Res 2007, 6:4127-4134.
49. El Ayed M., Bonnel D., Longuespee R., Castelier C., Franck J., Vergara D., et al. MALDI imaging mass spectrometry in ovarian cancer for tracking, identifying, and validating biomarkers. Med Sci Monit 2010, 16:BR233-BR245.
50. Groseclose M.R., Andersson M., Hardesty W.M., Caprioli R.M. Identification of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry. J Mass Spectrom 2007, 42:254-262.
51. Lemaire R., Desmons A., Tabet J.C., Day R., Salzet M., Fournier I. Direct analysis and MALDI imaging of formalin-fixed, paraffin-embedded tissue sections. J Proteome Res 2007, 6:1295-1305.
52. Franck J., Arafah K., Barnes A., Wisztorski M., Salzet M., Fournier I. Improving tissue preparation for matrix-assisted laser desorption ionization mass spectrometry imaging. Part 1: using microspotting. Anal Chem 2009, 81:8193-8202.
53. Djidja M.C., Claude E., Snel M.F., Francese S., Scriven P., Carolan V., et al. Novel molecular tumour classification using MALDI-mass spectrometry imaging of tissue micro-array. Anal Bioanal Chem 2010, 397:587-601.
54. Gustafsson J.O., Oehler M.K., McColl S.R., Hoffmann P. Citric acid antigen retrieval (CAAR) for tryptic peptide imaging directly on archived formalin-fixed paraffin-embedded tissue. J Proteome Res 2010, 9:4315-4328.
55. Schober Y., Schramm T., Spengler B., Rompp A. Protein identification by accurate mass matrix-assisted laser desorption/ionization imaging of tryptic peptides. Rapid Commun Mass Spectrom 2011, 25:2475-2483.
56. Stauber J., MacAleese L., Franck J., Claude E., Snel M., Kaletas B.K., et al. On-tissue protein identification and imaging by MALDI-ion mobility mass spectrometry. J Am Soc Mass Spectrom 2010, 21:338-347.
57. Djidja M.C., Claude E., Snel M.F., Scriven P., Francese S., Carolan V., et al. MALDI-ion mobility separation-mass spectrometry imaging of glucose-regulated protein 78kDa (Grp78) in human formalin-fixed, paraffin-embedded pancreatic adenocarcinoma tissue sections. J Proteome Res 2009, 8:4876-4884.
58. McLean J.A., Ridenour W.B., Caprioli R.M. Profiling and imaging of tissues by imaging ion mobility-mass spectrometry. J Mass Spectrom 2007, 42:1099-1105.
59. Franck J., El Ayed M., Wisztorski M., Salzet M., Fournier I. On-tissue N-terminal peptide derivatizations for enhancing protein identification in MALDI mass spectrometric imaging strategies. Anal Chem 2009, 81:8305-8317.
60. Debois D., Bertrand V., Quinton L., De Pauw-Gillet M.C., De Pauw E. MALDI-in source decay applied to mass spectrometry imaging: a new tool for protein identification. Anal Chem 2010, 82:4036-4045.
61. Zimmerman T.A., Debois D., Mazzucchelli G., Bertrand V., De Pauw-Gillet M.C., De Pauw E. An analytical pipeline for MALDI in-source decay mass spectrometry imaging. Anal Chem 2011, 83:6090-6097.
62. Brown R.S., Lennon J.J. Sequence-specific fragmentation of matrix-assisted laser-desorbed protein/peptide ions. Anal Chem 1995, 67:3990-3999.
63. Hardouin J. Protein sequence information by matrix-assisted laser desorption/ionization in-source decay mass spectrometry. Mass Spectrom Rev 2007, 26:672-682.
64. Van Berkel G.J., Kertesz V., Koeplinger K.A., Vavrek M., Kong A.N. Liquid microjunction surface sampling probe electrospray mass spectrometry for detection of drugs and metabolites in thin tissue sections. J Mass Spectrom 2008, 43:500-508.
65. Kertesz V., Van Berkel G.J. Liquid microjunction surface sampling coupled with high-pressure liquid chromatography-electrospray ionization-mass spectrometry for analysis of drugs and metabolites in whole-body thin tissue sections. Anal Chem 2010, 82:5917-5921.
66. Kertesz V., Van Berkel G.J. Fully automated liquid extraction-based surface sampling and ionization using a chip-based robotic nanoelectrospray platform. J Mass Spectrom 2010, 45:252-260.
67. Deininger S.O., Ebert M.P., Futterer A., Gerhard M., Rocken C. MALDI imaging combined with hierarchical clustering as a new tool for the interpretation of complex human cancers. J Proteome Res 2008, 7:5230-5236.
68. Wisztorski M., Franck J., Salzet M., Fournier I. MALDI direct analysis and imaging of frozen versus FFPE tissues: what strategy for which sample?. Methods Mol Biol 2010, 656:303-322.
69. Schadt S., Kallbach S., Almeida R., Sandel J. Investigation of figopitant and its metabolites in rat tissue by combining whole-body autoradiography with liquid extraction surface analysis mass spectrometry. Drug Metab Dispos 2012, 40:419-425.
70. Eikel D., Vavrek M., Smith S., Bason C., Yeh S., Korfmacher W.A., et al. Liquid extraction surface analysis mass spectrometry (LESA-MS) as a novel profiling tool for drug distribution and metabolism analysis: the terfenadine example. Rapid Commun Mass Spectrom 2011, 25:3587-3596.
71. Stegemann C., Drozdov I., Shalhoub J., Humphries J., Ladroue C., Didangelos A., et al. Comparative lipidomics profiling of human atherosclerotic plaques. Circ Cardiovasc Genet 2011, 4:232-242.
72. Blatherwick E.Q., Van Berkel G.J., Pickup K., Johansson M.K., Beaudoin M.E., Cole R.O., et al. Utility of spatially-resolved atmospheric pressure surface sampling and ionization techniques as alternatives to mass spectrometric imaging (MSI) in drug metabolism. Xenobiotica 2011, 41:720-734.
73. Walther D.M., Mann M. Accurate quantification of more than 4000 mouse tissue proteins reveals minimal proteome changes during aging. Mol Cell Proteomics 2011, 10. [M110 004523].
74. Gozal Y.M., Dammer E.B., Duong D.M., Cheng D., Gearing M., Rees H.D., et al. Proteomic analysis of hippocampal dentate granule cells in frontotemporal lobar degeneration: application of laser capture technology. Front Neurol 2011, 2:24.
75. Besson D., Pavageau A.H., Valo I., Bourreau A., Belanger A., Eymerit-Morin C., et al. A quantitative proteomic approach of the different stages of colorectal cancer establishes OLFM4 as a new nonmetastatic tumor marker. Mol Cell Proteomics 2011, 10. [M111 009712].
76. Baeumlisberger D., Rohmer M., Arrey T.N., Mueller B.F., Beckhaus T., Bahr U., et al. Simple dual-spotting procedure enhances nLC-MALDI MS/MS analysis of digests with less specific enzymes. J Proteome Res 2011, 10:2889-2894.
77. Brewis I.A., Brennan P. Proteomics technologies for the global identification and quantification of proteins. Adv Protein Chem Struct Biol 2010, 80:1-44.