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Review

High-throughput proteomics using matrix-assisted laser desorption/ ionization mass spectrometry

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Pages 407-420 | Published online: 09 Jan 2014

References

  • McLuckey SA, Wells JM. Mass analysis at the advent of the 21st century. Chem. Rev. 101, 571–606 (2001).
  • Martin RL, Brancia FL. Analysis of high mass peptides using a novel matrix-assisted laser desorption/ionisation quadrupole ion trap time-of-flight mass spectrometer. Rapid Commun. Mass Spectrom. 17, 1358–1365 (2003).
  • Douglas DJ, Frank AJ, Mao D. Linear ion traps in mass spectrometry. Mass Spectrom. Rev. 24, 1–29 (2005).
  • Ackloo S, Loboda A. Applications of a matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometer. l. Metastable decay and collision-induced dissociation for sequencing peptides. Rapid Commun. Mass Spectrom. 19, 213–220 (2005).
  • Syka JE, Marto JA, Bai DL et al. Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J. Proteome Res. 3, 621–626 (2004).
  • Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 422, 198–207 (2003).
  • Mann M, Hendrickson RC, Pandey A. Analysis of proteins and proteomes by mass spectrometry. Ann. Rev. Biochem. 70, 437–473 (2001).
  • Blueggel M, Chamrad D, Meyer HE. Bioinformatics in proteomics. Curr. Pharm. Biotechnol. 5, 79–88 (2004).
  • Pedrioli PG, Eng JK, Hubley R et al. A common open representation of mass spectrometry data and its application to proteomics research. Nature Biotechnol. 22, 1459–1466 (2004).
  • Boguski MS, McIntosh MW. Biomedical informatics for proteomics. Nature 422, 233–237 (2003).
  • Patterson SD. Data analysis – the Achilles heel of proteomics. Nature Biotechnol. 21, 221–222 (2003).
  • Kearney P, Thibault P. Bioinformatics meets proteomics – bridging the gap between mass spectrometry data analysis and cell biology. J. Bioinform. Comput. Biol. 1, 183–200 (2003).
  • Fenyo D, Beavis RC. Informatics and data management in proteomics. Trends Biotechnol. 20, S35–S38 (2002).
  • Hancock WS, Wu SL, Stanley RR, Gombocz EA. Publishing large proteome datasets: scientific policy meets emerging technologies. Trends Biotechnol. 20, S39–S44 (2002).
  • Dreisewerd K. The desorption process in MALDI. Chem. Rev. 103, 395–426 (2003).
  • Karas M, Kruger R. Ion formation in MALDI: the cluster ionization mechanism. Chem. Rev. 103, 427–440 (2003).
  • Knochenmuss R, Zenobi R. MALDI ionization: the role of in-plume processes. Chem. Rev. 103, 441–452 (2003).
  • Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60, 2299–2301 (1988).
  • Rappsilber J, Moniattes M, Nielsen ML, Podtelejnikov AV, Mann M. Experiences and perspectives of MALDI MS and MS/MS in proteomic research. Int. J. Mass Spectrom. 226, 223–237 (2003).
  • Mamyrin BA. Time-of-flight mass spectrometry (concepts, achievements, and prospects). Int. J. Mass Spectrom. 206, 251–266 (2001).
  • Cech NB, Enke CG. Practical implications of some recent studies in electrospray ionization fundamentals. Mass Spectrom. Rev. 20, 362–387 (2001).
  • Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM. Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64–71 (1989).
  • Tang K, Page JS, Smith RD. Charge competition and the linear dynamic range of detection in electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 15, 1416–1423 (2004).
  • Steen H, Jebanathirajah JA, Springer M, Kirschner MW. Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS. Proc. Natl Acad. Sci. USA 102, 3948–3953 (2005).
  • Tomer KB. Separations combined with mass spectrometry. Chem. Rev. 101, 297–328 (2001).
  • Washburn MP, Wolters D, Yates JR III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature Biotechnol. 19, 242–247 (2001).
