![Page 1: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/1.jpg)
Research and Innovation Centre
Jan Stanstrup†, Steffen Neumann‡, and Urska Vrhovsek††Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all’Adige (TN), Italy‡Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
The Role of Retention Timein Untargeted MetabolomicsCaparica-Lisbon, 21st September 2015
![Page 2: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/2.jpg)
Research and Innovation Centre
From feature to identified compound
Match to authentic standard MSI LEVEL I
Match to public MS library MSI LEVEL IINo orthogonal data: only spectra
Compound not in any MS library MSI LEVEL III/IV
Orthogonal data: e.g. spectra + retention time
![Page 3: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/3.jpg)
Research and Innovation Centre
From feature to identified compound
Match to authentic standard MSI LEVEL I
Match to public MS library MSI LEVEL IINo orthogonal data: only spectra
Compound not in any MS library MSI LEVEL III/IV
Orthogonal data: e.g. spectra + retention time
![Page 4: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/4.jpg)
Research and Innovation Centre
From feature to identified compound
Match to authentic standard MSI LEVEL I
Match to public MS library MSI LEVEL IINo orthogonal data: only spectra
Compound not in any MS library MSI LEVEL III/IV
Orthogonal data: e.g. spectra + retention time
![Page 5: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/5.jpg)
Research and Innovation Centre
From feature to identified compound
Match to authentic standard MSI LEVEL I
Match to public MS library MSI LEVEL IINo orthogonal data: only spectra
Compound not in any MS library MSI LEVEL III/IV
Orthogonal data: e.g. spectra + retention time
![Page 6: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/6.jpg)
Research and Innovation Centre
MSI LEVEL II: match to public db
But are you sure that the spectra of your unknown couldn’t match other isomers equally well?
You got your match to a database spectra.
![Page 7: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/7.jpg)
Research and Innovation Centre
![Page 8: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/8.jpg)
Research and Innovation Centre
1) Examine mass spectra No way to discriminate
![Page 9: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/9.jpg)
Research and Innovation Centre
1) Examine mass spectra No way to discriminate2) Check spectra libraries Still cannot be sure
![Page 10: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/10.jpg)
Research and Innovation Centre
"Piled Higher and Deeper" by Jorge Cham www.phdcomics.com
1) Examine mass spectra No way to discriminate2) Check spectra libraries Still cannot be sure
![Page 11: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/11.jpg)
Research and Innovation Centre
"Piled Higher and Deeper" by Jorge Cham www.phdcomics.com
1) Examine mass spectra No way to discriminate2) Check spectra libraries Still cannot be sure3) Buy all standards (if available) Expensive!
![Page 12: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/12.jpg)
Research and Innovation Centre
"Piled Higher and Deeper" by Jorge Cham www.phdcomics.com
1) Examine mass spectra No way to discriminate2) Check spectra libraries Still cannot be sure3) Buy all standards (if available) Expensive!
![Page 13: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/13.jpg)
Research and Innovation Centre
"Piled Higher and Deeper" by Jorge Cham www.phdcomics.com
1) Examine mass spectra No way to discriminate2) Check spectra libraries Still cannot be sure3) Buy all standards (if available) Expensive!
So can we at least limit the number of isomersby using the information we already have?
![Page 14: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/14.jpg)
Research and Innovation Centre
Why retention time information is usually neglected
Retention time is specific to the chromatographic system and there are no RT references
No coordinated efforts to share and exploit RT info.
![Page 15: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/15.jpg)
Research and Innovation Centre
aAbate-Pella D, et al. (2015). Retention Projection Enables Accurate Calculation of Liquid Chromatographic Retention Times Across Labs and Methods. J Chromatogr.
Prediction from structure (QSRR) Projection from isocratic runsa
PredRetb
Accuracy Low Very high High to medium
Universality (any structure) High Low Medium
Additional lab work None Lots None
Model complexity High Low Low
Current approaches to retention time prediction and their characteristics
![Page 16: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/16.jpg)
Research and Innovation Centre
Ret
entio
n tim
e (m
in)
1
2
3
4
Predicted logD-6 -4 -2 0 2 4
Stanstrup, J., Gerlich, M., Dragsted, L. O., & Neumann, S. (2013). Metabolite profiling and beyond: Approaches for the rapid processing and annotation of human blood serum mass spectrometry data Metabolomics and Metabolite Profiling. Analytical and Bioanalytical Chemistry, 405(15), 5037–5048.
