Literature DB >> 23440717

omniSpect: an open MATLAB-based tool for visualization and analysis of matrix-assisted laser desorption/ionization and desorption electrospray ionization mass spectrometry images.

R Mitchell Parry1, Asiri S Galhena, Chaminda M Gamage, Rachel V Bennett, May D Wang, Facundo M Fernández.   

Abstract

We present omniSpect, an open source web- and MATLAB-based software tool for both desorption electrospray ionization (DESI) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) that performs computationally intensive functions on a remote server. These functions include converting data from a variety of file formats into a common format easily manipulated in MATLAB, transforming time-series mass spectra into mass spectrometry images based on a probe spatial raster path, and multivariate analysis. OmniSpect provides an extensible suite of tools to meet the computational requirements needed for visualizing open and proprietary format MSI data.

Entities:  

Mesh：

Year:  2013        PMID： 23440717      PMCID： PMC4983445          DOI： 10.1007/s13361-012-0572-y

Source DB:  PubMed          Journal:  J Am Soc Mass Spectrom        ISSN： 1044-0305            Impact factor:   3.109


  12 in total

1.  Learning the parts of objects by non-negative matrix factorization.

Authors:  D D Lee; H S Seung
Journal:  Nature       Date:  1999-10-21       Impact factor: 49.962

Review 2.  Mass spectrometric imaging of small molecules.

Authors:  Ales Svatos
Journal:  Trends Biotechnol       Date:  2010-06-25       Impact factor: 19.536

3.  Tools and strategies for visualization of large image data sets in high-resolution imaging mass spectrometry.

Authors:  Ivo Klinkert; Liam A McDonnell; Stefan L Luxembourg; A F Maarten Altelaar; Erika R Amstalden; Sander R Piersma; Ron M A Heeren
Journal:  Rev Sci Instrum       Date:  2007-05       Impact factor: 1.523

4.  Mass imaging and identification of biomolecules with MALDI-QIT-TOF-based system.

Authors:  Shuichi Shimma; Yuki Sugiura; Takahiro Hayasaka; Nobuhiro Zaima; Mineo Matsumoto; Mitsutoshi Setou
Journal:  Anal Chem       Date:  2008-01-01       Impact factor: 6.986

5.  Effect of surface free energy on PDMS transfer in microcontact printing and its application to ToF-SIMS to probe surface energies.

Authors:  Li Yang; Naoto Shirahata; Gaurav Saini; Feng Zhang; Lei Pei; Matthew C Asplund; Dirk G Kurth; Katsuhiko Ariga; Ken Sautter; Takashi Nakanishi; Vincent Smentkowski; Matthew R Linford
Journal:  Langmuir       Date:  2009-05-19       Impact factor: 3.882

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

Authors:  Takahiro Hayasaka; Naoko Goto-Inoue; Masaru Ushijima; Ikuko Yao; Akiko Yuba-Kubo; Masatoshi Wakui; Shigeki Kajihara; Masaaki Matsuura; Mitsutoshi Setou
Journal:  Anal Bioanal Chem       Date:  2011-03-17       Impact factor: 4.142

7.  Elastic net-based framework for imaging mass spectrometry data biomarker selection and classification.

Authors:  Fengqing Zoe Zhang; Don Hong
Journal:  Stat Med       Date:  2010-12-29       Impact factor: 2.373

8.  AMASS: algorithm for MSI analysis by semi-supervised segmentation.

Authors:  Jocelyne Bruand; Theodore Alexandrov; Srinivas Sistla; Maxence Wisztorski; Céline Meriaux; Michael Becker; Michel Salzet; Isabelle Fournier; Eduardo Macagno; Vineet Bafna
Journal:  J Proteome Res       Date:  2011-08-25       Impact factor: 4.466

9.  An analytical pipeline for MALDI in-source decay mass spectrometry imaging.

Authors:  Tyler A Zimmerman; Delphine Debois; Gabriel Mazzucchelli; Virginie Bertrand; Marie-Claire De Pauw-Gillet; Edwin De Pauw
Journal:  Anal Chem       Date:  2011-07-06       Impact factor: 6.986

10.  Deblurring molecular images using desorption electrospray ionization mass spectrometry.

Authors:  R Parry; Asiri S Galhena; Facundo M Fernandez; May D Wang
Journal:  Conf Proc IEEE Eng Med Biol Soc       Date:  2009
View more
  17 in total

1.  Imaging mass spectrometry for natural products discovery: a review of ionization methods.

Authors:  Joseph E Spraker; Gordon T Luu; Laura M Sanchez
Journal:  Nat Prod Rep       Date:  2020-02-26       Impact factor: 13.423

2.  ChiMS: Open-source instrument control software platform on LabVIEW for imaging/depth profiling mass spectrometers.

Authors:  Yang Cui; Luke Hanley
Journal:  Rev Sci Instrum       Date:  2015-06       Impact factor: 1.523

3.  MALDI-mass spectrometric imaging for the investigation of metabolites in Medicago truncatula root nodules.

Authors:  Erin Gemperline; Lingjun Li
Journal:  J Vis Exp       Date:  2014-03-05       Impact factor: 1.355

Review 4.  Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry.

Authors:  Nico Verbeeck; Richard M Caprioli; Raf Van de Plas
Journal:  Mass Spectrom Rev       Date:  2019-10-11       Impact factor: 10.946

Review 5.  Mass spectrometry imaging to detect lipid biomarkers and disease signatures in cancer.

Authors:  Matthias Holzlechner; Eliseo Eugenin; Brendan Prideaux
Journal:  Cancer Rep (Hoboken)       Date:  2019-12

6.  DetectTLC: Automated Reaction Mixture Screening Utilizing Quantitative Mass Spectrometry Image Features.

Authors:  Chanchala D Kaddi; Rachel V Bennett; Martin R L Paine; Mitchel D Banks; Arthur L Weber; Facundo M Fernández; May D Wang
Journal:  J Am Soc Mass Spectrom       Date:  2015-10-27       Impact factor: 3.109

7.  Imaging regiospecific lipid turnover in mouse brain with desorption electrospray ionization mass spectrometry.

Authors:  Richard H Carson; Charlotte R Lewis; Mercede N Erickson; Anna P Zagieboylo; Bradley C Naylor; Kelvin W Li; Paul B Farnsworth; John C Price
Journal:  J Lipid Res       Date:  2017-07-25       Impact factor: 5.922

8.  A public repository for mass spectrometry imaging data.

Authors:  Andreas Römpp; Rui Wang; Juan Pablo Albar; Andrea Urbani; Henning Hermjakob; Bernhard Spengler; Juan Antonio Vizcaíno
Journal:  Anal Bioanal Chem       Date:  2015-03       Impact factor: 4.142

9.  The application of Gaussian mixture models for signal quantification in MALDI-TOF mass spectrometry of peptides.

Authors:  John Christian G Spainhour; Michael G Janech; John H Schwacke; Juan Carlos Q Velez; Viswanathan Ramakrishnan
Journal:  PLoS One       Date:  2014-11-05       Impact factor: 3.240

10.  Whole Reproductive System Non-Negative Matrix Factorization Mass Spectrometry Imaging of an Early-Stage Ovarian Cancer Mouse Model.

Authors:  Martin R L Paine; Jaeyeon Kim; Rachel V Bennett; R Mitchell Parry; David A Gaul; May D Wang; Martin M Matzuk; Facundo M Fernández
Journal:  PLoS One       Date:  2016-05-09       Impact factor: 3.240
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.