High Throughput Small Molecule DetectionSkyline User Group Meeting 6/4/2017

Yang Zhang

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Amyris: from sugar to product

FARNESENE (C15)

SUGARSOURCE

MONOTERPENES (C10)

ISOPRENE (C5)

ARTEMISININANTI-MALARIAL (C15)

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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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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