  • Pappin DJC, Hojrup P, Bleasby AJ. Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 3, 327–332 (1993).
  • Naaby-Hansen S, Waterfield MD, Cramer R. Proteomics – post-genomic cartography to understand gene function. Trends Pharmacol. Sci. 22, 376–384 (2001).
  • O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007–4021 (1975).
  • Klose J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26, 231–243 (1975).
  • Chaurand P, Luetzenkirchen F, Spengler B. Peptide and protein identification by matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay time-of-flight mass spectrometry. J. Am. Soc. Mass Spectrom. 10, 91–103 (1999).
  • Spengler B. Post-source decay analysis in matrix-assisted laser desorption/ionization mass spectrometry of biomolecules. J. Mass Spectrom. 32, 1019–1036 (1997).
  • Steen H, Mann M. The ABC’s (and XYZ’s) of peptide sequencing. Nature Rev. Mol. Cell Biol. 5, 699–711 (2004).
  • Yergey AL, Coorssen JR, Backlund PS Jr et al. De novo sequencing of peptides using MALDI/TOF-TOF. J. Am. Soc. Mass Spectrom. 13, 784–791 (2002).
  • Bienvenut WV, Deon C, Pasquarello C et al. Matrix-assisted laser desorption/ionization-tandem mass spectrometry with high resolution and sensitivity for identification and characterization of proteins. Proteomics 2, 868–876 (2002).
  • 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. 376, 952–965 (2003).
  • Shevchenko A, Loboda A, Ens W, Standing KG. MALDI quadrupole time-of-flight mass spectrometry: a powerful tool for proteomic research. Anal. Chem. 72, 2132–2141 (2000).
  • Krutchinsky AN, Zhang W, Chait BT. Rapidly switchable matrix-assisted laser desorption/ionization and electrospray quadrupole-time-of-flight mass spectrometry for protein identification. J. Am. Soc. Mass Spectrom. 11, 493–504 (2000).
  • Krutchinsky AN, Kalkum M, Chait BT. Automatic identification of proteins with a MALDI-quadrupole ion trap mass spectrometer. Anal. Chem. 73, 5066–5077 (2001).
  • Ong SE, Foster LJ, Mann M. Mass spectrometric-based approaches in quantitative proteomics. Methods 29, 124–130 (2003).
  • Moritz B, Meyer HE. Approaches for the quantification of protein concentration ratios. Proteomics 3, 2208–2220 (2003).
  • Oda Y, Huang K, Cross FR, Cowburn D, Chait BT. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl Acad. Sci. USA 96, 6591–6596 (1999).
  • Pratt JM, Petty J, Riba-Garcia I et al. Dynamics of protein turnover, a missing dimension in proteomics. Mol. Cell Proteomics 1, 579–591 (2002).
  • Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154–1169 (2004).
  • Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol. 17, 994–999 (1999).
  • Tao WA, Aebersold R. Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Curr. Opin. Biotechnol. 14, 110–118 (2003).
  • Brancia FL, Montgomery H, Tanaka K, Kumashiro S. Guanidino labeling derivatization strategy for global characterization of peptide mixtures by liquid chromatography matrix-assisted laser desorption/ionization mass spectrometry. Anal. Chem. 76, 2748–2755 (2004).
  • Beardsley RL, Reilly JP. Optimization of guanidination procedures for MALDI mass mapping. Anal. Chem. 74, 1884–1890 (2002).
  • Stewart NA, Pham VT, Choma CT, Kaplan H. Improved peptide detection with matrix-assisted laser desorption/ionization mass spectrometry by trimethylation of amino groups. Rapid Commun. Mass Spectrom. 16, 1448–1453 (2002).
  • Pashkova A, Moskovets E, Karger BL. Coumarin tags for improved analysis of peptides by MALDI-TOF MS and MS/MS. 1. Enhancement in MALDI MS signal intensities. Anal. Chem. 76, 4550–4557 (2004).
