Laser desorption ionization mass spectrometry of protein tryptic digests on nanostructured silicon plates

Journal of Proteomics

Volumn 75, Issue 7, 2012, Pages 1973-1990

  Dupré, Mathieu ^a   Coffinier, Yannick ^a   Boukherroub, Rabah ^a   Cantel, Sonia ^a   Martinez, Jean ^a   Enjalbal, Christine ^a  

^a CNRS   (France)

Author keywords

LDI MS; Nanostructured silicon; Peptide sequencing; PMF; SALDI MS; Tryptic peptides

Indexed keywords

BETA CASEIN; CYTOCHROME C; FIBRINOGEN; NANOMATERIAL; PROTEIN; SILICON;

AMINO ACID SEQUENCE; ARTICLE; CONTACT ANGLE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR WEIGHT; PEPTIDE ANALYSIS; PRIORITY JOURNAL; SCANNING ELECTRON MICROSCOPY;

PEPTIDES; PROTEINS; PROTEOLYSIS; PROTEOMICS; SILICON; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84858750855     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2011.12.039     Document Type: Article

References (49)

1. Sunner J., Dratz E., Chen Y.-C. Graphite surface-assisted laser desorption/ionization time-of-flight mass spectrometry of peptides and proteins from liquid solutions. Anal Chem 1995, 67:4335-4342.
2. Wei J., Buriak J.M., Siuzdak G. Desorption/Ionization Mass Spectrometry on porous silicon. Nature 1999, 399:243-246.
3. Peterson D.S. Matrix-free methods for laser desorption/ionization mass spectrometry. Mass Spectrom Rev 2007, 26:19-34.
4. Zhang Q., Zou H., Guo Z., Zhang Q., Chen X., Ni J. Matrix-assisted laser desorption/ionization mass spectrometry using porous silicon and silica gel as matrix. Rapid Commun Mass Spectrom 2001, 15:217-223.
5. Okuno S., Arakawa R., Okamoto K., Matsui Y., Seki S., Kozawa T., et al. Requirements for laser-induced desorption/ionization on submicrometer structures. Anal Chem 2005, 77:5364-5369.
6. n of small molecules. 1. Imaging of cerebrosides directly from rat brain tissue. Anal Chem 2007, 79:2373-2385.
7. n of small molecules. 2. Direct profiling and MS imaging of small metabolites from fruits. Anal Chem 2007, 79:6575-6584.
8. Black C., Poile C., Langley J., Herniman J. The use of pencil lead as a matrix and calibrant for matrix-assisted laser desorption/ionization. Rapid Commun Mass Spectrom 2006, 20:1053-1060.
9. Woldegiorgis A., Kieseritzky F.V., Dahlstedt E., Hellberg J., Brinck T., Roeraade J. Polymer-assisted laser desorption/ionization analysis of small molecular weight compounds. Rapid Commun Mass Spectrom 2004, 18:841-852.
10. Chen C.-T., Chen Y.-C. Desorption/ionization mass spectrometry on nanocrystalline titania sol-gel-deposited films. Rapid Commun Mass Spectrom 2004, 18:1956-1964.
11. Law K.P., Larkin J.R. Recent advances in SALDI-MS techniques and their chemical and bioanalytical applications. Anal Bioanal Chem 2011, 399:2597-2622.
12. Xu S., Li Y., Zou H., Qiu J., Guo Z., Guo B. Carbon nanotubes as assisted matrix for laser desorption/ionization time-of-flight mass spectrometry. Anal Chem 2003, 75:6191-6195.
13. Go E.P., Apon J.V., Luo G., Saghatelian A., Daniels R.H., Sahi V., et al. Desorption/ionization on silicon nanowires. Anal. Chem. 2005, 77:1641-1646.
14. McLean J.A., Stumpo K.A., Russell D.H. Size-selected (2-10nm) gold nanoparticles for matrix assisted laser desorption ionization of peptides. J Am Chem Soc 2005, 127:5304-5305.
