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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Digested peptides
Digestion
Proteins
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MS(MS/MS)
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State BState B
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LC-MS data
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
MS
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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: