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

Yuan Cao,Na Wang,Ailing Li,Hengsha Wang,Xuemin Zhang,Xiaomin Ying,Wuju Li

doi:10.1186/1472-6947-9-13

Abstract

BackgroundWith 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.ResultsHere 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.ConclusionBioSunMS 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/.

Highlights

With wide applications of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and surface-enhanced laser desorption/ionization time-offlight 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
Baseline subtraction and smoothing; Normalization; Automatic or manual peak detection; Peak alignment Support common MS format, such as mzML, mzXML, mzData, Graphics display for MS raw data and MS peaks t-test for feature selection; Support Vector Machine (SVM) or k-nearest neighbour (kNN)-based model construction; The Receiver Operation Characteristic (ROC) curve for the evaluation of model performance Client-server architecture for multi-user workgroups Plug-in framework for future development edit and save data
BioSunMS is a Rich Client Platform (RCP) application through bringing the power of lab's network to access and manage a large amount of information. It can be installed on Windows or Linux system

Summary

Results

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

Background

Results and discussion

Cannataro M