a workflow for quality assessment, quantitation and
TRANSCRIPT
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©2012, Genentech
Shadi Eshghi
A Workflow for Quality Assessment, Quantitation and
Statistical Inference of Targeted Proteomics Data using Skyline
and Panorama
Skyline User MeetingJune 4, 2017
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©2012, Genentech
Data analysis is a challenge for development of clinical biomarkers using targeted mass spectrometry 2
Drug developmentResearch Pre-IND Phase I Phase II Phase III
(Pivotal) Clinical Practice
Triple Quad(High sensitivity)
Targeted MS for development of clinical biomarkers
100 patients
2 timepoints
40 target analytes
5 transitions per analyte
8,000 peak groups
40,000 transitions
An ideal data analysis pipeline would be:
High throughput
Reproducible
Objective
Automated
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©2012, Genentech
Panorama and skyline simplify data management and analysis for targeted MS assays
Centralized archiving model
Distributed analysis model
Peak Integration
QC
Quant
Stats
JASMS, November 2016
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©2012, Genentech
Enabling targeted MS post-processing on Panorama centralizes data archiving and analysis
JASMS, November 2016
Centralized archiving and analysis model
Automated and objective QC
Generation of results within minutespost data acquisition
QC Quant Stats
Peak Integration
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©2012, Genentech
Targeted MS data analysis pipeline
Peak Integration
Quality Checking
Data Integration
StatisticalInference
Quantitation
TargetedMSQC (WP 320)[Panorama compatible R package]
Skyline Skyline/Panorama (MP 637)
MSstats[Panorama compatible R package]
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©2012, Genentech
Samples 100
Peptides 30
Transitions 12000
High Quality 11500
Poor Quality 500
Remove all flagged transitions from downstream analysis
Samples
Pept
ides
Remove ☐
QC Summary
Remove ☐
Remove ☐
Chromatographic Peaks Peptide QC Summary
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©2012, Genentech
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©2012, Genentech MSStats Package Vignette
Peptide Sample Condition Concentration
Pep 1 A 0 h 0.13
Pep 2 A 0 h 0.24
Pep 1 B 48 h 0.48
Pep 2 B 48 h 0.19
Profile Plots Group Comparison
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©2012, Genentech
Acknowledgements
GenentechBiomarker Development
Rod MathewsPaul AugerVeronica AnaniaKristin WildsmithFrancesco Pingitore
Nonclinical BiostatsDanny SheinsonYuda Zhu
IT SupportJon SasanoJoshua Haznedar
Panorama PartnersJosh Eckels (Labkey)Brendan MacLean (UW)Vagisha Sharma (UW)Nick Shulman (UW)Michel Petrovic (Roche)Daniel Spellman (Merck)
Related ASMS Posters:
TargetedMSQC: WP 320Absolute Quant on Panorama: MP 637
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