自動化蛋白質定量系統 Automatic Protein Quantitation System

1. A L E L H F R P A A K M D G N D I P V K E D F S L K A G H A K G H E K P D E M E T L K D S E K S A K K K H L Y Q V K Q L F E L L A G I M M D H G V A K G W V G A G G Q G V Q G E L E M G V E G G F Q N L I I S L K L R M I K A G V A L K T F S L W E E Q D D G K F L S K V T E H A I A E L G H T H T P N H G A L Q S F E L Y We have developed the following software to support various experiments Relative quantitative proteomics LC Separation Multi-Q m/z Digestion State A MS analysis Labeling Label-free Digested peptides Alignment and cross assignment MaXIC-Q Proteins State B … IDEAL-Q MS/MS MS Elution time LC-MS data MS(MS/MS) Protein 1…….. Peptide 1…… Peptide 25…… Peptide 65…… Protein 2…….. Peptide 25…… Peptide 65…… Protein 5…….. Peptide 1…… Peptide 25…… Peptide 65…… Protein 2…….. Peptide 25…… Peptide 65…… Peptide identification 14N / 15N SILAC ICAT 16O / 18O iTRAQTM MS/MS spectra MS, MS/MS spectrum Protein & Peptide ID list 自動化蛋白質定量系統Automatic Protein Quantitation System • MS-based shotgun proteomics • The developed tools Please visit the developed tools: Protein 1……..0.5 Peptide 1……0.3 Peptide 25……0.6 Peptide 65……0.7 Protein 2……..1.2 Peptide 25……1.3 Peptide 65……1.2 • Multi-Q: http://ms.iis.sinica.edu.tw/Multi-Q/ (JPR 2006; NAR 2007.) • MaXIC-Q: http://ms64.iis.sinica.edu.tw/MaXIC-Q_web/index.html(NAR 2009) • IDEAL-Q: http://ms.iis.sinica.edu.tw/IDEAL-Q/ (MCP 2009) Protein & Peptide ratio • Workflow of label-free quantitation approach XIC of State B XIC of State A • Challenges • Peptide elutes at different time across experiments • peptide identified randomly across experiments • IDEAL-Q Purpose: Provide a automated quantitation software tool for label-free proteomics analysis. Methods: IDEAL algorithm to predict the elution time of peptides and SCI peptide validation to accurately profile protein expression. Results: IDEAL-Q can accurately quantify protein expressions and significantly increase the number of quantifiable proteins/peptides. IDEAL-Q is a fully automated software tool for label-free quantitation analysis. Unlike other label-free programs, IDEAL-Q uses an efficient algorithm, called IDEAL (ID-based Elution time Alignment based on Linear regression), to predict the elution time of unidentified peptides (i.e., peptides unidentified in this LC-MS run, but identified in other LC-MS runs). It also utilizes computational and statistical methods to evaluate the validity of detected peptide clusters and then quantify validated peptide clusters. IDEAL-Q is designed to adapt to different fractionation strategies for correct quantitation analysis. Furthermore, it provides graphical visualizations of peptide/protein information and statistical charts for quantitation results. Elution time prediction SCI validation (based on PIMS) XIC and PIMS constructions Peptide fraction/sample abundance 生物資訊實驗室 計畫主持人 許聞廉　特聘研究員 宋定懿　研究員