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MaxQuant enables high peptide identification rates, individual-ized p.p.b.-range mass accura-cies and proteome-wide protein
quantificationYoona Kim
University of California, San Diego
UCSD Mass Spectrometry Journal Club 12/03/10
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MaxQuant
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What is the MaxQuant? What’s benefits from MaxQuant? Conclusion Critisism
Outline
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Input : High resolution, quantitative MS data of SILAC-en-coded cell populations
MaxQuant
Output: Identified MS/MS spectra and protein quantification graph(x=protein ration/y=intensity)
What is the MaxQuant?
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Stable amino acid isotope-la-beled (SILAC) (1)
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Stable amino acid iso-tope-labeled (SILAC) (2)
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4. Visualization
3. Identification and validation
2. MS/MS Ion search - Mascot
1. Feature detection and peptide quantitation
MaxQuant’s pipeline
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2D peaks
1. Feature detection and peptide quantitation-Peak Detection (1)
3D peaks
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A bootstrap estimation over B = 150∵unknown atomic composition and intensity profiles overlap
1. Feature detection and peptide quantitation-Peak Detection (2)
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Step 1: All possible pairs of isotope patterns- The correlation test >0.5- Have equal charge, close enough in mass
Step 2 : Convolute two isotope patterns- K, R, KK, KR, RR, KKK, KKR, KRR, and RRR- Find the same atomic composition
1. Feature detection and peptide quantitation-SILAC pair detection (1)
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Ex. The peptide contains one K and no R- Heavy isotope labeled form ,
1. Feature detection and peptide quantitation-SILAC pair detection (2)
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1. Feature detection and peptide quantitation-SILAC pair detection (3)
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Posterior Error Probability - for calculating the false-discovery rate
3. Identification and validation
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3. Identification and validation–Peptide score distributions
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1. Improving peptide mass accu-racy
2. High rate of identified MS/MS spectra
3. Proteome-wide protein quantifiation
What’s the benefits from MaxQuant?
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1. Improving peptide mass ac-curacy
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2. High rate of identified MS/MS spectra
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Protein ratio = median(all SILAC peptide ra-tio)
P-value for detection of significant outlier ratio (significance A)
3. Proteome-wide protein quan-tifiation
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3. Proteome-wide protein quan-tifiation
Significance A Significance B
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MaxQuant improves◦ Peptide identification rates◦ Peptide mass accuracy◦ Proteom-wide protein quantification
Conclusion
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All experimental results are based on Mas-cot search◦ Mascot does not fully benefit from high-accuracy
(limit 0.25Da)
-> It is not working…!! (Sangtae said)
Critisism
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IF you have more ques-tions…..
Go MaxQunt summer schoolIt will be fun!!!