Exploring proteomics, macrophage phenotyping, extracellular vesicles, and lipidômica. Notes on methods, papers, and the journey through biochemical research at FMRP-USP.
A walkthrough of my LC–MS/MS workflow for plasma proteomics: sample preparation, protein digestion, data acquisition with MaxQuant, and post-processing in R. Focusing on sample QC and normalization decisions that saved me months of troubleshooting.
Getting started with EV isolation and lipidomic profiling using the Matyash method. This post covers why lipids matter in cell communication, how I optimized my workflow, and lessons learned with plasma-derived vs. cell-culture EVs.
A brief breakdown of a key proteomics paper on macrophage phenotyping. What were the key findings? Which figure made me rethink my approach? Why macrophage subtypes matter in lipid metabolism and inflammation.
Reflections on starting my doctorate at FMRP-USP in Ribeirão Preto and the prospect of a research period in Calgary. Navigating international research, funding (FAPESP), and building collaborations across continents.
Tips on folder structures, naming conventions, and metadata tracking for large proteomics and lipidomics datasets. Why your future self will thank you for being obsessive about data organization today.
Lessons on multiple testing correction, effect sizes, and why p-values alone won't save you. Practical examples from my own analyses and how I learned to think more critically about statistical reporting.
Welcome to my academic notes. I'm Pedro Nobre Azevedo, a PhD candidate in Biochemistry at the Federal University of São Paulo's Graduate Program in Biochemistry (FMRP-USP, São Paulo, Brazil), focused on proteomics and cell biology.
This blog documents my research journey: methods I've developed, papers that shaped my thinking, and reflections on the academic life. I write about proteomics, macrophage phenotyping, extracellular vesicles, lipidômica, and the tools I use daily (MaxQuant, R, Python, PyMOL).
Whether you're a fellow researcher, a curious student, or someone interested in how modern biochemistry works, I hope these notes offer value. Feel free to reach out for discussions, collaborations, or questions.