Imaging mass spectrometry data reduction: Automated feature identification and extraction

Journal of the American Society for Mass Spectrometry

Volumn 21, Issue 12, 2010, Pages 1969-1978

  McDonnell, Liam A ^a   van Remoortere, Alexandra ^a   de Velde, Nico ^b   van Zeijl, René J M ^a   Deelder, André M ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b UNIVERSITY OF APPLIED SCIENCES LEIDEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED FEATURES; COMPLEMENTARY ANALYSIS; DATA ANALYSIS; DATA LOAD; DATA SETS; DISCRETE VARIABLES; FILE SIZES; IMAGING MASS SPECTROMETRY; LOCALIZED FEATURES; MOLECULAR CLASS; MOLECULAR SIGNATURES; MULTI VARIATE ANALYSIS; MULTIPLE IMAGING; PARALLEL ANALYSIS; REDUCTION TOOLS;

FEATURE EXTRACTION; HISTOLOGY; MULTIVARIANT ANALYSIS; SECONDARY ION MASS SPECTROMETRY; STATISTICS; TISSUE;

DATA REDUCTION;

LIPID; PEPTIDE; PROTEIN;

ALGORITHM; ARTICLE; AUTOMATION; DATA ANALYSIS; DATA BASE; DATA EXTRACTION; MASS SPECTROMETRY; MOLECULAR BIOLOGY; MOLECULAR IMAGING; MULTIVARIATE ANALYSIS; STANDARDIZATION;

BIOLOGICAL MARKERS; BRAIN CHEMISTRY; DATABASES, FACTUAL; HISTOCYTOCHEMISTRY; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; LIPIDS; MOLECULAR IMAGING; MULTIVARIATE ANALYSIS; MUSCLES; NEOPLASMS; PANCREAS; PEPTIDES; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 78649529317     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2010.08.008     Document Type: Article

References (32)

