Non-linear gradients and retention time prediction?

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Phosphoserine Member
Phosphoserine Member
Posts: 20
Joined: Mon Apr 29, 2013 11:47 pm

Non-linear gradients and retention time prediction?

Postby botte » Tue Oct 15, 2013 12:50 am

Dear all,
I found this interesting paper by the Käll and Mechtler groups recommending non-linear gradients to optimize precursor yield over elution time:

Anal Chem. 2013 Aug 20;85(16):7777-85. doi: 10.1021/ac401145q. Epub 2013 Jul 24.
Optimized nonlinear gradients for reversed-phase liquid chromatography in shotgun proteomics.
Moruz L, Pichler P, Stranzl T, Mechtler K, Käll L.

Matches our own experience without the theoretical work, that e.g. breaking the gradient into two or three linear functions instead of a single linear function will improve protein ID especially for complex samples and long gradients.

But now my question - has anybody investigated the impact on this on processing software using iRT information, e.g. Skyline or Spectronaut? Will iRT (or other standard)-based corrections still apply, even if the resulting set of peptide retention times are not following a linear trend?

Sorry if this sounds like a stupid question, I am obviously lacking the information how RT alignment is implemented in the respective SW packages.

Glycine Member
Glycine Member
Posts: 5
Joined: Mon Oct 21, 2013 4:51 am

Non-linear gradients in Spectronaut

Postby oBernhardt » Mon Oct 21, 2013 5:03 am


In regards to Spectronaut, support for non-linear gradients is not yet available in the current Academic release of the Software. But the feature is planned for the next release. The iRT concept itself is applicable regardless whether it is used with a linear or non-linear gradient. It is just that the software and therefore the transformation function has to support it.
Please be advised though that non-linear gradients will influence the quantification since the number of data points per peak across your run will vary regarding to the steepness of your gradient at that point.

I hope that was what you where asking for. If you have any further questions about iRT (or Spectronaut) please feel free to contact us.


Oliver Bernhardt, MSc.
Lead Developer of Spectronaut
Biognosys AG

CH-8952 Zurich

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