Simplest QSRR model
![Page 17: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/17.jpg)
Research and Innovation Centre
Candidates after filtering as afunction of prediction accuracy
![Page 18: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/18.jpg)
Research and Innovation Centre
Median
Candidates after filtering as afunction of prediction accuracy
![Page 19: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/19.jpg)
Research and Innovation Centre
Median
Max
Candidates after filtering as afunction of prediction accuracy
![Page 20: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/20.jpg)
Research and Innovation Centre
aAbate-Pella D, et al. (2015). Retention Projection Enables Accurate Calculation of Liquid Chromatographic Retention Times Across Labs and Methods. J Chromatogr.
Prediction from structure (QSRR) Projection from isocratic runsa
PredRetb
Accuracy Low Very high Medium to high
Universality (any structure) High Low Low to medium
Additional lab work None Lots None
Model complexity High Low Low
Previous approaches to retention time prediction
![Page 21: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/21.jpg)
Research and Innovation Centre
aAbate-Pella D, et al. (2015). Retention Projection Enables Accurate Calculation of Liquid Chromatographic Retention Times Across Labs and Methods. J Chromatogr.bStanstrup, J., Neumann, S., & Vrhovsek, U. (2015). PredRet: Prediction of Retention Time by Direct Mapping between Multiple Chromatographic Systems. Analytical Chemistry.
Prediction from structure (QSRR) Projection from isocratic runsa
PredRetb
Accuracy Low Very high Medium to high
Universality (any structure) High Low Low to medium
Additional lab work None Lots None
Model complexity High Low Low
Previous approaches to retention time prediction
![Page 22: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/22.jpg)
Research and Innovation Centre
PredRet models
![Page 23: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/23.jpg)
Research and Innovation Centre
Compound overlap between systems in PredRet
![Page 24: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/24.jpg)
Research and Innovation Centre
![Page 25: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/25.jpg)
Research and Innovation Centre
![Page 26: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/26.jpg)
Research and Innovation Centre
![Page 27: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/27.jpg)
Research and Innovation Centre
"Piled Higher and Deeper" by Jorge Cham www.phdcomics.com
![Page 28: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/28.jpg)
Research and Innovation Centre
Accuracy of PredRet predictions
![Page 29: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/29.jpg)
Research and Innovation Centre
Candidates after filtering as afunction of prediction accuracy
![Page 30: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/30.jpg)
Research and Innovation Centre
Median
Max
Candidates after filtering as afunction of prediction accuracy
![Page 31: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/31.jpg)
Research and Innovation Centre
Median
Max
Median
Max
Candidates after filtering as afunction of prediction accuracy
![Page 32: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/32.jpg)
Research and Innovation Centre
![Page 33: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/33.jpg)
Research and Innovation Centre
![Page 34: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/34.jpg)
Research and Innovation Centre
Conclusions● PredRet allows sharing of retention time information and
across chromatographic systems
![Page 35: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/35.jpg)
Research and Innovation Centre
Conclusions● PredRet allows sharing of retention time information and
across chromatographic systems● The accuracy of PredRet can allow differentiation of isomers
![Page 36: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/36.jpg)
Research and Innovation Centre
Conclusions● PredRet allows sharing of retention time information and
across chromatographic systems● The accuracy of PredRet can allow differentiation of isomers
● Compound need to be in the database (someone need to record it)
![Page 37: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/37.jpg)
Research and Innovation Centre
Conclusions● PredRet allows sharing of retention time information and
across chromatographic systems● The accuracy of PredRet can allow differentiation of isomers
● Compound need to be in the database (someone need to record it)
● Chromatography needs to be similar (e.g. acidic C18-based)
![Page 38: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/38.jpg)
Research and Innovation Centre
Conclusions● PredRet allows sharing of retention time information and
across chromatographic systems● The accuracy of PredRet can allow differentiation of isomers
● Compound need to be in the database (someone need to record it)
● Chromatography needs to be similar (e.g. acidic C18-based)
● When people use PredRet the database expands
![Page 39: The Role of Retention Time in Untargeted Metabolomics](https://reader035.vdocuments.mx/reader035/viewer/2022062900/58edccbb1a28ab8c0b8b4655/html5/thumbnails/39.jpg)
Research and Innovation Centre
Thank you for your attention
Share the RTs!