High Throughput Small Molecule Detection - Skyline · 2017-06-06 · High Throughput Small Molecule...
Transcript of High Throughput Small Molecule Detection - Skyline · 2017-06-06 · High Throughput Small Molecule...
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High Throughput Small Molecule DetectionSkyline User Group Meeting 6/4/2017
Yang Zhang
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2 Copyright © 2017 Amyris, Inc. All rights reserved
Amyris: from sugar to product
FARNESENE (C15)
SUGARSOURCE
MONOTERPENES (C10)
ISOPRENE (C5)
ARTEMISININANTI-MALARIAL (C15)
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3 Copyright © 2017 Amyris, Inc. All rights reserved
DARPA M2K: from mg to kg in record time
Year 1 Attempt to
produce 450 molecules at
mg scale
Year 2150
molecules at gm scale
Year 350 molecules at g/L/h scale
Year 4Purify 1 Kg of 10 molecules
reduce the cost of scale up by 10X
Cheaper
increase molecule throughput by 20X
Greater
reduce the time to market by 4X
Faster
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Analytical workflow
Data Acquisition Data analysis• Peak integration• Peak alignment• Hit calling• Titer estimation
Data uploading• Generate reports• Save to database
Thousands of samples per
week covering 500+ molecules
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Peak integration without RT correction
Skyline picked the best peak at 4 minutes
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Get RT from standard or best guess in sample
Standard peak showsat 3.5 minute
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Correct RT
Correct peak to 3.4 minute
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8 Copyright © 2017 Amyris, Inc. All rights reserved
Skylinerunner + R: naïve peak integration
SkylineRunner.exe --in=skyline.sky--import-transition-list=transition.csv --out=skyline.sky
SkylineRunner.exe --in=skyline.sky –report-name=M2K--report-file=M2K.tsv --report-format=tsv--report-invariant --report-add=M2K.skyr --report-conflict-resolution=overwrite
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Skylinerunner + R: Retention time correction
SkylineRunner.exe --in=skyline.sky--import-transition-list=transition.csv --out=skyline.sky
SkylineRunner.exe --in=skyline.sky –report-name=M2K--report-file=M2K.tsv --report-format=tsv--report-invariant --report-add=M2K.skyr --report-conflict-resolution=overwrite
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Example output
Sample
Control
Blank
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Performance comparable to manual curation
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Hands-on time dropped from hours to minutes
Before:
Now:
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Acknowledgement