A place to put other resources found online. (excuse the mess while I organize this)
Videos:
- Brett Phinney UC Davis Proteomics Online 2d Short Course - I did one of these btw
- Other Brett videos
- David Tabb - often have slides in comments, ex. proteomics for clinical biomarkers
- Matt Padula - all things mass spec and proteomics
- May Institute - Stats!
- Mass Spec Everything w/Ben Katz
- Requisite flying ion video, but no dubstep - Stellar video; skip first minute or so
- Thermo Fisher Orbitrap Fusion Lumos Tribrid Mass Spectrometer
- Agilent Q-TOF Mass Spectrometer
- SCIEX QTRAP Mass Spectrometer
Great (Not So) British Proteomics Bake Off Videos
Blogs (proteomics):
- Orsburn Blog - Proteomics News - check out “Useful Stuff!” sidebar
- Phil Wilmarth blog/repo - it is both, but you can read the blog here and navigate the repo here. There are tutorials, vignettes, and slide decks throughout. For re-analysis I recommend the LFQ re-analysis of my sea lion urine data, and the re-analysis of Beynon data.
- Ron Beavis website - with all sorts of things (Main Site), specifically his unofficial dataset annotation
Tutorial/Overview Papers:
- The Anatomy and Taxonomy of Protein Structure by Jane S. Richardson
- An Introduction to Mass Spectrometry-Based Proteomics (Shuken 2023)
- Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry (Jiang et al. 2024) (or here with maybe easier section navigation)
- A beginner’s guide to mass spectrometry–based proteomics (Sinha and Mann 2020)
- Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications (Pino 2020)
- Technical advances in proteomics: new developments in data-independent acquisition (Hu et al, 2016)
- Instrumentation at the Leading Edge of Proteomics (Peters-Clarke et al. 2024)
- Posterior error probabilities and false discovery rates: two sides of the same coin (Kall 2008)
- Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases (Kall 2008)
- Nature Article: s41580-020-0231-2
QC Resources
- MacCoss QC
- RapidQC
- Our QC
- QC framework with Core for Life alliance (Chiva 2021 and 2024)
- Springer Article: 10.1186/s12910-026-01409-3
History:
- Ours
- Dayhoff review
- The history and philosophy of science: a taxonomy by Ernan McMullin, 1970
- The origin of the single-letter code for the amino acids - Dr. Margaret Oakley Dayhoff
- The backstory behind the FASTA format
- Hunt Lab Guide to de novo
Other fav papers:
- WOMBAT-P
- On the excessive use of coefficient of variation as a metric of quantitation quality in proteomics (Ivanov et al. 2023)
- The “blood” paper dump
- mRNA v Protein
- 30 essays on biology
Other blogs of note (not proteomics):
- Vince Buffalo (@vsbuffalo) Evolutionary genetics blog
- Andrej Karpathy (@karpathy) AI blog
- Daniël Lakens (@lakens) The 20% Statistician