Automated querying and identification of novel peptides using MALDI mass spectrometric imaging

Journal of Proteome Research

Volumn 10, Issue 4, 2011, Pages 1915-1928

  Bruand, Jocelyne ^a,h   Sistla, Srinivas ^b   Mériaux, Céline ^c   Dorrestein, Pieter C ^a,d,e   Gaasterland, Terry ^f   Ghassemian, Majid ^a   Wisztorski, Maxence ^c   Fournier, Isabelle ^c   Salzet, Michel ^c   MacAgno, Eduardo ^b   Bafna, Vineet ^g  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c UNIV LILLE   (France)

^d UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^e San Diego   (United States)

^f UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^g UNIVERSITY OF CALIFORNIA   (United States)

^h NONE   (United States)

Author keywords

MALDI imaging; mass spectrometry imaging; targeted peptide identification

Indexed keywords

HISTONE H2B; NEUROPEPTIDE;

AMINO ACID SEQUENCE; ANIMAL EXPERIMENT; ARTICLE; AUTOMATION; CENTRAL NERVOUS SYSTEM; IN SITU HYBRIDIZATION; LEECH; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION MASS SPECTROMETRY; NERVE FIBER; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; SIMULATION;

HIRUDO; HIRUDO MEDICINALIS;

EID: 79953709441     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr101159e     Document Type: Article

References (47)

