1. Concept of Data Extracting Software Import raw data select RT range calculate centroid value select m/z range repeat for all peptides repeat for all files RT m/z LCMS data file

2. Concept of Data Extracting Software MagTran (Zhang) HXExpress (Weis) Deuterator (Scripps) DXMS (UCSD) HDExpress (ExSAR) Import raw data select RT range calculate centroid value select m/z range repeat for all peptides repeat for all files

3. Comparison of Data Extracting Software nameMagTranHX-ExpressDeuteratorDXMSHDExpress ownerZ. ZhangDavid WeisScrippsUCSDExSAR availabilityfree expensivenot available MS typeall Finnegan, Waters Finnegan, ABI RT selectionmanual auto-poorauto m/z selectionmanualauto centroidauto otherstand aloneExcel basedweb basedstand alone

4. ExSAR’s HDExpress is still the best software. Better than UCSD’s DXMS due to the easiness of manual correction, which is always necessary. Scripps made Deuterator available via web. This software does not have good RT selection algorithm. While both HDExpress and DXMS can accommodate retention time shift in chromatogram, Deuterator can not. Software and automation should go hands in hands. Around Data Extracting Software