  • Keough T, Youngquist RS, Lacey MP. Sulfonic acid derivatives for peptide sequencing by MALDI MS. Anal. Chem. 75, 156A–165A (2003).
  • Hellman U, Bhikhabhai R. Easy amino acid sequencing of sulfonated peptides using post-source decay on a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer equipped with a variable voltage reflector. Rapid Commun. Mass Spectrom. 16, 1851–1859 (2002).
  • Marekov LN, Steinert PM. Charge derivatization by 4-sulfophenyl isothiocyanate enhances peptide sequencing by post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Mass Spectrom. 38, 373–377 (2003).
  • Wang D, Kalb SR, Cotter RJ. Improved procedures for N-terminal sulfonation of peptides for matrix-assisted laser desorption/ionization post-source decay peptide sequencing. Rapid Commun. Mass Spectrom. 18, 96–102 (2004).
  • Thompson AJ, Calnan D, Cramer R. Cysteic acid-mediated proteome analysis: selective generation and isolation of cysteic acid peptides for mass spectrometric sequencing. In: ASMS Conference on Mass Spectrometry; TN, USA. ThOCam 10, 35 (2004).
  • Nordhoff E, Egelhofer V, Giavalisco P et al. Large-gel two-dimensional electrophoresis-matrix assisted laser desorption/ionization-time of flight-mass spectrometry: an analytical challenge for studying complex protein mixtures. Electrophoresis 22, 2844–2855 (2001).
  • Gauss C, Kalkum M, Lowe M, Lehrach H, Klose J. Analysis of the mouse proteome. (I) Brain proteins: separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation. Electrophoresis 20, 575–600 (1999).
  • Rabilloud T. Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 2, 3–10 (2002).
  • Gobom J, Schuerenberg M, Mueller M, Theiss D, Lehrach H, Nordhoff E. α-cyano-4-hydroxycinnamic acid affinity sample preparation. A protocol for MALDI-MS peptide analysis in proteomics. Anal. Chem. 73, 434–438 (2001).
  • Schuerenberg M, Luebbert C, Eickhoff H, Kalkum M, Lehrach H, Nordhoff E. Prestructured MALDI-MS sample supports. Anal. Chem. 72, 3436–3442 (2000).
  • Zhang N, Li N, Li L. Liquid chromatography MALDI MS/MS for membrane proteome analysis. J. Proteome Res. 3, 719–727 (2004).
  • Mirgorodskaya E, Braeuer C, Fucini P, Lehrach H, Gobom J. Nanoflow liquid chromatography coupled to matrix-assisted laser desorption/ionization mass spectrometry: sample preparation, data analysis, and application to the analysis of complex peptide mixtures. Proteomics 5, 399–408 (2005).
  • Ericson C, Phung QT, Horn DM et al. An automated noncontact deposition interface for liquid chromatography matrix-assisted laser desorption/ionization mass spectrometry. Anal. Chem. 75, 2309–2315 (2003).
  • Krokhin OV, Craig R, Spicer V et al. An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC. Mol. Cell. Proteomics 3, 908–919 (2004).
  • Qian W-J, Camp DG, II, Smith RD. High-throughput proteomics using Fourier transform ion cyclotron resonance mass spectrometry. Expert Rev. Proteomics 1, 87–95 (2004).
  • Figeys D. Adapting arrays and lab-on-a-chip technology for proteomics. Proteomics 2, 373–382 (2002).
  • Weinberger SR, Morris TS, Pawlak M. Recent trends in protein biochip technology. Pharmacogenomics 1, 395–416 (2000).
  • Leisner A, Rohlfing A, Berkenkamp S, Hillenkamp F, Dreisewerd K. Infrared laser post-ionization of large biomolecules from an IR-MALD(I) plume. J. Am. Soc. Mass Spectrom. 15, 934–941 (2004).
  • Cramer R, Corless S. Liquid ultraviolet matrix-assisted laser desorption/ionization – mass spectrometry for automated proteomic analysis. Proteomics 5, 360–370 (2005).
