Combining filter-aided sample preparation and pseudoshotgun technology to profile the proteome of a low number of early passage human melanoma cells

Journal of Proteome Research

Volumn 12, Issue 2, 2013, Pages 1040-1048

  Maurer, Margarita ^a   Müller, André C ^b   Wagner, Christine ^a   Huber, Marie L ^a,b   Rudashevskaya, Elena L ^b,c   Wagner, Stephan N ^a   Bennett, Keiryn L ^b  

^a Universitatsklinik fur Dermatologie   (Austria)

^b ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

^c MEDICAL UNIVERSITY OF VIENNA   (Austria)

Author keywords

FASP; in situ digest; metastatic melanoma; orbitrap; proteomic profile; pseudoshotgun; SDS removal; ultrasensitive proteomics

Indexed keywords

PROTEOME;

ARTICLE; CANCER CELL CULTURE; CELL COMPONENT; CELL COUNT; CELL LYSATE; FEASIBILITY STUDY; FILTER AIDED SAMPLE PREPARATION; FUNCTIONAL PROTEOMICS; HUMAN; HUMAN CELL; MELANOMA CELL; METASTATIC MELANOMA; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONTENT; PSEUDOSHOTGUN;

CELL COUNT; CHROMATOGRAPHY, LIQUID; FILTRATION; HUMANS; LIMIT OF DETECTION; MELANOMA; NEOPLASM PROTEINS; PEPTIDE FRAGMENTS; PROTEOLYSIS; PROTEOME; SKIN NEOPLASMS; TANDEM MASS SPECTROMETRY; TRYPSIN; TUMOR CELLS, CULTURED;

EID: 84873354356     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr301009u     Document Type: Article

References (35)

