MSiMass list: A public database of identifications for protein MALDI MS imaging

Journal of Proteome Research

Volumn 13, Issue 2, 2014, Pages 1138-1142

  McDonnell, Liam A ^a,b   Walch, Axel ^c   Stoeckli, Markus ^d   Corthals, Garry L ^e  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b Pisa Science Foundation   (Italy)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

^d NOVARTIS PHARMA AG   (Switzerland)

^e UNIVERSITY OF TURKU   (Finland)

Author keywords

database; mass spectrometry imaging; MSI; protein identification

Indexed keywords

BIOLOGICAL MARKERS; DATABASES, PROTEIN; PROTEINS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TRYPSIN;

EID: 84893856169     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400620y     Document Type: Article

References (34)

1. McDonnell, L. A.; Heeren, R. M. A. Imaging Mass Spectrometry Mass Spectrom. Rev. 2007, 26, 606-643
2. Balluff, B.; Elsner, M.; Kowarsch, A.; Rauser, S.; Meding, S.; Schumacher, C.; Feith, M.; Herrmann, K.; Röcken, C.; Schmid, R. M.; Höfler, H.; Walch, A.; Ebert, M. P. Classification of HER2/neu Status in Gastric Cancer Using a Breast-Cancer Derived Proteome Classifier J. Proteome Res. 2010, 9, 6317-6322
3. Cazares, L. H.; Troyer, D.; Mendrinos, S.; Lance, 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 (17) 5541-5551
4. Lazova, R.; Seeley, E. H.; Keenan, M.; Gueorguieva, R.; Caprioli, R. M. Imaging mass spectrometry-a new and promising method to differentiate spitz nevi from spitzoid malignant melanomas Am. J. Dermatopathol. 2012, 34, 82-90
5. Lemaire, R.; Menguellet, S. A.; Stauber, J.; Marchaudon, V.; Lucot, J. P.; Collinet, P.; Farine, M. O.; Vinatier, D.; Day, R.; Ducoroy, P.; Salzet, M.; Fournier, I. Specific MALDI Imaging and Profiling for Biomarker Hunting and Validation: Fragment of the 11S Proteasome Activator Complex, Reg a Fragment, is a New Potential Ovary Cancer Biomarker J. Proteome Res. 2007, 6 (11) 4127-4134
6. Rauser, S.; Marquardt, C.; Balluff, B.; Deininger, S. O.; Albers, C.; Belau, E.; Hartmer, R.; Suckau, D.; Specht, K.; Ebert, M. P.; 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
7. Schwamborn, K.; Caprioli, R. M. Molecular imaging by mass spectrometry-looking beyond classical histology Nat. Rev. Cancer 2010, 10, 639-646
8. Schwamborn, K.; Krieg, R. C.; Uhlig, S.; Ikenberg, H.; Wellmann, A. MALDI Imaging as a Specific Diagnostic Tool for Routine Cervical Cytology Specimens Int. J. Mol. Med. 2010, 27, 417-421
9. Willems, S. M.; van Remoortere, A.; van Zeijl, R.; Deelder, A. M.; McDonnell, L. A.; Hogendoorn, P. C. W. Imaging Mass Spectrometry of Myxoid Sarcomas Identifies Proteins and Lipids Specific to Tumor Type and Grade, and Reveals Biochemical Intratumor Heterogeneity J. Pathol. 2010, 222, 400-409
10. Balluff, B.; Rauser, S.; Meding, S.; Elsner, M.; Schoene, C.; Feuchtinger, A.; Schuhmacher, C.; Novotny, A.; Juetting, U.; Maccarrone, G.; Sarioglu, H.; Ueffing, M.; Braselmann, H.; Zitzelsberger, H.; Schmid, R. M.; Hoefler, H.; Ebert, M. P.; Walch, A. MALDI Imaging Identifies Prognostic Seven-Protein Signature of Novel Tissue Markers in Intestinal-Type Gastric Cancer Am. J. Pathol. 2011, 179, 2720-2729
