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

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

Relative quantitative proteomicsRelative quantitative proteomics

LabelingLabeling Label-freeLabel-free

MSMS MS/MSMS/MS

14N / 15N14N / 15N SILACSILAC ICATICAT 16O / 18O

16O / 18O iTRAQTMiTRAQTM

IDEAL-QIDEAL-Q

MaXIC-QMaXIC-Q

We have developed the following software to support

various experiments

Multi-QMulti-Q

MS-based shotgun proteomics

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Digestion

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State BState B

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Protein & Peptide ID list

Protein 1…….. Peptide 1…… Peptide 25…… Peptide 65……Protein 2…….. Peptide 25…… Peptide 65……

Elution time

m/z

Protein & Peptide ratio

Protein 1……..0.5 Peptide 1……0.3 Peptide 25……0.6 Peptide 65……0.7Protein 2……..1.2 Peptide 25……1.3 Peptide 65……1.2

Protein 1……..0.5 Peptide 1……0.3 Peptide 25……0.6 Peptide 65……0.7Protein 2……..1.2 Peptide 25……1.3 Peptide 65……1.2

XIC of State A

XIC of State B

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Protein 5…….. Peptide 1…… Peptide 25…… Peptide 65……Protein 2…….. Peptide 25…… Peptide 65……

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Workflow of label-free quantitation approach

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)

Challenges1. Peptide elutes at different time across

experiments2. peptide identified randomly across

experiments

IDEAL-QPurpose: 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 predictionElution time prediction

XIC and PIMS constructionsXIC and PIMS constructions

SCI validation (based on PIMS)SCI validation (based on PIMS)

Peptide fraction/sample abundancePeptide fraction/sample abundance

The developed tools

Please visit the developed tools: