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Proteored Multicentric Experiment 8 (PME8) Quantitative Targeted Analysis in Proteomics. An Assesment Study (QTAPAS). ProteoRed WG1-WG2 Meeting Pamplona, December 10th 2013. Total 27 Participant Laboratories ( February - April 2013). 20 SRM data sets. 10 PRM data sets:.
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ProteoredMulticentric Experiment 8 (PME8) QuantitativeTargetedAnalysis in Proteomics. AnAssesmentStudy (QTAPAS) ProteoRed WG1-WG2 Meeting Pamplona, December 10th 2013
Total 27 ParticipantLaboratories (February- April 2013) 20 SRM data sets 10 PRM data sets: 3 QTOF 7 OT
SIGMA-ALDRICH MSQC1 • 6 Digestedproteins : • 25-fold concentrationrange – 3 concentrationtiers • Quantified UV beforedigestion • 2-3 labeledpeptides/ protein • L/H ratios 0.2-50 • Quantified AAA
SAMPLE SET YeastDigest + Spiked MSQC1, 5 differentconcentrations fmol/ microgramYeastLysateDigest
QTAPAS - PME8 SRM ANALYSIS RECOMMENDED GUIDELINES • 1- LC conditions: • Nano LC- system: • Column: 75 mm x 15 cm C18 • Sample load: 1 mg yeast digest/injection • Flow rate: 300-500 nL /min • Gradient: 0-35% Acetonitrile in 90 min 3- Analysis design: - Samples A through E Replica 1 (from most diluted to most concentrated) - Blank runs (enough to secure clean baseline) - Samples A through E Replica 2 - Blank runs - Samples A through E Replica 3
LINEARITY OF RESPONSE Average of 30 datasets – Error bars: StdDev. Tier 1
ABSOLUTE QUANTIFICATION INTER LABORATORY VARIABILITY %CV 30 datasets Average of 30 datasets , three replicas averaged
ABSOLUTE QUANTIFICATION INTER LABORATORY VARIABILITY N=20 N=7
ABSOLUTE QUANTIFICATION INTER LABORATORY VARIABILITY N=20 N=3
ABSOLUTE QUANTIFICATION Comparisonbytype of measurement
ABSOLUTE QUANTIFICATION INTRA- vs INTER LABORATORY VARIABILITY Average, %CV 3 replicas - Average, %CV 30 datasets
INTRA- vs INTER LABORATORY VARIABILITY Average, %CV 3 replicas - Average, %CV 30 datasets
REPRODUCIBILITY OF TRANSITION PATTERN Transitionsignaldistribution Average 3 replicas Normalizeddotproducttoaveragedistribution
Analysis of pure MSQC1 (withoutyeastbackground) Forcomparison: Possibleeffects of complexbackground 3 Vials x 10 mg 200 nginjection – 80 fmol min
CONCLUSIONS • The results demonstrate a good degree of reproducibility of targeted quantification measurements by SRM at different laboratories, irrespective of the method of analysis and the spectrometer used. • The average Inter-Laboratory %CV of the measured absolute protein amounts ranges from less than 10%CV for Tier 1 proteins, to 40-60% for the proteins at the lowest concentrations. • The pattern of relative intensities of the transitions monitored is fairly consistent among different instruments and fragmentation modes, underscoring the utility of spectral databases for the design of quantification methods. • The results obtained at each laboratory allow the assessment of the limitations in sensitivity and limits of quantification under the diverse analytical conditions used