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compomics / DeepLC

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
https://iomics.ugent.be/deeplc
Apache License 2.0
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negative retention times #34

Closed Seb-Leb closed 2 years ago

Seb-Leb commented 2 years ago

I am using DeepLC through the MS2PIP website along with the intensity predictor for a list of peptides. Many of the peptides are assigned a negative retention time and I am not sure how to interpret that result. Thank you for your help!

RobbinBouwmeester commented 2 years ago

Dear Seb-Leb, there are several possibilities, but it is most likely that these values are iRT values (the default as returned by the MS2PIP webserver). Although negative retention times would nor make sense, iRT values can be negative. These values can be negative because they are indexed using specific points and peptides retention times are "normalized" towards these specific points.

RobbinBouwmeester commented 2 years ago

This article should help you in understanding iRT values:

https://doi.org/10.1002/pmic.201100463

RobbinBouwmeester commented 2 years ago

I will close this issue for now, you can always contact me with any of your questions.

Seb-Leb commented 2 years ago

That settles it, thank you!