  • Chen CT, Chen YC. Desorption/ionization mass spectrometry on nanocrystalline titania sol-gel-deposited films. Rapid Commun. Mass Spectrom. 18, 1956–1964 (2004).
  • Go EP, Prenni JE, Wei J et al. Desorption/ionization on silicon time-of-flight/time-of-flight mass spectrometry. Anal. Chem. 75, 2504–2506 (2003).
  • Thomas JJ, Shen Z, Crowell JE, Finn MG, Siuzdak G. Desorption/ionization on silicon (DIOS): a diverse mass spectrometry platform for protein characterization. Proc. Natl Acad. Sci. USA 98, 4932–4937 (2001).
  • Go EP, Apon JV, Luo G et al. Desorption/ionization on silicon nanowires. Anal. Chem. 77, 1641–1646 (2005).
  • Rosenblatt KP, Bryant-Greenwood P, Killian JK et al. Serum proteomics in cancer diagnosis and management. Ann. Rev. Med. 55, 97–112 (2004).
  • Conrads TP, Zhou M, Petricoin EF III, Liotta L, Veenstra TD. Cancer diagnosis using proteomic patterns. Expert Rev. Mol. Diagn. 3, 411–420 (2003).
  • Cottingham K. Clinical proteomics: are we there yet? Anal. Chem. 75, 472A–476A (2003).
  • Bright JJ, Claydon MA, Soufian M, Gordon DB. Rapid typing of bacteria using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry and pattern recognition software. J. Microbiol. Methods 48, 127–138 (2002).
  • Fenselau C, Demirev PA. Characterization of intact microorganisms by MALDI mass spectrometry. Mass Spectrom. Rev. 20, 157–171 (2001).
  • Arnold RJ, Reilly JP. Fingerprint matching of E. coli strains with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of whole cells using a modified correlation approach. Rapid Commun. Mass Spectrom. 12, 630–636 (1998).
  • Stattin P, Hakama M. Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res. 62, 3609–3614 (2002).
  • Diamandis EP. Point: proteomic patterns in biological fluids: do they represent the future of cancer diagnostics? Clin. Chem. 49, 1272–1275 (2003).
  • Rockhill B. Proteomic patterns in serum and identification of ovarian cancer. Lancet 360, 169; author reply 170–161 (2002).
  • Pearl DC. Proteomic patterns in serum and identification of ovarian cancer. Lancet 360, 169–170; author reply 170–161 (2002).
  • Diamandis EP. Proteomic patterns in serum and identification of ovarian cancer. Lancet 360, 170; author reply 170–171 (2002).
  • Caprioli RM, Farmer TB, Gile J. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal. Chem. 69, 4751–4760 (1997).
  • Chaurand P, Schwartz SA, Caprioli RM. Assessing protein patterns in disease using imaging mass spectrometry. J. Proteome Res. 3, 245–252 (2004).
  • Stoeckli M, Chaurand P, Hallahan DE, Caprioli RM. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nature Med. 7, 493–496 (2001).
  • Spengler B, Hubert M. Scanning microprobe matrix-assisted laser desorption ionization (SMALDI) mass spectrometry: instrumentation for sub-micrometer resolved LDI and MALDI surface analysis. J. Am. Soc. Mass Spectrom. 13, 735–748 (2002).
  • Luxembourg SL, Mize TH, McDonnell LA, Heeren RM. High-spatial resolution mass spectrometric imaging of peptide and protein distributions on a surface. Anal. Chem. 76, 5339–5344 (2004).
  • Altelaar AF, van Minnen J, Jimenez CR, Heeren RM, Piersma SR. Direct molecular imaging of Lymnaea stagnalis nervous tissue at subcellular spatial resolution by mass spectrometry. Anal. Chem. 77, 735–741 (2005).
  • McDonnell LA, Piersma SR, MaartenAltelaar AF et al. Subcellular imaging mass spectrometry of brain tissue. J. Mass Spectrom. 40, 160–168 (2005).

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