Isotopo is an application created within SPP1316 with the ability of performing quantitative mass spectrometry to readily mixtures of materials labeled with stable isotopes.

Figure. 1: Isotopo

Isotopo is the ability of processing experimental isotopomers data (output of GC-MS) and provides obtained results (output) both in textual and visual formats, for better understanding and analysis. Processable (input) data consists of following elements i.e. Metabolite Information, Mass to Charge Ratio (M/Z) Values, Actual Relative Intensity (RI) Values and Standard Relative Intensity Values and Number of Carbon Atom Fragments. Isotopo is capable of analyzing three RIs value sets observed during GC-MS experiment against one M/Z value set with one Standard RI value set. The resultant (output) information is consists of following results i.e. Mass Calculations (Mo, M-1, M maximum), Natural Abundances (NA), Relative Abundances (RA), Fractional Molar Abundances (FRA), Absolute Enrichment, Mean RA, Standard Deviation RA and a Spectrum of calculated RA. It provides output of each processed RI along with average of three.

Isotopo consists of seven integrated modules i.e. Analyzer, Fragment Viewer, Spectrum Viewer, Results Viewer, Relative Abundance 1, 2 and 3.

Isotopo Analyzer, as shown in Figure 1 & 2, is capable of taking input from user in two ways i.e. loading from input file or entering manually at run time. The resultant information of this module consists of following results i.e. M-1, Mo, Mmax, Mean RI Values, NA with %, RA with %, Absolute 13C NA Enrichment with %, Absolute 13C RA Enrichment with %, Mean RA and Standard Deviation RA.

Figure. 2: Isotopo Analyzer

Isotopo Fragment Viewer, as shown in Figure 3, provides the information about estimated Abundances against for each Fragment. It also allows user to export (save) new fragment output file and import (open) existing output fragment file.

Figure. 3: Isotopo Fragment Viewer

Isotopo Spectrum Viewer, as shown in Figure 4, provides visual presentation of drawn spectrum, consisting of RA and NA per Fragment. It provides some useful options to take help in improving visualization at run time e.g. zoom in/out, highlighting values and exporting output as image etc.

Figure. 4: Isotopo Spectrum Viewer

Isotopo Results Viewer, as shown in Figure 5, provides the over all inputted and system's output information. It also allows user to export (save) new output file and import (open) existing system output file.

Figure. 5: Isotopo Results Viewer

Isotopo Relative Abundance 1, 2 and 3, as shown in Figure 6, provides resultant information obtained against each processed RI Value.

Figure. 6: Isotopo Relative Abundance (1)

Isotopo also provides a Data Management System for Experimental Data Manipulation and Management, as shown in Figure 7.

Figure. 7: Isotopo Data Management System

Isotopo provides an additional independent modules i.e. Data Viewer, which helps user in working with output (files) generated by Isotopo Data Analyzer as shown in Figure 8.

Isotopo is implemented in Microsoft Visual Studio Dot Net (C#), following V-Model SDLC, integrating formal unified modelling language to scheme from different perspectives and incorporating human computer interaction guidelines, principles and patterns.

Isotopo is a freely available software application for the academic use with an open license. Please write a request at provided contacts.

Contact Person:

Dr. Zeeshan AHMED
Scientific Software Engineer

Prof. Thomas Dandekar Group;
Funct. Genomics & Systems Biology.
Department of Bioinformatics;
Biocenter, University of Wuerzburg.
Am Hubland 97074,
Wuerzburg Germany.

Related Recent Publication:

• Dandekar T., Fieselmann A., Saman M. and Ahmed Z., Software Applications toward Quantitative Metabolic Flux Analysis and Visualization. Briefings in Bioinformatics, Oxford University Press, First Published Online November 9, 2012. [E. Pub., Ahead of print]
• Ahmed Z., Saman M., and Dandekar T. Computational Feature Performance and Domain Specific Architecture Evaluation of Software Applications towards Metabolic Flux Analysis. Recent Patents on Computer Science, Bentham Science, Vol.5, No. 3, 99. 165-176, December 2012.
• Ahmed Z., Saman M., and Dandekar T., Formal UML Modelling of Isotopo, Bioinformatical Software for Mass Isotopomers Distribution Analysis. Software Engineering, SAP, Vol. 2 No. 5, pp. 147-159, November 2012.

• Ahmed Z., Huber C., Saman Z., Hensel M., Schomburg D., Münch R., Eylert E., Eisenreich. W, Dandekar T. A Platform for Facile Analysis and Management of facile Quantitative Mass Isotopomers. [In submission]

Conference Appearances:

• Ahmed Z., Eisenreich E., Dandekar T. Intelligent Metabolic Isotopomer Data Extraction, Classification, Standardization and Management, New England Database Summit (NEDB), CSAIL, the Massachusetts Institute of Technology (MIT), USA, 2013.
• Ahmed Z., Saman M., Eisenreich E., Dandekar T. Isotopo Towards Quantitative Mass Isotopomers Distribution Analysis using Spectral Data. 9th Symposium on the Practical Applications of Mass Spectrometry in the Biotechnology Industry (Mass Spec 2012), CASSS, Page 40, ID P-101, San Diego, CA USA, 2012.
• Ahmed Z., Saman M., Eisenreich E. Dandekar. Isotopo: Software towards Quantitative MIDA, Visualization and Data Management, 5th Annual New England Data Base Summit (NEDB), CSAIL, The Massachusetts Institute of Technology (MIT), USA, 2012.
• Ahmed Z. Saman M., Liang C., Dandekar T. et al. Intelligent Information Management for efficient Computational Biology. Intelligent Information Management, Information and Communication Technology Research (ICT), Information and Networking Day, European Commission, Jean Monnet Conference Centre, Luxembourg, 2011.

Thesis

• Ahmed Z. Bioinformatics Software for Metabolic and Health Care Data Management (Doctoral Dissertation). Department of Bioinformatics, Theodor-Boveri-Institute of Biosciences, Faculty of Biology, Life sciences, Advisors: Prof. Dr. Thomas Dandekar & PD. Dr. Wolfgang Eisenreich, 20.12.2012.