1. Hudgin, R. L.; Ashwell, G. Studies on the role of glycosyltransferases in the hepatic binding of asialoglycoproteins J. Biol. Chem. 1974, 249 (22) 7269-72
2. Wessel, D.; Flugge, U. I. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids Anal. Biochem. 1984, 138 (1) 141-3
3. Puchades, M.; Westman, A.; Blennow, K.; Davidsson, P. Removal of sodium dodecyl sulfate from protein samples prior to matrix-assisted laser desorption/ionization mass spectrometry Rapid Commun. Mass Spectrom. 1999, 13 (5) 344-9
4. Botelho, D.; Wall, M. J.; Vieira, D. B.; Fitzsimmons, S.; Liu, F.; Doucette, A. Top-down and bottom-up proteomics of SDS-containing solutions following mass-based separation J. Proteome Res. 2010, 9 (6) 2863-70
5. Shevchenko, A.; Tomas, H.; Havlis, J.; Olsen, J. V.; Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes Nat. Protoc. 2006, 1 (6) 2856-60
6. Shevchenko, A.; Wilm, M.; Vorm, O.; Jensen, O. N.; Podtelejnikov, A. V.; Neubauer, G.; Mortensen, P.; Mann, M. A strategy for identifying gel-separated proteins in sequence databases by MS alone Biochem. Soc. Trans. 1996, 24 (3) 893-6
7. Shevchenko, A.; Wilm, M.; Vorm, O.; Mann, M. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels Anal. Chem. 1996, 68 (5) 850-8
8. Wisniewski, J. R.; Zougman, A.; Nagaraj, N.; Mann, M. Universal sample preparation method for proteome analysis Nat. Methods 2009, 6 (5) 359-62
9. Wisniewski, J. R.; Zougman, A.; Mann, M. Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome J. Proteome Res. 2009, 8 (12) 5674-8
10. 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 (7) 3040-9
11. Sabel, M. S.; Liu, Y.; Lubman, D. M. Proteomics in melanoma biomarker discovery: great potential, many obstacles Int. J. Proteomics 2011, 2011, 181890
12. Han, M. J.; Wang, H.; Beer, L. A.; Tang, H. Y.; Herlyn, M.; Speicher, D. W. A systems biology analysis of metastatic melanoma using in-depth three-dimensional protein profiling Proteomics 2010, 10 (24) 4450-62
13. Caron, J.; Mange, A.; Guillot, B.; Solassol, J. Highly sensitive detection of melanoma based on serum proteomic profiling J. Cancer Res. Clin. Oncol. 2009, 135 (9) 1257-64
14. Wilson, L. L.; Tran, L.; Morton, D. L.; Hoon, D. S. Detection of differentially expressed proteins in early-stage melanoma patients using SELDI-TOF mass spectrometry Ann. N.Y. Acad. Sci. 2004, 1022, 317-22
15. Mian, S.; Ugurel, S.; Parkinson, E.; Schlenzka, I.; Dryden, I.; Lancashire, L.; Ball, G.; Creaser, C.; Rees, R.; Schadendorf, D. Serum proteomic fingerprinting discriminates between clinical stages and predicts disease progression in melanoma patients J. Clin. Oncol. 2005, 23 (22) 5088-93
16. Hood, B. L.; Grahovac, J.; Flint, M. S.; Sun, M.; Charro, N.; Becker, D.; Wells, A.; Conrads, T. P. Proteomic analysis of laser microdissected melanoma cells from skin organ cultures J. Proteome Res. 2010, 9 (7) 3656-63
17. Campoli, M. R.; Chang, C. C.; Kageshita, T.; Wang, X.; McCarthy, J. B.; Ferrone, S. Human high molecular weight-melanoma-associated antigen (HMW-MAA): a melanoma cell surface chondroitin sulfate proteoglycan (MSCP) with biological and clinical significance Crit. Rev. Immunol. 2004, 24 (4) 267-96
18. Giorgianni, F.; Cappiello, A.; Beranova-Giorgianni, S.; Palma, P.; Trufelli, H.; Desiderio, D. M. LC-MS/MS analysis of peptides with methanol as organic modifier: improved limits of detection Anal. Chem. 2004, 76 (23) 7028-38
19. Bennett, K. L.; Funk, M.; Tschernutter, M.; Breitwieser, F. P.; Planyavsky, M.; Ubaida Mohien, C.; Muller, A.; Trajanoski, Z.; Colinge, J.; Superti-Furga, G.; Schmidt-Erfurth, U. Proteomic analysis of human cataract aqueous humour: Comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ(R)-labelled specimens J. Proteomics 2011, 74 (2) 151-66
20. Olsen, J. V.; de Godoy, L. M.; Li, G.; Macek, B.; Mortensen, P.; Pesch, R.; Makarov, A.; Lange, O.; Horning, S.; Mann, M. Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap Mol. Cell. Proteomics 2005, 4 (12) 2010-21
21. Colinge, J.; Masselot, A.; Giron, M.; Dessingy, T.; Magnin, J. OLAV: towards high-throughput tandem mass spectrometry data identification Proteomics 2003, 3 (8) 1454-63
22. Altelaar, A. F.; Heck, A. J. Trends in ultrasensitive proteomics Curr. Opin. Chem. Biol. 2012, 16 (1-2) 206-13
23. 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 (6) 2262-71
24. Di Palma, S.; Stange, D.; van de Wetering, M.; Clevers, H.; Heck, A. J.; Mohammed, S. Highly sensitive proteome analysis of FACS-sorted adult colon stem cells J. Proteome Res. 2011, 10 (8) 3814-9
25. Waanders, L. F.; Chwalek, K.; Monetti, M.; Kumar, C.; Lammert, E.; Mann, M. Quantitative proteomic analysis of single pancreatic islets Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (45) 18902-7
26. Masuda, T.; Sugiyama, N.; Tomita, M.; Ishihama, Y. Microscale phosphoproteome analysis of 10 000 cells from human cancer cell lines Anal. Chem. 2011, 83 (20) 7698-703
27. Kocher, T.; Swart, R.; Mechtler, K. Ultra-high-pressure RPLC hyphenated to an LTQ-Orbitrap Velos reveals a linear relation between peak capacity and number of identified peptides Anal. Chem. 2011, 83 (7) 2699-704
28. Bernard, K.; Litman, E.; Fitzpatrick, J. L.; Shellman, Y. G.; Argast, G.; Polvinen, K.; Everett, A. D.; Fukasawa, K.; Norris, D. A.; Ahn, N. G.; Resing, K. A. Functional proteomic analysis of melanoma progression Cancer Res. 2003, 63 (20) 6716-25
29. Brychtova, S.; Fiuraskova, M.; Hlobilkova, A.; Brychta, T.; Hirnak, J. Nestin expression in cutaneous melanomas and melanocytic nevi J. Cutaneous Pathol. 2007, 34 (5) 370-5
30. Fusi, A.; Reichelt, U.; Busse, A.; Ochsenreither, S.; Rietz, A.; Maisel, M.; Keilholz, U. Expression of the stem cell markers nestin and CD133 on circulating melanoma cells J. Invest. Dermatol. 2011, 131 (2) 487-94
31. Carta, F.; Demuro, P. P.; Zanini, C.; Santona, A.; Castiglia, D.; D'Atri, S.; Ascierto, P. A.; Napolitano, M.; Cossu, A.; Tadolini, B.; Turrini, F.; Manca, A.; Sini, M. C.; Palmieri, G.; Rozzo, A. C. Analysis of candidate genes through a proteomics-based approach in primary cell lines from malignant melanomas and their metastases Melanoma Res. 2005, 15 (4) 235-44
32. Choksawangkarn, W.; Edwards, N.; Wang, Y.; Gutierrez, P.; Fenselau, C. Comparative study of workflows optimized for in-gel, in-solution, and on-filter proteolysis in the analysis of plasma membrane proteins J. Proteome Res. 2012, 11 (5) 3030-4
33. Wisniewski, J. R.; Zielinska, D. F.; Mann, M. Comparison of ultrafiltration units for proteomic and N-glycoproteomic analysis by the filter-aided sample preparation method Anal. Biochem. 2011, 410 (2) 307-9
34. Ashburner, M.; Ball, C. A.; Blake, J. A.; Botstein, D.; Butler, H.; Cherry, J. M.; Davis, A. P.; Dolinski, K.; Dwight, S. S.; Eppig, J. T.; Harris, M. A.; Hill, D. P.; Issel-Tarver, L.; Kasarskis, A.; Lewis, S.; Matese, J. C.; Richardson, J. E.; Ringwold, M.; Rubin, G. M.; Sherlock, G. G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nat. Genet. 2000, 25 (1) 25-9
35. Lin, W. M.; Baker, A. C.; Beroukhim, R.; Winckler, W.; Feng, W.; Marmion, J. M.; Laine, E.; Greulich, H.; Tseng, H.; Gates, C.; Hodi, F. S.; Dranoff, G.; Sellers, W. R.; Thomas, R. K.; Meyerson, M.; Golub, T. R.; Dummer, R.; Herlyn, M.; Getz, G.; Garraway, L. A. Modeling genomic diversity and tumor dependency in malignant melanoma Cancer. Res. 2008, 68 (3) 664-73