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Development of imaging mass spectrometry (IMS) dataset extractor software, IMS convolution

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Abstract

Imaging mass spectrometry (IMS) is a powerful tool for detecting and visualizing biomolecules in tissue sections. The technology has been applied to several fields, and many researchers have started to apply it to pathological samples. However, it is very difficult for inexperienced users to extract meaningful signals from enormous IMS datasets, and the procedure is time-consuming. We have developed software, called IMS Convolution with regions of interest (ROI), to automatically extract meaningful signals from IMS datasets. The processing is based on the detection of common peaks within the ordered area in the IMS dataset. In this study, the IMS dataset from a mouse eyeball section was acquired by a mass microscope that we recently developed, and the peaks extracted by manual and automatic procedures were compared. The manual procedure extracted 16 peaks with higher intensity in mass spectra averaged in whole measurement points. On the other hand, the automatic procedure using IMS Convolution easily and equally extracted peaks without any effort. Moreover, the use of ROIs with IMS Convolution enabled us to extract the peak on each ROI area, and all of the 16 ion images on mouse eyeball tissue were from phosphatidylcholine species. Therefore, we believe that IMS Convolution with ROIs could automatically extract the meaningful peaks from large-volume IMS datasets for inexperienced users as well as for researchers who have performed the analysis.

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References

  1. Hayasaka T, Goto-Inoue N, Zaima N, Kimura Y, Setou M (2009) Organ-specific distributions of lysophosphatidylcholine and triacylglycerol in mouse embryo. Lipids 44(9):837–848

    Article  CAS  Google Scholar 

  2. Shimma S, Sugiura Y, Hayasaka T, Zaima N, Matsumoto M, Setou M (2008) Mass imaging and identification of biomolecules with MALDI-QIT-TOF-based system. Anal Chem 80(3):878–885

    Article  CAS  Google Scholar 

  3. Groseclose MR, Andersson M, Hardesty WM, Caprioli RM (2007) Identification of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry. J Mass Spectrom 42(2):254–262

    Article  CAS  Google Scholar 

  4. Shimma S, Sugiura Y, Hayasaka T, Hoshikawa Y, Noda T, Setou M (2007) MALDI-based imaging mass spectrometry revealed abnormal distribution of phospholipids in colon cancer liver metastasis. J Chromatogr B Analyt Technol Biomed Life Sci 855(1):98–103

    Article  CAS  Google Scholar 

  5. Chaurand P, Cornett DS, Caprioli RM (2006) Molecular imaging of thin mammalian tissue sections by mass spectrometry. Curr Opin Biotechnol 17(4):431–436

    Article  CAS  Google Scholar 

  6. Khatib-Shahidi S, Andersson M, Herman JL, Gillespie TA, Caprioli RM (2006) Direct molecular analysis of whole-body animal tissue sections by imaging MALDI mass spectrometry. Anal Chem 78(18):6448–6456

    Article  CAS  Google Scholar 

  7. Hattori K, Kajimura M, Hishiki T, Nakanishi T, Kubo A, Nagahata Y, Ohmura M, Yachie-Kinoshita A, Matsuura T, Morikawa T, Nakamura T, Setou M, Suematsu M (2010) Paradoxical ATP elevation in ischemic penumbra revealed by quantitative imaging mass spectrometry. Antioxid Redox Signal 13(8):1157–1167

    Article  CAS  Google Scholar 

  8. Hayasaka T, Goto-Inoue N, Zaima N, Shrivas K, Kashiwagi Y, Yamamoto M, Nakamoto M, Setou M (2010) Imaging mass spectrometry with silver nanoparticles reveals the distribution of fatty acids in mouse retinal sections. J Am Soc Mass Spectrom 21(8):1446–1454

    Article  CAS  Google Scholar 

  9. Andersson M, Groseclose MR, Deutch AY, Caprioli RM (2008) Imaging mass spectrometry of proteins and peptides: 3D volume reconstruction. Nat Methods 5(1):101–108

    Article  CAS  Google Scholar 

  10. Goto-Inoue N, Hayasaka T, Sugiura Y, Taki T, Li YT, Matsumoto M, Setou M (2008) High-sensitivity analysis of glycosphingolipids by matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight imaging mass spectrometry on transfer membranes. J Chromatogr B Analyt Technol Biomed Life Sci 870(1):74–83

    Article  CAS  Google Scholar 

  11. Goto-Inoue N, Hayasaka T, Zaima N, Setou M (2009) The specific localization of seminolipid molecular species on mouse testis during testicular maturation revealed by imaging mass spectrometry. Glycobiology 19(9):950–957

    Article  CAS  Google Scholar 

  12. Shimma S, Furuta M, Ichimura K, Yoshida Y, Setou M (2006) A novel approach to in situ proteome analysis using a chemical inkjet printing technology and MALDI-QIT-TOF tandem mass spectrometer. Surf Int Anal 38:1712–1714

    Article  CAS  Google Scholar 

  13. Sugiura Y, Shimma S, Setou M (2006) Thin sectioning improves the peak intensity and signla-to-noise ratio in direct tissue mass spectrometry. J Mass Spectrom Soc Jpn 54:45–48

