JMSACL Journal Club with Benjamin Owusu
About this Episode
Recent Episodes from MSACL
MSACL 2023 : A Chat with Jennifer Van Eyk on her Distinguished Contribution Award Lecture
MSACL 2023 : A Chat with Tim Collier on his Michael S Bereman Award Lecture
The MetaProteomics Initiative : The Cornerstone of Comprehensive Molecular Analysis of the Microbiome Ecosystem
Paper Spray Mass Spectrometry in Clinical Application
The triple quadrupole: Innovation, serendipity and persistence
JMSACL Journal Club : Supervised Machine Learning for Mass Spectrometry Data Analysis: Experts' Opinion
We will be talking with Thomas Durant and Edward Lee about recent advances in machine learning (ML) for mass spectrometry (MS) data analysis. The primary focus will be the alignment of these two fields (ML and MS) and how this offers a promising synergy that can be used to optimize workflows, improve result quality, and enhance our understanding of high-dimensional datasets, as well as their inherent relationship with disease biology. We will also dig deeper to understand a basic overview of ML and an ML-based experiment. Overall, we will have a opportunity go through the fundamental principles of supervised ML, outline the steps that are classically involved in an ML-based experiment, and discuss the purpose of good ML practice in the context of a binary MS classification problem.
Fireside Chat with Christopher Rose on Single Cell Proteomics
JMSACL Journal Club : Understanding X-Chromosome Deletion Disorder using metabolomics and lipidomics
X linked disorders are considerably rare and research analysing human samples is under-represented. Research undertaken in this study used neural progenitor cells from an afflicted patient to begin exploring this rare disorder. While most experimental work focuses on the neurodevelopmental impacts of X-chromosome associated diseases, this work demonstrates that they should also be considered metabolic disorders owing to their perturbations on metabolite and lipid biochemistry. This work aims to use mass spectrometry to improve our understanding of these conditions and guide novel interventions by characterizing disease associated metabolic alterations.
Novel Techniques using Silicon (in silico) and Gold to Improve Imaging Results
Untargeted small molecule machine learning for MSI
Cameron Shedlock (until 14:00)
Mass spectrometry imaging returns large dimensionally complex datasets. Traditional analysis in imaging utilizes a mindset focused on target molecule identification that parses data with a narrow view of molecular exploration. These data analysis methods are specifically focused on exploring differences between a traditional organic acid matrix when compared to using nanoparticles for MSI, which results in very different ionization of small molecules. Analysis methods have taken a shotgun approach using both supervised and unsupervised machine learning to reveal critical trends in MSI datasets. A workflow is being prepared which enables select regions of interest to be compared using powerful machine learning algorithms to offer a holistic approach to data analysis and class comparison.
Mass spectrometry imaging using gold nanoparticles
Kate Stumpo, PhD
Mass spectrometry imaging (MSI) is a powerful analytical method for the simultaneous analysis of hundreds of compounds within a biological sample. Despite the broad applicability of this technique, there is a critical need for advancements in methods for small molecule detection. Some molecular classes of small molecules are more difficult than others to ionize, e.g., neurotransmitters (NTs). The chemical structure of NTs (i.e., primary, secondary, and tertiary amines) affects ionization and has been a noted difficulty in the literature. In order to achieve detection of NTs using MSI, strategies must focus on either changing the chemistry of target molecules to aid in detection or focus on new methods of ionization. This presentation will introduce a new method of ionization, using gold nanoparticles (AuNPs), and the bigger picture of NPs for MSI.