Challenges in Lipidomics Biomarker Identification: Avoiding the Pitfalls and Improving Reproducibility
Abstract
:1. Introduction
2. Materials and Methods
2.1. PANC-1 Lipid Extraction LC–MS Dataset
2.2. Comparison of Outputs
2.3. Post-Software Quality Control Checks of Data
3. Results
3.1. Comparison of MS DIAL and Lipostar Outputs
3.2. Data-Driven Investigation of Putative Lipid Identifications
3.3. Manual Investigation of Putative Lipid Identifications
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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MS DIAL Identified Features | Actual tR (min) | Predicted tR (min) | Δ (min) |
---|---|---|---|
Inconsistencies in tR: saturation | |||
TG C51H92O6 | 7.42 | 7.49 | 0.07 |
TG C51H94O6 | 7.55 | 7.57 | 0.02 |
TG C51H96O6 | 7.69 | 7.65 | −0.04 |
TG C51H98O6 | 6.62 | 7.74 | 1.12 |
Inconsistencies in tR: headgroups | |||
DG C36H61D7O5 | 6.55 | 6.52 | −0.03 |
PC C36H64NO8P | 6.50 | 5.42 | −1.08 |
MS DIAL Identified Features | tR (min) | Lipostar Identified Features | tR (min) |
---|---|---|---|
Identification problems: co-elution of lipids | |||
DG 34:0|DG 16:0_18:0 | 6.78 | DG (15:0/16:0/0:0) | 6.78 |
TG 41:1;O|TG 9:0_17:0_15:1;O | 6.78 | DG (15:1/18:1/0:0) | 6.78 |
Cer 42:2;O2|Cer 18:1;O2/24:1 | 6.80 | TG (13:0/13:0/16:0) | 6.78 |
Cer 42:2;O2|Cer 18:1;O2/24:1 | 6.80 | DG (15:0/18:1/0:0) | 6.79 |
Cer (51:1) | 6.80 | ||
Identification problems: misidentifications | |||
PC 37:7|PC 15:1_22:6 | 6.00 | PE (40:7) | 6.00 |
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von Gerichten, J.; Saunders, K.; Bailey, M.J.; Gethings, L.A.; Onoja, A.; Geifman, N.; Spick, M. Challenges in Lipidomics Biomarker Identification: Avoiding the Pitfalls and Improving Reproducibility. Metabolites 2024, 14, 461. https://doi.org/10.3390/metabo14080461
von Gerichten J, Saunders K, Bailey MJ, Gethings LA, Onoja A, Geifman N, Spick M. Challenges in Lipidomics Biomarker Identification: Avoiding the Pitfalls and Improving Reproducibility. Metabolites. 2024; 14(8):461. https://doi.org/10.3390/metabo14080461
Chicago/Turabian Stylevon Gerichten, Johanna, Kyle Saunders, Melanie J. Bailey, Lee A. Gethings, Anthony Onoja, Nophar Geifman, and Matt Spick. 2024. "Challenges in Lipidomics Biomarker Identification: Avoiding the Pitfalls and Improving Reproducibility" Metabolites 14, no. 8: 461. https://doi.org/10.3390/metabo14080461