ppb range mass accuracies and proteomewide protein quantification Yoona Kim University of California San Diego UCSD Mass Spectrometry Journal Club 120310 MaxQuant ID: 723070
Download Presentation The PPT/PDF document "MaxQuant enables high peptide identific..." is the property of its rightful owner. Permission is granted to download and print the materials on this web site for personal, non-commercial use only, and to display it on your personal computer provided you do not modify the materials and that you retain all copyright notices contained in the materials. By downloading content from our website, you accept the terms of this agreement.
Slide1
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
Yoona Kim University of California, San Diego
UCSD Mass Spectrometry Journal Club
12/03/10Slide2
MaxQuantSlide3Slide4
What is the MaxQuant?What’s benefits from MaxQuant?Conclusion
CritisismOutlineSlide5
What is the
MaxQuant?Slide6
Stable amino acid isotope-labeled (SILAC) (1)Slide7
Stable amino acid isotope-labeled (SILAC) (2)Slide8
MaxQuant’s
pipelineSlide9
2D peaks 1. Feature detection and peptide
quantitation-Peak Detection (1)
3
D peaks Slide10
A bootstrap estimation over B = 150∵unknown atomic composition and intensity profiles overlap
1. Feature detection and peptide quantitation-Peak Detection (2)Slide11
Step 1: All possible pairs of isotope patternsThe correlation test >0.5
Have equal charge, close enough in massStep 2 : Convolute two isotope patternsK, R, KK, KR, RR, KKK, KKR, KRR, and RRRFind the same atomic composition
1. Feature detection and peptide
quantitation
-
SILAC pair detection (1)Slide12
Ex. The peptide contains one K and no RHeavy isotope labeled form ,
1. Feature detection and peptide quantitation-SILAC pair detection (2)Slide13
1. Feature detection and peptide quantitation-
SILAC pair detection (3)Slide14
Posterior Error Probability - for calculating the false-discovery rate3. Identification and validationSlide15
3. Identification and validation–Peptide score distributionsSlide16
What’s the benefits from
MaxQuant?Slide17
1. Improving peptide mass accuracySlide18
2. High rate of identified MS/MS spectraSlide19
Protein ratio = median(all SILAC peptide ratio)P-value for detection of significant outlier ratio (significance A)
3. Proteome-wide protein quantifiationSlide20
3. Proteome-wide protein quantifiationSignificance A
Significance BSlide21
MaxQuant improvesPeptide identification ratesPeptide mass accuracyProteom-wide protein quantification
ConclusionSlide22
All experimental results are based on Mascot searchMascot does not fully benefit from high-accuracy (limit 0.25Da)-> It is not working…!! (Sangtae
said)CritisismSlide23
IF you have more questions…..
Go
MaxQunt
summer school
It will be fun!!!