15. 2 surface-assisted laser desorption/ionization mass spectrometry. Anal Chem 2005, 77:5912-5919.
16. Hua L., Chen J., Ge L., Tan S.N. Silver nanoparticles as matrix for laser desorption/ionization mass spectrometry of peptides. J. Nanoparticle Res. 2007, 9:1133-1138.
17. Kawasaki H., Yonezawa T., Watanabe T., Arakawa R. Platinum nanoflowers for surface-assisted laser desorption/ionization mass spectrometry of biomolecules. J Phys Chem C 2007, 111:16278-16283.
18. Yalcin T., Li L. Cobalt coated substrate for matrix-free analysis of small molecules by laser desorption/ionization mass spectrometry. Appl Surf Sci 2009, 256:1309-1312.
19. Bi H., Qiao L., Busnel J.-M., Devaud V., Liu B., Girault H.H. TiO(2) printed aluminum foil: single-use film for a laser desorption/ionization target plate. Anal Chem 2009, 81:1177-1183.
20. Seino T., Sato H., Yamamoto A., Nemoto A., Torimura M., Tao H. Matrix-free laser desorption/ionization mass spectrometry using self-assembled germanium Nanodots. Anal Chem 2007, 79:4827-4832.
21. Watanabe T., Kawasaki H., Yonezawa T., Arakawa R. Surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) of low molecular weight organic compounds and synthetic polymers using zinc oxide (ZnO) nanoparticles. J Mass Spectrom 2008, 43:1063-1071.
22. Taira S., Kitajima K., Katayanagi H., Ichiishi E., Ichiyanagi Y. Manganese oxide nanoparticle-assisted laser desorption/ionization mass spectrometry for medical applications. Sci. Technol. Adv. Mater. 2009, 10:034602.
23. Chiang C.-K., Yang Z., Lin Y.-W., Chen W.-T., Lin H.-J., Chang H.-T. Detection of proteins and protein-ligand complexes using HgTe nanostructure matrixes in surface-assisted laser desorption/ionization mass spectrometry. Anal Chem 2010, 82:4543-4550.
24. 2 nanorods for improved MALDI-MS analysis of cyclodextrins, peptides, and phosphoproteins. Anal Bioanal Chem 2010, 396:1115-1125.
25. Wyatt M.F., Ding S., Stein B.K., Brenton A.G., Daniels R.H. Analysis of various organic and organometallic compounds using nanostructure-assisted laser desorption/ionization time-of-flight mass spectrometry (NALDI-TOFMS). J Am Soc Mass Spectrom 2010, 21:1256-1259.
26. Shenar N., Martinez J., Enjalbal C. Laser desorption/ionization mass spectrometry on porous silica and alumina for peptide mass fingerprinting. J Am Soc Mass Spectrom 2008, 19:632-644.
27. Shenar N., Cantel S., Martinez J., Enjalbal C. Comparison of inert supports in laser desorption/ionization mass spectrometry of peptides: pencil lead, porous silica gel, DIOS-chip and NALDITM target. Rapid Commun Mass Spectrom 2009, 23:2371-2379.
28. Coffinier Y., Szunerits S., Drobecq H., Melnyk O., Boukherroub R. Diamond nanowires for highly sensitive matrix-free mass spectrometry analysis of small molecules. Nanoscale 2012, 4:231-238.
29. Coffinier Y., Janel S., Addad A., Blossey R., Gengembre L., Payen E., et al. Preparation of superhydrophobic silicon nanowires surfaces. Langmuir 2007, 23:1608-1611.
30. Piret G., Coffinier Y., Roux C., Melnyk O., Boukherroub R. Biomolecule and nanoparticle transfer on patterned and heterogeneously wetted superhydrophobic silicon nanowire surfaces. Langmuir 2008, 24:1670-1672.
31. Piret G., Drobecq H., Coffinier Y., Melnyk O., Boukherroub R. Matrix-free laser desorption/ionization mass spectrometry on silicon nanowire arrays prepared by chemical etching of crystalline silicon. Langmuir 2009, 26:1354-1361.