    Article  CAS  Google Scholar 

  14. Harada T, Yuba-Kubo A, Sugiura Y, Zaima N, Hayasaka T, Goto-Inoue N, Wakui M, Suematsu M, Takeshita K, Ogawa K, Yoshida Y, Setou M (2009) Visualization of volatile substances in different organelles with an atmospheric-pressure mass microscope. Anal Chem 81(21):9153–9157

    Article  CAS  Google Scholar 

  15. Yao I, Sugiura Y, Matsumoto M, Setou M (2008) In situ proteomics with imaging mass spectrometry and principal component analysis in the Scrapper-knockout mouse brain. Proteomics 8(18):3692–3701

    Article  CAS  Google Scholar 

  16. Brulet M, Seyer A, Edelman A, Brunelle A, Fritsch J, Ollero M, Laprevote O (2010) Lipid mapping of colonic mucosa by cluster TOF-SIMS imaging and multivariate analysis in cftr knockout mice. J Lipid Res 51(10):3034–3045

    Article  CAS  Google Scholar 

  17. Wong JW, Cagney G, Cartwright HM (2005) SpecAlign–processing and alignment of mass spectra datasets. Bioinformatics 21(9):2088–2090

    Article  CAS  Google Scholar 

  18. Norris JL, Cornett DS, Mobley JA, Andersson M, Seeley EH, Chaurand P, Caprioli RM (2007) Processing MALDI mass spectra to improve mass spectral direct tissue analysis. Int J Mass Spectrom 260(2–3):212–221

    CAS  Google Scholar 

  19. Yang C, He Z, Yu W (2009) Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis. BMC Bioinform 10:4

    Article  Google Scholar 

  20. Nguyen N, Huang H, Oraintara S, Vo A (2009) Peak detection in mass spectrometry by Gabor filters and envelope analysis. J Bioinform Comput Biol 7(3):547–569

    Article  CAS  Google Scholar 

  21. Ushijima M, Miyata S, Eguchi S, Kawakita M, Yoshimoto M, Iwase T, Akiyama F, Sakamoto G, Nagasaki K, Miki Y, Noda T, Hoshikawa Y, Matsuura M (2007) Common peak approach using mass spectrometry data sets for predicting the effects of anticancer drugs on breast cancer. Can Inf 3:285–293

    Google Scholar 

  22. Fushiki T, Fujisawa H, Eguchi S (2006) Identification of biomarkers from mass spectrometry data using a "common" peak approach. BMC Bioinform 7:358

    Article  Google Scholar 

  23. Hayasaka T, Goto-Inoue N, Sugiura Y, Zaima N, Nakanishi H, Ohishi K, Nakanishi S, Naito T, Taguchi R, Setou M (2008) Matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight (MALDI-QIT-TOF)-based imaging mass spectrometry reveals a layered distribution of phospholipid molecular species in the mouse retina. Rapid Commun Mass Spectrom 22(21):3415–3426

    Article  CAS  Google Scholar 

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Acknowledgments

The authors are grateful to Tsuyoshi Adachi (Tokai Information Systems Corporation) and Kurando Hosaka (Kansai Medical University) for providing considerable support to our research. The authors acknowledge support for this work through a Grant-in-Aid for SENTAN from the Japan Science and Technology Agency (to M.S.), and by a Grant-in-Aid for Young Scientists S (to M.S.) and for Young Scientists B (to T.H.).

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Authors and Affiliations

  1. Department of Molecular Anatomy, Molecular Imaging Frontier Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431–3192, Japan

    Takahiro Hayasaka, Naoko Goto-Inoue & Mitsutoshi Setou

  2. Bioinformatics Group, Genome Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koutou-ku, Tokyo, 135–8550, Japan

    Masaru Ushijima & Masaaki Matsuura

  3. Department of Medical Chemistry, Kansai Medical University, 10–15 Fumizono-cho, Moriguchi, Osaka, 570–8506, Japan

    Ikuko Yao

  4. Department of Biochemistry and Integrative Medical Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160–8582, Japan

    Akiko Yuba-Kubo & Masatoshi Wakui

  5. Department of Laboratory Medicine, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160–8582, Japan

    Masatoshi Wakui

  6. Technology Research Laboratory, Shimadzu Corporation, 3-9-4 Soraku-gun, Seika-cho, Kyoto, 619–0237, Japan

    Shigeki Kajihara

Authors
  1. Takahiro Hayasaka
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  2. Naoko Goto-Inoue
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  3. Masaru Ushijima
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  4. Ikuko Yao
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  5. Akiko Yuba-Kubo
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  6. Masatoshi Wakui
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  7. Shigeki Kajihara
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  8. Masaaki Matsuura
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  9. Mitsutoshi Setou
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Corresponding author

Correspondence to Mitsutoshi Setou.

Additional information

Published in the special issue on MALDI Imaging with Guest Editor Olivier Laprévote.

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Hayasaka, T., Goto-Inoue, N., Ushijima, M. et al. Development of imaging mass spectrometry (IMS) dataset extractor software, IMS convolution. Anal Bioanal Chem 401, 183–193 (2011). https://doi.org/10.1007/s00216-011-4778-9

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  • DOI: https://doi.org/10.1007/s00216-011-4778-9

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