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Proteomic analysis by 2DICAL

About 2DICAL(2-Dimensional Image Converted Analysis of LCMS)

2DICAL analyzed the data of mass-to-charge ratio (m/z), peak intensity, retention time (RT), and each sample generated by liquid chromatography and mass spectrometry as the elemental data. It deployed various two-dimensional images with different combinations of axes using these four elements. From the m/z-RT image, peaks derived from the same peptide in the direction of acquiring time were integrated. By adding algorisms to ensure reproducibility of m/z and RT, the same peak was compared precisely across different samples, and a statistical comparison of identical peaks in different samples led to the discovery of specific differentially expressed peptide peaks.

 Basic image of 2DICAL

 Combining each spectrum generated on retention time (RT), the intensity is plotted in the gray scale mode on the plane with the axes of m/z (mass to charge ratio) and RT.

Basic image of 2DICAL

References related to 2DICAL

  1. Kagami Y, Ono M, Yoshida K. Plk1 phosphorylation of CAPH2 triggers chromosome condensation by condensin II at the early phase of mitosis. Sci Rep. 2017; in press
  2. Yoshimaru T, Ono M, Bando Y, Chen YA, Mizuguchi K, Shima H, Komatsu M, Imoto I, Izumi K, Honda J, Miyoshi Y, Sasa M, Katagiri T. A-kinase anchoring protein BIG3 coordinates oestrogen signalling in breast cancer cells. Nat Commun. 2017; 8:15427. PMID: 28555617
  3. Kamita M, Mori T, Sakai Y, Ito S, Gomi M, Miyamoto Y, Harada A, Niida S, Yamada T, Watanabe K, Ono M. Proteomic analysis of ligamentum flavum from patients with lumbar spinal stenosis. Proteomics. 2015; 15: 1622-1630. PMID: 25641790
  4. Atsumi Y, Minakawa Y, Ono M, Dobashi S, Shinohe K, Shinohara A, Takeda S, Takagi M, Takamatsu N, Nakagama H, Teraoka H, Yoshioka K. ATM and SIRT6/SNF2H Mediate Transient H2AX Stabilization When DSBs Form by Blocking HUWE1 to Allow Efficient gammaH2AX Foci Formation. Cell Rep. 2015; 13:2728-2740. PMID: 26711340
  5. Arai E, Gotoh M, Tian Y, Sakamoto H, Ono M, Matsuda A, Takahashi Y, Miyata S, Totsuka H, Chiku S, Komiyama M, Fujimoto H, Matsumoto K, Yamada T, Yoshida T, Kanai Y. Alterations of the spindle checkpoint pathway in clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas. Int J Cancer. 2015; 137:2589-2606. PMID: 26061684
  6. Taira N, Yamaguchi T, Kimura J, Lu ZG, Fukuda S, Higashiyama S, Ono M, Yoshida K. Induction of amphiregulin by p53 promotes apoptosis via control of microRNA biogenesis in response to DNA damage. Proc Natl Acad Sci U S A. 2014; 111:717-722. PMID: 24379358
  7. Matsukawa S, Morita KI, Negishi A, Harada H, Nakajima Y, Shimamoto H, Tomioka H, Tanaka K, Ono M, Yamada T, Omura K. Galectin-7 as a potential predictive marker of chemo- and/or radio-therapy resistance in oral squamous cell carcinoma. Cancer Med. 2014; 3:349-36. PMID: 24515895
  8. Kagami Y, Nihira K, Wada S, Ono M, Honda M, Yoshida K. Mps1 phosphorylation of condensin II controls chromosome condensation at the onset of mitosis. J Cell Biol. 2014; 205:781-790. PMID: 24934155
  9. Yoneyama T, Ohtsuki S, Ono M, Ohmine K, Uchida Y, Yamada T, Tachikawa M, Terasaki T. Quantitative targeted absolute proteomics-based large-scale quantification of proline-hydroxylated alpha-fibrinogen in plasma for pancreatic cancer diagnosis. J Proteome Res. 2013; 12:753-762. PMID: 23298340
  10. Takahashi RU, Takeshita F, Honma K, Ono M, Kato K, Ochiya T. Ribophorin II regulates breast tumor initiation and metastasis through the functional suppression of GSK3beta. Sci Rep. 2013; 3:2474. PMID: 23959174
  11. Singh SK, Maeda K, Eid MM, Almofty SA, Ono M, Pham P, Goodman MF, Sakaguchi N. GANP regulates recruitment of AID to immunoglobulin variable regions by modulating transcription and nucleosome occupancy. Nat Commun. 2013; 4:1830. PMID: 23652018
  12. Nakano T, Matsushima-Hibiya Y, Yamamoto M, Takahashi-Nakaguchi A, Fukuda H, Ono M, Takamura-Enya T, Kinashi H, Totsuka Y. ADP-ribosylation of guanosine by SCO5461 protein secreted from Streptomyces coelicolor. Toxicon. 2013; 63:55-63. PMID: 23212047
  13. Yokomizo A, Takakura M, Kanai Y, Sakuma T, Matsubara J, Honda K, Naito S, Yamada T, Ono M. Use of quantitative shotgun proteomics to identify fibronectin 1 as a potential plasma biomarker for clear cell carcinoma of the kidney. Cancer Biomarkers 2012; 10:175-183 PMID: 22674303
