High Level Intros to Metabolomics and Proteomics
This would probably be the most useful section for an intro class...
Small Molecule Metabolites: Discovery of Biomarkers and Therapeutic Targets (Qiu et al., 2023)
Comprehensive review of metabolomics focused on how small molecule metabolites can serve as biomarkers for disease diagnosis, prognosis, and treatment monitoring. Great for seeing how mass spectrometry-based profiling maps metabolic pathways to disease mechanisms.
Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry (Jiang et al., 2024)
Detailed handbook-style overview of the full bottom-up proteomics workflow, from protein extraction and digestion to LC-MS, data acquisition, and biological interpretation. Excellent “big picture” resource if you’re planning or interpreting proteomics experiments.
An Introduction to Mass Spectrometry-Based Proteomics (Shuken, 2023)
A very accessible guide to untargeted bottom-up proteomics with data-dependent acquisition. Walks through sample prep, peptide fragmentation, and protein quantification with clear figures and explanations, ideal as a first read in the area.
Hefty example of application and multi-omics
A Protein Network Map of Head and Neck Cancer Reveals PIK3CA Mutant Drug Sensitivity (Swaney et al., 2021)
High-content protein–protein interaction map in head and neck cancer that links specific PIK3CA mutations to HER3-targeted drug sensitivity. A concrete example of how proteomics, networks, and genomics combine to inform precision oncology.
More Operational and Instrumentation Usage and Operation
An Introduction to the Basic Principles and Concepts of Mass Spectrometry (Faull et al., 2008)
Classic introduction to the physics and hardware of mass spectrometry: ionization (ESI, laser desorption), mass analyzers (TOF, quadrupole, ion traps, Orbitrap), and detectors. Ideal if you want to truly understand what’s happening inside the instrument.
Model-Based Discovery of Circulating Biomarkers (Vogelsang et al., 2011)
Describes a model-based approach to discovering circulating protein biomarkers using tissue and cell culture systems instead of only direct serum profiling. Helpful for understanding how experimental design and quantitative proteomics link to clinically relevant markers.