MSiReader: An open-source interface to view and analyze high resolving power MS imaging files on matlab platform

Journal of the American Society for Mass Spectrometry

Volumn 24, Issue 5, 2013, Pages 718-721

  Robichaud, Guillaume ^a   Garrard, Kenneth P ^b   Barry, Jeremy A ^a   Muddiman, David C ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b North Carolina State University   (United States)

Author keywords

FT ICR MS; High mass resolving power; Mass spectrometry imaging; Open source; Software

Indexed keywords

DATA ANALYSIS TOOL; FT-ICR-MS; MASS RESOLVING POWER; MASS SPECTROMETRY IMAGING (MSI); MASS-SPECTROMETRY IMAGING; OPEN SOURCE APPLICATION; OPEN-SOURCE; USER FRIENDLY INTERFACE;

COMPUTER SOFTWARE; IMAGING TECHNIQUES; MATLAB;

MASS SPECTROMETRY;

ACCURACY; ALGORITHM; ARTICLE; COMPARATIVE STUDY; COMPUTER INTERFACE; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; IMAGING; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MASS SPECTROMETRY; MASS SPECTROMETRY IMAGING; WEB BROWSER;

ALGORITHMS; COMPUTATIONAL BIOLOGY; IMAGE PROCESSING, COMPUTER-ASSISTED; INTERNET; MASS SPECTROMETRY; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84879082437     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-013-0607-z     Document Type: Article

References (21)

1. Stoeckli, M.; Staab, D.; Staufenbiel, M.; Wiederhold, K.H.; Signor, L.: Molecular imaging of amyloid beta peptides in mouse brain sections using mass spectrometry. Anal. Biochem. 311(1), 33-39 (2002)
2. Jardin-Mathe, O.; Bonnel, D.; Franck, J.; Wisztorski, M.; Macagno, E.; Fournier, I.; Salzet, M.: MITICS (MALDI Imaging Team Imaging Computing System): a new open source mass spectrometry imaging software. J. Proteom. 71(3), 332-345 (2008)
3. Hester, A.B.; Bouschen, W.; Leisner, A.; Maass, K.; Paschke, C.; Spengler, B.: Proc. 53rd ASMS Conf Mass Spectrom Allied Top, San Antonio, Tx, June 05-09 (2005)
4. Smith, D.F.; Kharchenko, A.; Konijnenburg, M.; Klinkert, I.; Pasa-Tolic, L.; Heeren, R.M.: Advanced mass calibration and visualization for FT-ICR mass spectrometry imaging. J. Am. Soc. Mass Spectrom. 23(12), 1865-1872 (2012)
5. msimaging: http://www.maldi-msi.org/. Accessed 22 Dec 2012
6. Robichaud, G.; Barry, J.; Garrard, K.; Muddiman, D.: Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) imaging source coupled to a FT-ICR mass spectrometer. J. Am. Soc. Mass Spectrom. 24(1), 92-100 (2013)
7. Pedrioli, P.G.; Eng, J.K.; Hubley, R.; Vogelzang, M.; Deutsch, E.W.; Raught, B.; Pratt, B.; Nilsson, E.; Angeletti, R.H.; Apweiler, R.; Cheung, K.; Costello, C.E.; Hermjakob, H.; Huang, S.; Julian, R.K.; Kapp, E.; McComb, M.E.; Oliver, S.G.; Omenn, G.; Paton, N.W.; Simpson, R.; Smith, R.; Taylor, C.F.; Zhu, W.; Aebersold, R.: A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 22(11), 1459-1466 (2004)
8. ProteoWizard: http://proteowizard.sourceforge.net/. Accessed 22 Dec 2012
9. Kessner, D.; Chambers, M.; Burke, R.; Agus, D.; Mallick, P.: ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24(21), 2534-2536 (2008)
10. mzXML converter: http://tools.proteomecenter.org/wiki/index.php?title= Formats:mzXML. Accessed 22 Dec 2012
11. Römpp, A.; Schramm, T.; Hester, A.; Klinkert, I.; Heeren, R.; Stöckli, M.; Both, J.-P.; Brunelle, A.; Spengler, B.: Data mining in proteomics. Humana Press, New York (2010)
12. Schramm, T.; Hester, A.; Klinkert, I.; Both, J.P.; Heeren, R.M.; Brunelle, A.; Laprevote, O.; Desbenoit, N.; Robbe, M.F.; Stoeckli, M.; Spengler, B.; Rompp, A.: imzML - a common data format for the flexible exchange and processing of mass spectrometry imaging data. J. Proteom. 75(16), 5106-5110 (2012)
13. Martens, L.; Chambers, M.; Sturm, M.; Kessner, D.; Levander, F.; Shofstahl, J.; Tang, W.H.; Rompp, A.; Neumann, S.; Pizarro, A.D.; Montecchi-Palazzi, L.; Tasman, N.; Coleman, M.; Reisinger, F.; Souda, P.; Hermjakob, H.; Binz, P.A.; Deutsch, E.W.: mzML - a community standard for mass spectrometry data. Mol. Cell. Proteom. 10(1), R110 000133 (2011)
14. Race, A.M.; Styles, I.B.; Bunch, J.: Inclusive sharing of mass spectrometry imaging data requires a converter for all. J. Proteom. 75(16), 5111-5112 (2012)
15. Analyze 7.5: http://eeg.sourceforge.net/. Accessed 22 Dec 2012
16. McDonnell, L.A.; van Remoortere, A.; de Velde, N.; van Zeijl, R.J.M.; Deelder, A.M.: Imaging mass spectrometry data reduction: automated feature identification and extraction. J. Am. Soc. Mass Spectrom. 21(12), 1969-1978 (2010)
17. Sud, M.; Fahy, E.; Cotter, D.; Brown, A.; Dennis, E.A.; Glass, C.K.; Merrill Jr.; A.H.; Murphy, R.C.; Raetz, C.R.; Russell, D.W.; Subramaniam, S.L.M.S.D.: LIPID MAPS structure database. Nucleic Acids Res. 35(Database issue), D527-532 (2007)
18. LIPID MAPS Structure Database (LDMS): http://www.lipidmaps.org/data/ structure/index.html. Accessed 22 Dec 2012
19. Giancaspro, C.; Comisarow, M.B.: Exact interpolation of Fourier-transform spectra. Appl. Spectrosc. 37(2), 153-166 (1983)
20. Jones, E.A.; Deininger, S.O.; Hogendoorn, P.C.; Deelder, A.M.; McDonnell, L.A.: Imaging mass spectrometry statistical analysis. J. Proteom. 75(16), 4962-4989 (2012)
21. Open Source Initiative OSI - The BSD 3-Clause License: http://opensource.org/licenses/BSD-3-Clause. Accessed 22 Dec 2012