11. Elsner, M.; Rauser, S.; Maier, S.; Schone, C.; Balluff, B.; Meding, S.; Jung, G.; Nipp, M.; Sarioglu, H.; Maccarrone, G.; Aichler, M.; Ruchtinger, A.; Langer, R.; Jutting, U.; Feith, M.; Kuster, B.; Ueffing, M.; Zitzelsberger, H.; Hofler, H.; Walch, A. 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
12. Nipp, M.; Elsner, M.; Balluff, B.; Meding, S.; Sarioglu, H.; Ueffing, M.; Rauser, S.; Unger, K.; Hofler, H.; Walch, A.; Zitzelsberger, H. S100-A10, thioredoxin, and S100-A6 as biomarkers of papillary thyroid carcinoma with lymph node metastasis identified by MALDI Imaging J. Mol. Med. 2012, 90 (2) 163-174
13. Reyzer, M. L.; Caldwell, R. L.; Dugger, T. C.; Forbes, J. T.; Ritter, C. A.; Guix, M.; Arteaga, C. L.; Caprioli, R. M. Early Changes in Protein Expression Detected by Mass Spectrometry Predict Tumor Response to Molecular Therapeutics Cancer Res. 2004, 64 (24) 9093-9100
14. Eberlin, L. S.; Norton, I.; Dill, A. L.; Golby, A. J.; Ligon, K. L.; Santagata, S.; Cooks, R. G.; Agar, N. Y. R. Classifying Human Brain Tumors by Lipid Imaging with Mass Spectrometry Cancer Res. 2012, 72, 645-654
15. Thomas, A.; Patterson, N. H.; Marcinkiewicz, M. M.; Lazaris, A.; Metrakos, P.; Chaurand, P. Histology-driven data mining of lipid signatures from multiple imaging mass spectrometry analyses: application to human colorectal cancer liver metastasis biopsies Anal. Chem. 2013, 85 (5) 2860-2866
16. Picotti, P.; Rinner, O.; Stallmach, R.; Dautel, F.; Farrah, T.; Domon, B.; Wenschuh, H.; Aebersold, R. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes Nat. Methods 2010, 7 (1) 43-46
17. Hopfgartner, G.; Varesio, E.; Stoeckli, M. Matrix-assisted laser desorption/ionization mass spectrometric imaging of complete rat sections using a triple quadrupole linear ion trap Rapid Commun. Mass Spectrom. 2009, 23 (6) 733-736
18. 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
19. Stoeckli, M.; Chaurand, P.; Hallahan, D. E.; Caprioli, R. M. Imaging mass spectrometry: a new technology for the analysis of of protein expression in mammalian tissues Nat. Med. 2001, 7, 493-496
20. Yanagisawa, K.; Shyr, Y.; Xu, B. J.; Massion, P. P.; Larsen, P. H.; White, B. C.; Roberts, J. R.; Edgerton, M.; Gonzalez, A.; Nadaf, S.; Moore, J. H.; Caprioli, R. M.; Carbone, D. P. Proteomic Patterns of Tumour Subsets in Non-Small-Cell Lung Cancer Lancet 2003, 362 (9382) 433-439
21. Inutan, E. D.; Wager-Miller, J.; Mackie, K.; Trimpin, S. Laserspray ionization imaging of multiply charged ions using a commercial vacuum MALDI ion source Anal. Chem. 2012, 84 (21) 9079-9084
22. Inutan, E. D.; Richards, A. L.; Wager-Miller, J.; Mackie, K.; McEwen, C. N.; Trimpin, S. Laserspray ionization, a new method for protein analysis directly from tissue at atmospheric pressure with ultrahigh mass resolution and electron transfer dissociation Mol. Cell. Proteomics 2011, 10 (2) M110 000760