1. Lemaire, R.; Tabet, J. C.; Ducoroy, P.; Hendra, J. B.; Salzet, M.; Fournier, I. Solid ionic matrixes for direct tissue analysis and MALDI imaging Anal. Chem. 2006, 78, 809-819 (Pubitemid 43230188)
2. 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
3. Spengler, B.; Hubert, M.; Kaufmann, R. MALDI ion imaging and biological ion imaging with new scanning UV-laser microprobe. In Proceedings of the 42nd ASMS Conference on Mass Spectrometry and Allied Topics; ASMS: Santa Fe, NM, 2004.
4. Chaurand, P.; Stoeckli, M.; Caprioli, R. M. Direct profiling of proteins in biological tissue sections by MALDI mass spectrometry Anal. Chem. 1999, 71, 5263-5270 (Pubitemid 129563241)
5. Fournier, I.; Day, R.; Salzet, M. Direct analysis of neuropeptides by in situ MALDI-TOF mass spectrometry in the rat brain Neuro Endocrinol. Lett. 2003, 24, 9-14 (Pubitemid 36559493)
6. Dreisewerd, K.; Kingston, R.; Geraerts, W. P. M.; Li, K. W. Direct mass spectrometric peptide profiling and sequencing of nervous tissues to identify peptides involved in male copulatory behavior in lymnaea stagnalis Int. J. Mass Spectrom. Ion Processes 1997, 169-170, 291-299. Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (Pubitemid 127737178)
7. Jiménez, C. R.; Li, K. W.; Dreisewerd, K.; Spijker, S.; Kingston, R.; Bateman, R. H.; Burlingame, A. L.; Smit, A. B.; van Minnen, J.; Geraerts, W. P. Direct mass spectrometric peptide profiling and sequencing of single neurons reveals differential peptide patterns in a small neuronal network Biochemistry 1998, 37, 2070-2076 (Pubitemid 28099831)
8. Li, K. W.; Hoek, R. M.; Smith, F.; Jiménez, C. R.; van der Schors, R. C.; van Veelen, P. A.; Chen, S.; van der Greef, J.; Parish, D. C.; Benjamin, P. R. Direct peptide profiling by mass spectrometry of single identified neurons reveals complex neuropeptide-processing pattern J. Biol. Chem. 1994, 269, 30288-30292 (Pubitemid 24376500)
9. Caprioli, R. M.; Farmer, T. B.; Gile, J. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS Anal. Chem. 1997, 69, 4751-4760
10. Stoeckli, M.; Farmer, T. B.; Caprioli, R. M. Automated mass spectrometry imaging with a matrix-assisted laser desorption ionization time-of-flight instrument J. Am. Soc. Mass Spectrom. 1999, 10, 67-71 (Pubitemid 34450237)
11. Stoeckli, M.; Chaurand, P.; Hallahan, D. E.; Caprioli, R. M. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues Nat. Med. 2001, 7, 493-496 (Pubitemid 32298555)
12. McCombie, G.; Staab, D.; Stoeckli, M.; Knochenmuss, R. Spatial and spectral correlations in MALDI mass spectrometry images by clustering and multivariate analysis Anal. Chem. 2005, 77, 6118-6124 (Pubitemid 41436943)
13. Alexandrov, T.; Becker, M.; Deininger, S. O.; Ernst, G.; Wehder, L.; Grasmair, M.; von Eggeling, F.; Thiele, H.; Maass, P. Spatial segmentation of imaging mass spectrometry data with edge-preserving image denoising and clustering J. Proteome Res. 2010, 12, 6535-46
14. Blackshaw, S. E.; Henderson, L. P.; Malek, J.; Porter, D. M.; Gross, R. H.; Angstadt, J. D.; Levasseur, S. M.; Maue, R. A. Single-cell analysis reveals cell-specific patterns of expression of a family of putative voltage-gated sodium channel genes in the leech J. Neurobiol. 2003, 55, 355-371 (Pubitemid 36566153)
15. Burrell, B. D.; Sahley, C. L.; Muller, K. J. Progressive recovery of learning during regeneration of a single synapse in the medicinal leech J. Comp. Neurol. 2003, 457, 67-74 (Pubitemid 36172573)
16. Skierczynski, B. A.; Wilson, R. J.; Kristan, W. B.; Skalak, R. A model of the hydrostatic skeleton of the leech J. Theor. Biol. 1996, 181, 329-342 (Pubitemid 26333830)
17. Cazares, L. H.; Troyer, D.; Mendrinos, S.; Lamce, R. A.; Nyalwidhe, J. O.; Beydoun, H. A.; Clements, M. A.; Drake, R. R.; Semmes, O. J. Imaging Mass Spectrometry of a Specific Fragment of Mitogen-Activated Protein Kinase/Extracellular Signal-Regulated Kinase Kinase Kinase 2 Discriminates Cancer from Uninvolved Prostate Tissue Clin. Cancer Res. 2009, 15, 5541-5551
18. Rauser, S.; Marquardt, C.; Balluff, B.; Deininger, S.-O.; Albers, C.; Belau, E.; Hartmer, R.; Suckau, D.; Specht, K.; Ebert, M.; Schmitt, M.; Aubele, M.; Höfler, H.; Walch, A. Classification of HER2 receptor status in breast cancer tissues by MALDI imaging mass spectrometry J. Proteome Res. 2010, 9, 1854-1863
19. Schwamborn, K.; Caprioli, R. M. Molecular imaging by mass spectrometry - looking beyond classical histology Nat. Rev. Cancer 2010, 10, 639-646
20. El Ayed, M.; Bonnel, D.; Longuespée, R.; Castelier, C.; Franck, J.; Vergara, D.; Desmons, A.; Tasiemski, A.; Kenani, A.; Vinatier, D.; Day, R.; Fournier, I.; Salzet, M. MALDI imaging mass spectrometry in ovarian cancer for tracking, identifying, and validating biomarkers Med. Sci. Monit. 2010, 16, 233-245
21. 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
22. Seeley, E. H.; Caprioli, R. M. Molecular imaging of proteins in tissues by mass spectrometry Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 18126-18131
