Limits...
BioSunMS: a plug-in-based software for the management of patients information and the analysis of peptide profiles from mass spectrometry.

Cao Y, Wang N, Ying X, Li A, Wang H, Zhang X, Li W - BMC Med Inform Decis Mak (2009)

Bottom Line: Here we presented a plug-in-based software, BioSunMS, for both the management of patients information and serum peptide profiles-based statistical analysis.By integrating all functions into a user-friendly desktop application, BioSunMS provided a comprehensive solution for clinical researchers without any knowledge in programming, as well as a plug-in architecture platform with the possibility for developers to add or modify functions without need to recompile the entire application.BioSunMS provides a plug-in-based solution for managing, analyzing, and sharing high volumes of MALDI-TOF or SELDI-TOF MS data.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Taiping Road 27, Haidian district, Beijing 100850, PR China. labs.net@gmail.com

ABSTRACT

Background: With wide applications of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), statistical comparison of serum peptide profiles and management of patients information play an important role in clinical studies, such as early diagnosis, personalized medicine and biomarker discovery. However, current available software tools mainly focused on data analysis rather than providing a flexible platform for both the management of patients information and mass spectrometry (MS) data analysis.

Results: Here we presented a plug-in-based software, BioSunMS, for both the management of patients information and serum peptide profiles-based statistical analysis. By integrating all functions into a user-friendly desktop application, BioSunMS provided a comprehensive solution for clinical researchers without any knowledge in programming, as well as a plug-in architecture platform with the possibility for developers to add or modify functions without need to recompile the entire application.

Conclusion: BioSunMS provides a plug-in-based solution for managing, analyzing, and sharing high volumes of MALDI-TOF or SELDI-TOF MS data. The software is freely distributed under GNU General Public License (GPL) and can be downloaded from http://sourceforge.net/projects/biosunms/.

Show MeSH
The workflow charts of the BioSunMS. To construct model for patients classification using peptide profiles generated by MALDI-TOF MS or SELDI-TOF MS, following steps are suggested. The first step is to input patients information, then preprocessing of MS spectra data for each patient, linking MS peaks to each patient through sample ID, peak alignment and creation of data matrix, t-test based feature selection and SVM-based model construction. Finally, the ROC curve was used to evaluate the performance of the model.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2654546&req=5

Figure 2: The workflow charts of the BioSunMS. To construct model for patients classification using peptide profiles generated by MALDI-TOF MS or SELDI-TOF MS, following steps are suggested. The first step is to input patients information, then preprocessing of MS spectra data for each patient, linking MS peaks to each patient through sample ID, peak alignment and creation of data matrix, t-test based feature selection and SVM-based model construction. Finally, the ROC curve was used to evaluate the performance of the model.

Mentions: To access the BioSunMS server at client side, users must first log on with an authorized username and a given password. Users could also log on for analyzing spectral data without connecting to the server, when their computers are offline. The workflow of BioSunMS was illustrated in Figure 2, which was divided into four main parts as follows.


BioSunMS: a plug-in-based software for the management of patients information and the analysis of peptide profiles from mass spectrometry.

Cao Y, Wang N, Ying X, Li A, Wang H, Zhang X, Li W - BMC Med Inform Decis Mak (2009)

The workflow charts of the BioSunMS. To construct model for patients classification using peptide profiles generated by MALDI-TOF MS or SELDI-TOF MS, following steps are suggested. The first step is to input patients information, then preprocessing of MS spectra data for each patient, linking MS peaks to each patient through sample ID, peak alignment and creation of data matrix, t-test based feature selection and SVM-based model construction. Finally, the ROC curve was used to evaluate the performance of the model.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2654546&req=5

Figure 2: The workflow charts of the BioSunMS. To construct model for patients classification using peptide profiles generated by MALDI-TOF MS or SELDI-TOF MS, following steps are suggested. The first step is to input patients information, then preprocessing of MS spectra data for each patient, linking MS peaks to each patient through sample ID, peak alignment and creation of data matrix, t-test based feature selection and SVM-based model construction. Finally, the ROC curve was used to evaluate the performance of the model.
Mentions: To access the BioSunMS server at client side, users must first log on with an authorized username and a given password. Users could also log on for analyzing spectral data without connecting to the server, when their computers are offline. The workflow of BioSunMS was illustrated in Figure 2, which was divided into four main parts as follows.

Bottom Line: Here we presented a plug-in-based software, BioSunMS, for both the management of patients information and serum peptide profiles-based statistical analysis.By integrating all functions into a user-friendly desktop application, BioSunMS provided a comprehensive solution for clinical researchers without any knowledge in programming, as well as a plug-in architecture platform with the possibility for developers to add or modify functions without need to recompile the entire application.BioSunMS provides a plug-in-based solution for managing, analyzing, and sharing high volumes of MALDI-TOF or SELDI-TOF MS data.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Taiping Road 27, Haidian district, Beijing 100850, PR China. labs.net@gmail.com

ABSTRACT

Background: With wide applications of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), statistical comparison of serum peptide profiles and management of patients information play an important role in clinical studies, such as early diagnosis, personalized medicine and biomarker discovery. However, current available software tools mainly focused on data analysis rather than providing a flexible platform for both the management of patients information and mass spectrometry (MS) data analysis.

Results: Here we presented a plug-in-based software, BioSunMS, for both the management of patients information and serum peptide profiles-based statistical analysis. By integrating all functions into a user-friendly desktop application, BioSunMS provided a comprehensive solution for clinical researchers without any knowledge in programming, as well as a plug-in architecture platform with the possibility for developers to add or modify functions without need to recompile the entire application.

Conclusion: BioSunMS provides a plug-in-based solution for managing, analyzing, and sharing high volumes of MALDI-TOF or SELDI-TOF MS data. The software is freely distributed under GNU General Public License (GPL) and can be downloaded from http://sourceforge.net/projects/biosunms/.

Show MeSH