  14. Takakura M, Yokomizo A, Tanaka Y, Kobayashi M, Jung G, Banno M, Sakuma T, Imada K, Oda Y, Kamita M, Honda K, Yamada T, Naito S, Ono M. Carbonic anhydrase I as a new plasma biomarker for prostate cancer. ISRN Oncology 2012; 2012:10 pages PMID: 23213568
  15. Ono M, Kamita M, Murakoshi Y, Matsubara J, Honda K, Miho B, Sakuma T, Yamada T. Biomarker Discovery of Pancreatic and Gastrointestinal Cancer by 2DICAL: 2-Dimensional Image-Converted Analysis of Liquid Chromatography and Mass Spectrometry. Int J Proteomics 2012; 2012:897412 PMID: 22844596
  16. Miyamoto T, Kitamura N, Ono M, Nakamura Y, Yoshida M, Kamino H, Murai R, Yamada T, Arakawa H. Identification of 14-3-3gamma as a Mieap-interacting protein and its role in mitochondrial quality control. Sci Rep 2012; 2:379 PMID: 22532927
  17. Fukawa T, Ono M, Matsuo T, Uehara H, Miki T, Nakamura Y, Kanayama H, Katagiri T. DDX31 regulates the p53-HDM2 pathway and rRNA gene transcription through its interaction with NPM1 in renal cell carcinomas. Cancer Res 2012; 72:5867-5877 PMID: 23019224
  18. Murakoshi Y, Honda K, Sasazuki S, Ono M, Negishi A, Matsubara J, Sakuma T, Kuwabara H, Nakamori S, Sata N, Nagai H, Ioka T, Okusaka T, Kosuge T, Shimahara M, Yasunami Y, Ino Y, Tsuchida A, Aoki T, Tsugane S, Yamada T. Plasma biomarker discovery and validation for colorectal cancer by quantitative shotgun mass spectrometry and protein microarray. Cancer Sci 2011; 102:630-638 PMID: 21199170
  19. Matsubara J, Honda K, Ono M, Tanaka YN, Kobayashi M, Jung G, Yanagisawa K, Sakuma T, Nakamori S, Sata N, Nagai H, Ioka T, Okusaka T, Kosuge T, Tsuchida A, Shimahara M, Yasunami Y, Chiba T, Hirohashi S, Yamada T. Reduced Plasma Level of CXC Chemokine Ligand 7 in Patients with Pancreatic Cancer. Cancer Epidemiol Biomarkers Prev 2011; 20:160-171 PMID: 21148121
  20. Matsubara J, Honda K, Ono M, Sekine S, Tanaka Y, Kobayashi M, Jung G, Sakuma T, Nakamori S, Sata N, Nagai H, Ioka T, Okusaka T, Kosuge T, Tsuchida A, Shimahara M, Yasunami Y, Chiba T, Yamada T. Identification of Adipophilin as a Potential Plasma Biomarker for Colorectal Cancer using Label-free Quantitative Mass Spectrometry and Protein Microarray. Cancer Epidemiol Biomarkers Prev 2011; 20:2195-2203 PMID: 21828233
  21. Matsubara J, Ono M, Honda K, Negishi A, Ueno H, Okusaka T, Furuse J, Furuta K, Sugiyama E, Saito Y, Kaniwa N, Sawada J, Shoji A, Sakuma T, Chiba T, Saijo N, Hirohashi S, Yamada T. Survival prediction for pancreatic cancer patients receiving gemcitabine treatment. Mol Cell Proteomics 2010; 9:695-704 PMID: 20061307
  22. Ono M, Matsubara J, Honda K, Sakuma T, Hashiguchi T, Nose H, Nakamori S, Okusaka T, Kosuge T, Sata N, Nagai H, Ioka T, Tanaka S, Tsuchida A, Aoki T, Shimahara M, Yasunami Y, Itoi T, Moriyasu F, Negishi A, Kuwabara H, Shoji A, Hirohashi S, Yamada T. Prolyl 4-hydroxylation of a-fibrinogen a novel protein modification revealed by plasma proteomics. J Biol Chem 2009; 284:29041-29049 PMID: 19696023
  23. Negishi A, Ono M, Handa Y, Kato H, Yamashita K, Honda K, Shitashige M, Satow R, Sakuma T, Kuwabara H, Omura K, Hirohashi S, Yamada T. Large-scale quantitative clinical proteomics by label-free liquid chromatography and mass spectrometry. Cancer Sci 2009, 100:514-519 PMID: 19154406
  24. Negishi A, Masuda M, Ono M, Honda K, Shitashige M, Satow R, Sakuma T, Kuwabara H, Nakanishi Y, Kanai Y, Omura K, Hirohashi S, Yamada T. Quantitative proteomics using formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma. Cancer Sci 2009; 100:1605-1611 PMID: 19522851
  25. Matsubara J, Ono M, Yamada T. Predictive Markers for Chemotherapy Toxicity: an Important Factor in Personalized Therapy. EUROPEAN JOURNAL OF CLINICAL & MEDICAL ONCOLOGY 2009; 1:1-6
  26. Matsubara J, Ono M, Negishi A, Ueno H, Okusaka T, Furuse J, Furuta K, Sugiyama E, Saito Y, Kaniwa N, Sawada J, Honda K, Sakuma T, Chiba T, Saijo N, Hirohashi S, Yamada T. Identification of a Predictive Biomarker for Hematologic Toxicities of Gemcitabine. J Clin Oncol 2009; 27:2261-2268 PMID: 19289617
  27. Ono M, Shitashige M, Honda K, Isobe T, Kuwabara H, Matsuzuki H, Hirohashi S, Yamada T. Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry. Mol Cell Proteomics 2006; 5:1338-1347 PMID: 16552026