32. Lapierre F., Piret G., Drobecq H., Melnyk O., Coffinier Y., Thomy V., et al. High sensitive matrix-free mass spectrometry analysis of peptides using silicon nanowires-based digital microfluidic device. Lab Chip 2011, 11:1620-1628.
33. Piret G., Desmet R., Diesis E., Drobecq H., Segers J., Rouanet C., et al. Chips from chips: application to the study of antibody responses to methylated proteins. J Proteome Res 2010, 9:6467-6478.
34. Michalski A., Cox J., Mann M. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res 2011, 10:1785-1793.
35. Beck M., Schmidt A., Malmstroem J., Claassen M., Ori A., Szymborska A., et al. The quantitative proteome of a human cell line. Mol Syst Biol 2011, 549:1-8.
36. Nagaraj N., Wisniewski J.R., Geiger T., Cox J., Kircher M., Kelso J., et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 2011, 548:1-8.
37. Falkner J.A., Kachman M., Veine D.M., Walker A., Strahler J.R., Andrews P.C. Validated MALDI-TOF/TOF mass spectra for protein standards. J Am Soc Mass Spectrom 2007, 18:850-855.
38. Shenar N., Sommerer N., Martinez J., Enjalbal C. Comparison of LID versus CID activation modes in tandem mass spectrometry of peptides. J Mass Spectrom 2009, 44:621-632.
39. Dupré M., Cantel S., Verdié P., Martinez J., Enjalbal C. Sequencing Lys-N proteolytic peptides by ESI and MALDI tandem mass spectrometry. J Am Soc Mass Spectrom 2011, 22:265-279.
40. Dupré M., Cantel S., Martinez J., Enjalbal C. Occurrence of C-terminal residue exclusion in peptide fragmentation by ESI and MALDI tandem mass spectrometry. J Am Soc Mass Spectrom 2012, 23:330-346.
41. Stewart J.M., Young J.D. Solid Phase Peptide Synthesis-Second Edition 1984, Pierce Chemical Company, Rockford, Illinois.
42. Nonaka T., Hashimoto Y., Takio K. Kinetic characterization of lysine-specific metalloendopeptidases from Grifola frondosa and Pleurotus ostreatus fruiting bodies. J Biochem 1998, 124:157-162.
43. Krokhin O.V., Ying S., Cortens J.P., Ghosh D., Spicer V., Ens W., et al. Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS. Anal Chem 2006, 78:6265-6269.
44. Mouls L., Subra G., Aubagnac J.-L., Martinez J., Enjalbal C. Tandem mass spectrometry of amidated peptides. J Mass Spectrom 2006, 41:1470-1483.
45. Nordström A., Apon J.V., Uritboonthai W., Go E.P., Siuzdak G. Surfactant enhanced Desorption/Ionization on Silicon (DIOS) mass spectrometry. Anal Chem 2006, 78:272-278.
46. Macht M., Asperger A., Deininger S.-O. Comparison of laser-induced dissociation and high-energy collision induced dissociation using matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) for peptide and protein identification. Rapid Commun Mass Spectrom 2004, 18:2093-2105.
47. Suckau D., Resemann A., Schuerenberg M., Hufnagel P., Franzen J., Holle A. A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics. Anal Bioanal Chem 2003, 376:952-965.
48. Moneti G., Francese S., Mastrobuoni G., Pieraccini G., Seraglia R., Valitutti G., et al. Do collisions inside the collision cell play a relevant role in CID-LIFT experiments? J. Mass Spectrom. 2007, 42:117-126.
49. Paizs B., Suhai S. Fragmentation pathways of protonated peptides. Mass Spectrom Rev 2005, 24:508-548.