1. Karas M., Bachmann D., Bahr U., Hillenkamp F. Matrix-Assisted Ultraviolet Laser Desorption of Nonvolatile Compounds. Int. J. Mass Spectrom. Ion Processes 1987, 78:53-68.
2. Chaurand P., Sanders M.E., Jensen R.A., Caprioli R.M. Proteomics in Diagnostic Pathology-Profiling and Imaging Proteins Directly in Tissue Sections. Am. J. Pathol 2004, 165:1057-1068.
3. Cornett D.S., Reyzer M.L., Chaurand P., Caprioli R.M. MALDI Imaging Mass Spectrometry: Molecular Snapshots of Biochemical Systems. Nat. Methods 2007, 4:828-833.
4. McDonnell L.A., Heeren R.M.A. Imaging Mass Spectrometry. Mass Spectrom. Rev 2007, 26:606-643.
5. McDonnell L.A., Willems S.M., Corthals G.L., van Remoortere A., van Zeijl R.J.M., Deelder A.M. Imaging Mass Spectrometry in Cancer Research: Past Experiences and Future Possibilities. J. Proteom 2010, 73:1921-1944.
6. 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, 15:5541-5551.
7. Schwamborn K., Krieg R.C., Reska M., Jakse G., Knuechel R., Wellmann A. Identifying Prostate Carcinoma by MALDI-Imaging. Int. J. Mol. Med 2007, 20:155-159.
8. Groseclose M.R., Massion P.P., Chaurand P., Caprioli R.M. High-Throughput Proteomic Analysis of Formalin-Fixed Paraffin-Embedded Tissue Microarrays Using MALDI Imaging Mass Spectrometry. Proteomics 2008, 8:3715-3724.
9. 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 α fragment, is a New Potential Ovary Cancer Biomarker. J. Proteome Res 2007, 6:4127-4134.
10. Pevsner P.H., Melamed J., Remsen T., Kogos A., Francois F., Kessler P., Stern A., Anand S. Mass Spectrometry MALDI Imaging of Colon Cancer Biomarkers: A New Diagnostic Paradigm. Biomarkers Med 2009, 3:55-69.
11. Oppenheimer S.R., Mi D., Sanders M.E., Caprioli R.M. Molecular Analysis of Tumor Margins by MALDI Mass Spectrometry in Renal Carcinoma. J. Proteome Res 2010, 9:2182-2190.
12. Deininger S.O., Ebert M.P., Fütterer A., Gerhard M., Röcken C. MALDI Imaging Combined with Hierarchical Clustering as a New Tool for the Interpretation of Complex Human Cancers. J. Proteome Res 2008, 7:5230-5236.
13. Eijkel G.B., Kükrer Kaletaş B., van der Wiel I.M., Kros M., Luider T.M., Heeren R.M.A. Correlating MALDI and SIMS Imaging Mass Spectrometric Datasets of Biological Tissue Surfaces. Surf. Interface Anal 2009, 41:675-685.
14. Hanselmann M., Kirchner M., Renard B.Y., Amstalden E.R., Glunde K., Heeren R.M.A., Hamprecht F.A. Concise Representation of Mass Spectrometry Images by Probabilistic Latent Semantic Analysis. Anal. Chem 2008, 80:9649-9658.
15. Hanselmann M., Kothe U., Kirchner M., Renard B.Y., Amstalden E.R., Glunde K., Heeren R.M.A., Hamprecht F.A. Toward Digital Staining using Imaging Mass Spectrometry and Random Forests. J. Proteome Res 2009, 8:3558-3567.
16. 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.
17. McDonnell L.A., van Remoortere A., van Zeijl R.J.M., Deelder A.M. Mass Spectrometry Image Correlation: Quantifying Co-Localization. J. Proteome Res 2008, 7:3619-3627.
18. van de Plas, R.; Ojeda, F.; Dewil, M.; van Den Bosch, L.; De Moor, B.; Waelkens, E. Prospective Exploration of Biochemical Tissue Composition Via Imaging Mass Spectrometry Guided by Principal Component Analysis. Proceedings of the Pacific Symposium on Biocomputing 12 (PSB); Maui, Hawaii, January, 2007; pp 458-469.
19. Golub G.H., van Loanb C.F. Matrix Computationsb 1996, John Hopkins University Pressb, Baltimoreb.
20. Broersen A., van Liere R., Altelaar A.F.M., Heeren R.M.A., McDonnell L.A. Automated, Feature-Based Image Alignment for High-Resolution Imaging Mass Spectrometry of Large Biological Samples. J. Am. Soc. Mass Spectrom 2008, 19:823-832.
21. Coombes K.R., Tsavachidis S., Morris J.S., Baggerly K.A., Hung M.-C., Kuerer H.M. Improved Peak Detection and Quantification of Mass Spectrometry Data Acquired from Surface-Enhanced Laser Desorption and Ionization by Denoising Spectra with the Undecimated Discrete Wavelet Transform. Proteomics 2005, 5:4107-4117.
22. van de Plas, R.; de Moor, B.; Waelkens, E. Discrete Wavelet Transform-based Multiivariate Exploration of Tissue via Imaging Mass Spectrometry. Proceedings of the 23rd Annual ACM Symposium on Allied Computing (ACM SAC); Fortaleza, Brazil, March, 2008.
23. Vogt F., Banerji S., Booksh K. Utilizing Three-Dimensional Wavelet Transforms for Accelerated Evaluation of Hyperspectral Image Cubes. J. Chemometr 2004, 18:350-362.
24. Bradley, A. P. Proceedings of the 7th International Conference on Digital Image Computing: Techniques and Applications; Sydney, Australia, December, 2003; p. 29-38.
25. McDonnell L.A., van Remoortere A., van Zeijl R.J.M., Dalebout H., Bladergroen M.R., André M.D. Automated Imaging MS: Toward High Throughput Imaging Mass Spectrometry. J. Proteom 2009, 73:1279-1282.
26. Puolitaival S.M., Burnum K.E., Cornett D.S., Caprioli R.M. Solvent-Free Matrix Drycoating for MALDI Imaging of Phospholipids. J. Am. Soc. Mass Spectrom 2008, 19:882-886.
27. Mantini D., Petrucci F., Pieragostino D., Del Boccio P., Di Nicola M., Di Ilio C., Federici G., Sacchetta P., Comani S., Urbani A. LIMPIC: A Computational Method for the Separation of Protein MALDI-TOF-MS Signals from Noise. BMC Bioinformatics 2007, 8:101.
28. Kang S., Shim H.S., Lee J.S., Kim D.S., Kim H.Y., Hong S.H., Kim P.S., Yoon J.H., Cho N.H. Molecular Proteomics Imaging of Tumor Interfaces by Mass Spectrometry. J. Proteome Res 2010, 9:1157-1164.
29. 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.
30. Jones J.J., Stump M.J., Fleming R.C., Lay J.O., Wilkins C.L. Strategies and Data Analysis Techniques for Lipid and Phospholipid Chemistry Elucidation by Intact Cell MALDI FTMS. J. Am. Soc. Mass Spectrom 2004, 15:1665-1674.
31. Marshall A.G., Hendrickson C.L., Jackson G.S. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry: A Primer. Mass Spectrom. Rev 1998, 17:1-35.
32. Kelly P.C., Horlick G. Practical Considerations for Digitizing Analog Signals. Anal. Chem 1973, 45:518-527.