Thursday, May 14, 2009

Baseline correction for automated integration of NMR JCAMP-DX files

We were initially getting a surprisingly large solubility measurement for one of our solutes (spectrum from ONSC-EXP077). After investigating, it was clear that the discrepancy was originating from a peak with a sloping baseline:


The web service was integrating all of the area beneath the peak and the raised baseline. After discussing the situation with Andrew Lang, he modified his code to exclude the area beneath a linearly sloping baseline. Andy's code is Open Source and made available here, including detailed instructions for anyone wishing to implement it themselves. This modified web service is included in the most recent Google Spreadsheet template for semi-automated measurement of solubility using NMR.

The progress of science is a clumsy walk toward a non-attainable ideal of full understanding and control. With every experiment we have to re-question what think we know as variables change. This is why I am so passionate about Open Notebook Science and having all stakeholders interact at the level of the individual experiment. We caught this issue early and we were able to deal with it because our computational collaborator was engaged in details with the chemists and responsive.

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1 Comments:

At 3:13 PM, Anonymous Rich Apodaca said...

Jean-Claude - excellent work, and thanks for using the MIT License!

 

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