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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/.

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The interface for MS data display. The preprocessing of MS data for a particular patient was demonstrated, which included baseline subtraction, normalization, and automatic or manual peak extraction.
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Figure 3: The interface for MS data display. The preprocessing of MS data for a particular patient was demonstrated, which included baseline subtraction, normalization, and automatic or manual peak extraction.

Mentions: The second step in the workflow is to import spectral files to the BioSunMS. After importing a spectral file, BioSunMS uses the Bioconductor PROcess package developed by Li [23] to process the spectral data. The PROcess package contains a collection of functions for removing baseline drifts, detecting peaks and aligning peaks for a set of biomarkers. In the Spectra View which uses the JFreeChart package [24] for visualization of spectral information, users can identify or erase the peaks in a spectrum manually. Labeled peaks are shown in the Peak View. After data processing, the peak list can be saved to the database corresponding to the sample ID (Figure 3). Users can upload the "raw" spectral files to the ftp server for backup.


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 interface for MS data display. The preprocessing of MS data for a particular patient was demonstrated, which included baseline subtraction, normalization, and automatic or manual peak extraction.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: The interface for MS data display. The preprocessing of MS data for a particular patient was demonstrated, which included baseline subtraction, normalization, and automatic or manual peak extraction.
Mentions: The second step in the workflow is to import spectral files to the BioSunMS. After importing a spectral file, BioSunMS uses the Bioconductor PROcess package developed by Li [23] to process the spectral data. The PROcess package contains a collection of functions for removing baseline drifts, detecting peaks and aligning peaks for a set of biomarkers. In the Spectra View which uses the JFreeChart package [24] for visualization of spectral information, users can identify or erase the peaks in a spectrum manually. Labeled peaks are shown in the Peak View. After data processing, the peak list can be saved to the database corresponding to the sample ID (Figure 3). Users can upload the "raw" spectral files to the ftp server for backup.

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