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Realised by ALMS™
developer of the AIDS-HIV Reference project
Abstract No.: ThP-038
Session: Bioinformatics
Presentation date: Thu, Aug 31, 2006
Presentation time: 14:30 – 16:00

Development of an Application Software for Top-down and Bottom-up Proteomics with FT-ICR MS

Hun-Young So1, Byungjoo Kim1, Yong-Hyeon Yim1, Seonghee Ahn1, Eujin Hwang1, Jinyoung Park Park2, Sanghyun Lee2, Kihwan Kim2, Hyunjin Kim2, Younghun Cho2

1 KRISS, Daejeon, Korea
2 CBSbio Science, Daejeon, Korea

Correspondence address: Hun-Young So, KRISS, 1 Doryong-dong, Yuseong-gu, Daejeon, 305-600 Korea.

Keywords: Computer Program; Data Analysis; Mass Spectrometry, Fourier Transform; Proteomic.

Novel aspect: Application software for top-down and bottom-up proteomics.


Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR MS) is a rapidly emerging alternative to other types of mass spectrometers for proteome analysis due to its high resolving power, mass accuracy, sensitivity, and flexibility. Accurate mass measurement capability of FT-ICR MS has been proven as a significant tool for improving level of confidence in peptide and protein identification in bottom-up approach. Also information-rich fragmentation techniques available with a FT-ICR MS, electron capture dissociation (ECD) and infrared multiphoton dissociation (IRMPD), allowed the identification and characterization of intact protein ions by top-down approach. However, all of the advantages of FT-ICR MS could not be fully demonstrated because there is a gap between the complexity of FT-ICR MS spectra and capability of interpretation of the information by softwares. So it is still necessary to develop integrated software applicable for interpretating mass spectra of proteins and peptides obtained from a high-end FT-ICR MS. Therefore a few FT-ICR MS laboratories have developed and equipped with their own customized softwares. In this presentation, we will describe integrated application software, under development in our laboratory and provisionally named MassPeaks, for the identification and characterization of proteins and peptides by either/both top-down and bottom-up approach. This software includes modules performing Fourier signal analysis, deconvolution of ion peaks, peptide mass mapping with utilizing the advantage of high mass accuracy of FT-ICR MS, de novo interpretation and DB searching for MS/MS spectra of peptide and protein ions. This software has function of storage and management of experimental data and protein DB. This application software will be installed in our laboratory to be used with a 12 Tesla FT-ICR MS from IonSpec Corporation. This software will be improved to process any transient data obtained from any FT-ICR MS from other manufacturers.