23. Quanico, J.; Franck, J.; Dauly, C.; Strupat, K.; Dupuy, J.; Day, R.; Salzet, M.; Fournier, I.; Wisztorski, M. Development of liquid microjunction extraction strategy for improving protein identification from tissue sections J. Proteomics 2013, 79, 200-218
24. Harris, G. A.; Nicklay, J. J.; Caprioli, R. M. Localized in Situ Hydrogel-Mediated Protein Digestion and Extraction Technique for on-Tissue Analysis Anal. Chem. 2013, 85, 2717-2723
25. Rohner, T. C.; Staab, D.; Stoeckli, M. MALDI mass spectrometric imaging biological tissue sections Mech. Ageing Dev. 2004, 126 (1) 177-185
26. Scholz, B.; Sköld, K.; Kultima, K.; Fernandez, C.; Waldemarson, S.; Savitski, M. M.; Söderquist, M.; Borén, M.; Stella, R.; Andrén, P.; Zubarev, R.; James, P. Impact of temperature dependent sampling procedures in proteomics and peptidomics-A characterization of the liver and pancreas post mortem degradome Mol. Cell. Proteomics 2011, 10, M900229-MCP200
27. Jones, E. A.; Schmitz, N.; Waaijer, C. J. F.; Frese, C. K.; van Remoortere, A.; van Zeijl, R. J. M.; Heck, A. J. R.; Hogendoorn, P. C. W.; Deelder, A. M.; Altelaar, A. F. M.; Bovée, J. V. M. G.; McDonnell, L. A. Imaging Mass Spectrometry-based Molecular Histology Differentiates Microscopically Identical and Heterogeneous Tumors J. Proteome Res. 2013, 12, 1847-1855
28. Maier, S. K.; Hahne, H.; Gholami, A. M.; Balluff, B.; Meding, S.; Schoene, C.; Walch, A. K.; Kuster, B. Comprehensive identification of proteins from MALDI imaging Mol. Cell. Proteomics 2013, mcp.M113.027599
29. Lagarrigue, M.; Alexandrov, T.; Dieuset, G.; Perrin, A.; Lavigne, R.; Baulac, S.; Thiele, H.; Martin, B.; Pineau, C. New analysis workflow for MALDI imaging mass spectrometry: application to the discovery and identification of potential markers of childhood absence epilepsy J. Proteome Res. 2012, 11 (11) 5453-5463
30. Houel, S.; Abernathy, R.; Renganathan, K.; Meyer-Arendt, K.; Ahn, N. G.; Old, W. M. Quantifying the impact of chimera MS/MS spectra on peptide identification in large scale proteomics studies J. Proteome Res. 2010, 9 (8) 4152-4160
31. Schober, Y.; Schramm, T.; Spengler, B.; Römpp, A. Protein identification by accurate mass matrix-assisted laser desorption/ionization imaging of tryptic peptides Rapid Commun. Mass Spectrom. 2011, 25, 2475-2483
32. Yang, Y.; Zhang, S.; Howe, K.; Wilson, D. B.; Moser, F.; Irwin, D.; Thannhauser, T. W. A comparison of nLC-ESI-MS/MS and nLC-MALDI-MS/MS for GeLC-based protein identification and iTRAQ-based shotgun quantitative proteomics J. Biomol. Tech 2007, 18 (4) 226-237
33. Mann, M.; Kulak, N. A.; Nagaraj, N.; Cox, J. The Coming Age of Complete, Accurate, and Ubiquitous Proteomes Mol. Cell 2013, 49, 583-590
34. Uhlen, M.; Oksvold, P.; Fagerberg, L.; Lundberg, E.; Jonasson, K.; Forsberg, M.; Zwahlen, M.; Kampf, C.; Wester, K.; Hober, S.; Wernerus, H.; Byörling, L.; Ponten, F. Towards a knowledge-based Human Protein Atlas Nat. Biotechnol. 2010, 28, 1248-1250