23. Shimma, S.; Sugiura, Y.; Hayasaka, T.; Zaima, N.; Matsumoto, M.; Setou, M. Mass imaging and identification of biomolecules with MALDI-QIT-TOF-based system Anal. Chem. 2008, 80, 878-885 (Pubitemid 351206881)
24. Goodwin, R. J.; Pennington, S. R.; Pitt, A. R. Protein and peptides in pictures: imaging with MALDI mass spectrometry Proteomics 2008, 8, 3785-3800
25. Stauber, J.; Macaleese, L.; Franck, J.; Claude, E.; Snel, M.; Küyeakrer Kaletas, B.; Wiel, I. M.; Wisztorski, M.; Fournier, I.; Heeren, R. M. On-Tissue Protein Identification and Imaging by MALDI-Ion Mobility Mass Spectrometry J. Am. Soc. Mass Spectrom. 2010, 21 (3) 338-347
26. Mallick, P. Computational prediction of proteotypic peptides for quantitative proteomics Nat. Biotechnol. 2007, 25, 125-131 (Pubitemid 46098780)
27. Chen, R.; Jiang, X.; Prieto Conaway, M. C.; Mohtashemi, I.; Hui, L.; Viner, R.; Li, L. Mass Spectral Analysis of Neuropeptide Expression and Distribution in the Nervous System of the Lobster Homarus americanus J. Proteome Res. 2010, 9 (2) 818-832
28. Lee, J. E.; Atkins, N.; Hatcher, N. G.; Zamdborg, L.; Gillette, M. U.; Sweedler, J. V.; Kelleher, N. L. Endogenous peptide discovery of the rat circadian clock: a focused study of the suprachiasmatic nucleus by ultrahigh performance tandem mass spectrometry Mol. Cell. Proteomics 2010, 9, 285-297
29. Macagno, E. R.; Gaasterland, T.; Edsall, L.; Bafna, V.; Soares, M. B.; Scheetz, T.; Casavant, T.; Da Silva, C.; Wincker, P.; Tasiemski, A.; Salzet, M. Construction of a Medicinal Leech Transcriptome Database and Its Application to the Identification of Leech Homologs of Neural and Innate Immune Genes BMC Genomics 2010, 11, 407
30. Frank, A.; Tanner, S.; Bafna, V.; Pevzner, P. Peptide sequence tags for fast database search in mass-spectrometry J. Proteome Res. 2005, 4, 1287-1295 (Pubitemid 41208683)
31. Nardelli-Haefliger, D.; Shankland, M. Lox10, a member of the NK-2 homeobox gene class, is expressed in a segmental pattern in the endoderm and in the cephalic nervous system of the leech Helobdella Development 1993, 118, 877-892 (Pubitemid 23232794)
32. Norris, J. L.; Cornett, D. S.; Mobley, J. A.; Andersson, M.; Seeley, E. H.; Chaurand, P.; Caprioli, R. M. Processing MALDI Mass Spectra to Improve Mass Spectral Direct Tissue Analysis Int. J. Mass Spectrom. 2007, 260, 212-221
33. Macagno, E. R. Number and distribution of neurons in leech segmental ganglia J. Comp. Neurol. 1980, 190, 283-302
34. Lefebvre, C.; Salzet, M. Annelid neuroimmune system Curr. Pharm. Des. 2003, 9, 149-158 (Pubitemid 36131711)
35. Sawyer, R. Leech biology and behaviour; Oxford University Press: New York, 1986.
36. Zerbst-Boroffka, I.; Wenning, A. Mechanism of regulatory salt and water excretion in the leech, Hirudo medicinalis L. Zool. Beitr. N. F. 1986, 30, 359-377
37. Zerbst-Boroffka, I.; Bazin, B.; Wenning, A. Chloride secretion drives urine formation in leech nephridia J. Exp. Biol. 1997, 200, 2217-2227 (Pubitemid 27372565)
38. Schikorski, D.; Cuvillier-Hot, V.; Leippe, M.; Boidin-Wichlacz, C.; Slomianny, C.; Macagno, E.; Salzet, M.; Tasiemski, A. Microbial challenge promotes the regenerative process of the injured central nervous system of the medicinal leech by inducing the synthesis of antimicrobial peptides in neurons and microglia J. Immunol. 2008, 181, 1083-1095
39. Xu, Y.; Bolton, B.; Zipser, B.; Jellies, J.; Johansen, K. M.; Johansen, J. Gliarin and macrolin, two novel intermediate filament proteins specifically expressed in sets and subsets of glial cells in leech central nervous system J. Neurobiol. 1999, 40, 244-253 (Pubitemid 29343308)
40. Thompson, J. D.; Higgins, D. G.; Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 1994, 22, 4673-4680 (Pubitemid 24354800)
41. Altschul, S. F.; Madden, T. L.; Schãffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 1997, 25, 3389-3402 (Pubitemid 27359211)
42. Amstalden van Hove, E. R.; Smith, D. F.; Heeren, R. M. A concise review of mass spectrometry imaging J. Chromatogr., A 2010, 1217 (25) 3946-3954
43. Giepmans, B. N.; Adams, S. R.; Ellisman, M. H.; Tsien, R. Y. The fluorescent toolbox for assessing protein location and function Science 2006, 312, 217-224
44. 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 (Pubitemid 46724026)
45. Johansen, K. M.; Johansen, J. Filarin, a novel invertebrate intermediate filament protein present in axons and perikarya of developing and mature leech neurons J. Neurobiol. 1995, 27, 227-239
46. Weake, V. M.; Lee, K. K.; Guelman, S.; Lin, C. H.; Seidel, C.; Abmayr, S. M.; Workman, J. L. SAGA-mediated H2B deubiquitination controls the development of neuronal connectivity in the Drosophila visual system EMBO J. 2008, 27, 394-405 (Pubitemid 351161655)
47. Weake, V. M.; Workman, J. L. Histone ubiquitination: triggering gene activity Mol. Cell 2008, 29, 653-663 (Pubitemid 351400924)