Category Archives: Resource Library

Scalable Peptide MRM Transition Prediction for High-Throughput Proteomics via Hashing-Based Sequence Encoding

Peptide analysis via Multiple Reaction Monitoring (MRM) is indispensable for quantification and/or biomarker validation and drug development, yet its reliance on experimental transition optimization limits scalability. Current computational models for small molecules fail to address peptide-specific complexities, such as sequence-dependent fragmentation and charge-state variability. We introduce a novel framework that combines hashing-based peptide fragment encoding with gradient-boosted decision trees to predict MRM transitions efficiently. This method eliminates bottlenecks in experimental workflows, enabling rapid, resource-efficient transition identification without compromising accuracy—a critical advancement for high-throughput proteomics pipelines.

Molecular Structure and Mass Spectral Data Quality Driven Processing of High-Resolution Mass Spectrometry Data for Pharmacokinetics Studies

Our inability to comprehensively process high resolution mass spectrometry data for quantitative analysis has long been an impediment to the broader adoption of this powerful technique. We have developed an approach that agnostically and automatically identifies all ions related to the compound in both the MS and MSMS data. The algorithm uses the structure of the molecule to automatically select the optimal compound related MS and MSMS signals, and parameters (extraction window, S/N) to provide the best overall method to meet the assay acceptance criteria defined by the user. Results using this structure and data driven approach are presented for pharmacokinetic data that were collected using the same set of samples analyzed on both QQQ and HRMS instruments.

Plasma lipidomics analysis reveals altered profile of triglycerides and phospholipids in children with Medium-Chain Acyl-CoA dehydrogenase deficiency

July 2024

Inês M S Guerra, Helena B Ferreira, Tatiana Maurício, Marisa Pinho, Luísa Diogo, Sónia Moreira, Laura Goracci, Stefano Bonciarelli, Tânia Melo, Pedro Domingues, M Rosário Domingues, Ana S P Moreira

Abstract

Keywords: Lipid profile; Lipidomics; Mass spectrometry; Medium‐chain acyl‐CoA dehydrogenase deficiency (MCADD); Phospholipids (PL); Plasma analysis; Triacylglycerols (TG).

Unmasking the lipid landscape: carbamazepine induces alterations in Leydig cell lipidome

February 2025

Inês Nobre, Inês M. S. Guerra, Marisa Pinho, Ana D. Martins, Laura Goracci, Stefano Bonciarelli, Tânia Melo, Pedro Domingues, Artur Paiva, Pedro F. Oliveira, M. Rosário Domingues

Abstract

Leydig cells rely on lipids and fatty acids (FA) for essential functions like maintaining structural integrity, energy metabolism, and steroid hormone synthesis, including testosterone production. Carbamazepine (CBZ), a common anticonvulsant medication, can influence lipid metabolism and profiles, potentially impacting Leydig cell function and testosterone levels. Understanding this interplay is crucial to optimize treatment strategies for individuals requiring CBZ therapy while mitigating any adverse effects on male reproductive health. This study focuses on evaluating the effects of selected CBZ concentrations on the lipid homeostasis of BLTK-1 murine Leydig cells. By employing liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS), we aimed to uncover the specific changes in lipid profiles induced by CBZ exposure (25 and 200 μM). FA analysis demonstrated a significant decrease in FA 22:6 n-3 with increasing CBZ concentration and an increase in the n-6/n-3 ratio. Furthermore, changes in the lipidome, particularly in lipid species belonging to phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), and sphingomyelin (SM) classes were observed. PE and PC lipid species were significantly elevated in Leydig cells exposed to 200 μM CBZ, whereas PG and SM species were downregulated. CBZ treatment significantly altered the Leydig cell phospholipidome, suggesting specific phospholipids such as PG 40:4, PG 34:1, PC O-32:1, PC 32:2, and PE P-38:6, which exhibited the lowest p-values, as potential biomarkers for clinical assessment of CBZ’s impact on Leydig cells. These findings underscore the intricate relationship between CBZ exposure and alterations in lipid profiles, offering potential insights for monitoring and mitigating the drug’s effects on male reproductive health.

Phosphatidylethanolamine species with n-3 and n-6 fatty acids modulate macrophage lipidome and attenuate responses to LPS stimulation

April 2025

Tatiana Maurício, Inês M. S. Guerra, Marisa Pinho, Tânia Melo, Stefano Bonciarelli, Laura Goracci, Bruno Neves, Rosário Domingues, Pedro Domingues

Abstract

Phospholipids are increasingly recognized as key regulators of biological processes, including macrophage polarization and function. Among these, phosphatidylethanolamine (PE), a major constituent of cell membranes, is pivotal in maintaining cellular structure and function, yet the mechanisms through which native PE species influence macrophage immunometabolism remain largely unexplored. This study investigates the effects of two native PE species, PE 18:0/22:6 and PE 18:0/20:4, on the lipidome of resting and LPS-activated macrophages. Using C18 HPLC-MS/MS, we identified 337 lipid molecular species across 15 lipid subclasses, 332 of which varied significantly among conditions. Both PE 18:0/22:6 and PE 18:0/20:4 supplementation modulated the macrophage lipidome without inducing a pro-inflammatory phenotype under basal conditions. Notably, supplementation with PE 18:0/22:6 and PE 18:0/20:4 significantly increased lipid classes such as PE, PE O-, SM, CL, PG, LPE and PS, producing unique lipid profiles. Pre-treatment with PE 18:0/22:6 and PE 18:0/20:4 partially attenuated LPS-induced lipidomic changes, significantly reducing lipid classes like PC, including PC O- and PC P-, and Cer, which are typically linked to inflammation. While PE 18:0/20:4, from an individual lipid species perspective, may promote certain lipid profiles compatible with pro-inflammatory signaling pathways, particularly under inflammatory conditions, PE 18:0/22:6 seems to foster a lipid profile more supportive of inflammation resolution. This behaviour of PE 18:0/22:6 and PE 18:0/20:4 highlights the intricate complexity of lipid-mediated immunomodulation and emphasizes the critical role of cellular context in determining the functional outcomes of phospholipid supplementation in macrophage lipid metabolism and immune responses.