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
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 fusion lumos https://www.thermofisher.com/order/catalog/product/FETD2-10002?SID=srch-srp-FETD2-10002 agilent q-tof https://www.youtube.com/watch?v=W-DRL-V2Rkg sciex q-trap https://www.youtube.com/watch?v=VUmcxNLHu4Y
Great (Not So) British Proteomics Bake Off Videos PAW Pipeline - https://www.youtube.com/watch?v=ycRccM1myDE MetaMorpheus - https://www.youtube.com/watch?v=aM9c-weYBng
Blogs (proteomics):
Orsburn blog (check out “Useful Stuff!” sidebar - https://proteomicsnews.blogspot.com/
Phil Wilmarth blog/repo - it is both, but you can read blog here https://pwilmart.github.io/blog/ and navigate repo here https://github.com/pwilmart/Start_Here. There are tutorials, vignettes, and slide decks throughout. For re-analysis I recommend the LFQ re-analysis of my sea lion urine data (https://github.com/pwilmart/Sea_lion_urine_SpC), and the re-analysis of Beynon data https://github.com/pwilmart/Mammalian_sperm_PXD003164.
Ron Beavis website with all sorts of things (https://www.somecrazyblogger.org/a/index), specifically his unofficialy dataset annotation https://www.somecrazyblogger.org/a/tweets?s=pxd
Tutorial/Overview Papers:
The Anatomy and Taxonomy of Protein Structure by Jane S. Richardson
Shuken 2023 - An Introduction to Mass Spectrometry-Based Proteomics https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00838
Jiang et al. 2024 - Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry https://pubs.acs.org/doi/10.1021/acsmeasuresciau.3c00068 (or here with maybe easier section navigation https://jessegmeyerlab.github.io/proteomics-tutorial/ )
Sinha and Mann 20020 - A beginner’s guide to mass spectrometry–based proteomics https://portlandpress.com/biochemist/article/42/5/64/226371/A-beginner-s-guide-to-mass-spectrometry-based
Pino 2020 - Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications https://portlandpress.com/biochemsoctrans/article/48/5/1953/226710/Emerging-mass-spectrometry-based-proteomics?searchresult=1
Hu et al, 2016 - Technical advances in proteomics: new developments in data-independent acquisition https://f1000research.com/articles/5-419
Peters-Clarke et al. 2024 - Instrumentation at the Leading Edge of Proteomics https://pubs.acs.org/doi/10.1021/acs.analchem.3c04497
Kall 2008 - Posterior error probabilities and false discovery rates: two sides of the same coin https://pubmed.ncbi.nlm.nih.gov/18052118/
Kall 2008 - Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases https://pubs.acs.org/doi/10.1021/pr700600n
MacCoss QC RapidQC Our QC Chiva 2021 and 2024 QC framework with Core for Life alliance (https://coreforlife.eu)
History
Ours
Dayhoff review
The history and philosophy of science: a taxonomy by Ernan McMullin, 1970
The backstory behind the FASTA format https://youtu.be/7LA0IKsVloU
Other fav papers:
WOMBAT-P https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00636
Ivanov et al. 2023 - On the excessive use of coefficient of variation as a metric of quantitation quality in proteomics https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/full/10.1002/pmic.202300090
The “blood” paper dump
mRNA v Protein https://www.mcponline.org/article/S1535-9476(23)00098-1/fulltext https://www.nature.com/articles/s41576-020-0258-4
Other blogs of note (not proteomics):
Vince Buffalo (@vsbuffalo) Evolutionary genetics blog
Andrej Karpathy (@karpathy) AI blog
Daniël Lakens (@lakens) The 20% Statistician