Useful Links
Learning and Resources
Mass Spec and Proteomics
Mass Spec Pro, resource for basics about mass analyzers and other fundamental concepts
UniProt, high-quality, comprehensive, and freely accessible resource of protein sequence and functional information
PhosphoSitePlus, information about protein post-translational modifications (PTMs), e.g., phosphorylation, acetylation
Human Protein Atlas, via antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology
Cell Surface Protein Atlas, mass spectrometry-derived information about the cell surface protein repertoire (aka the surfaceome)
News in Proteomics Research blog by Dr. Ben Orsburn
An Introduction to Mass Spectrometry-Based Proteomics by Steven Shuken in JPR
Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry
Tutorials from David Tabb on YouTube
SUMS Mass Spec Fundamentals Seminars, including a glycoproteomics seminar from Nick
Videos from Mass Spec Summer School hosted by National Center for Quantitative Biology of Complex Systems (NCQBCS)
Glycoproteomics and Glycobiology
Essentials of Glycobiology, 4th Edition, freely available and widely recommended textbook
Nobel Prize lecture: Dr. Carolyn Bertozzi, Nobel Prize in Chemistry 2022
GlySpace Alliance, efforts from Glyco@Expasy (Swiss), GlyGen (US), and GlyCosmos (Japan)
GlyCosmos, web portal aiming to integrate the glycosciences with the life sciences
GlyComb, repository for glycoconjugate information, including glycopeptides, glycoproteins, glycolipids and glycosides
GlycoEpitope, information about carbohydrate antigens, ie, glycoepitopes, and antibodies
GlyGen, data integration and dissemination project for carbohydrate and glycoconjugate related data
GlyTouCan, the Glycan Repository
Glyco@Expasy, web-based glycoinformatics resources
Glycoinformatics Consortium (GLIC), a centralized source software repository for glycoscientists
GlyConnect, knowledgebase of glycoproteins spanning protein, glycosite and glycan information
Glycopedia, e-chapters on basic, intermediary and advanced topics of glycoscience
UniCarb-DB, glycomics MS database and repository
UniLectin, unified exploration platform for manuall curated and predicted lectins
GlycoShape, glycan structure database
Minimum Information Required for A Glycomics Experiment (MIRAGE)
Glycomics Institute of Alberta Educational Resources
Glycoinformatics videos on Swiss Institute of Bioinformatics YouTube channel
Institute for Glycomics at Griffith University
Coding and Data Analysis
Mass Spec Coding Club by Dr. Michael Marty on GitHub
Online R learning for applied statistics by Dr. Chenxin Li on GitHub
Quick data visualization using R by Dr. Chenxin Li on GitHub
CSMSL by Dr. Derek Bailey and Dr. Dain Brademan on GitHub
Glycosylator, a Python framework for the rapid modeling of glycans
GlyPy, Glycan Analysis and Glycoinformatics Library for Python from the Zaia lab
GlycoGlyph, open source glycan drawing and naming tool driven by JavaScript
DrawGlycan-SNFG, render glycans and glycopeptides with fragmentation info using the Symbolic Nomenclature for Glycans
FragPipe and MSFragger from the Nesvizhskii lab
MetaMorpheus from the Smith lab
Sage from Dr. Michael Lazear
Skyline ecosystem from the MacCoss Lab
Swiss Institute of Bioinformatics YouTube channel
Data Visualization, Points of View column from Nature Methods
Other
Inkscape, a powerful, free design tool
Bioicons, a free library of open-source icons for scientific illustrations using vector graphics software
Funding Opportunities, compiled and maintained by Johns Hopkins University
Research Culture: Why every lab needs a handbook, eLife 2023
How to organize your lab purchases and inventory, Nature 2023
Organizo, free organizational tools and more for scientists
Guide to a Postdoc from Dr. Ubadah Sabbagh, for "how to find, apply for, and choose a postdoc"
For Prospective PhD Students by Dr. Daniel Gonzales
Twelve Rules for Science (Yates Lab Version) by John Yates in JPR
Cell Mentor by Cell Press
Electronic Lab Notebook Comparison Matrix from the Longwood Medical Area Research Data Management Working Group
Scholar Googler by Ryan Morin to create word clouds from Google Scholar pages
Females in Mass Spectrometry (FeMS), community-led initiative to create a support network for women in the field of mass spec
Video of speech from Prof. Carolyn Bertozzi about diversity of thought in scientific breakthroughs
Societies
American Society for Mass Spectrometry (ASMS)
American Society for Biochemistry and Molecular Biology (ASBMB)
Human Proteome Organization (HUPO)
Society for Glycobiology (SFG)
Pacific Northwest Mass Spectrometry Discussion Group (PacMass)
American Association for Cancer Research (AACR)
Society for Immunotherapy of Cancer (SITC)
American Chemical Society (ACS)
ACS Division of Analytical Chemistry (ACS ANYL)
ACS Division of Carbohydrate Chemistry & Chemical Glycobiology (ACS Carb)
Conferences of interest
Conferences from Pastel BioScience
Upcoming Glyco Conferences by the Willis Glycobiology Lab
Mass Spec and Proteomics
Lake Arrowhead Conference on Mass Spectrometry, Lake Arrowhead, CA, Jan. 12 - 14, 2024
ASMS Sanibel Conference, St. Petersburg, FL, Jan. 21 - 24, 2024
Lorne Proteomics Symposium, Mantra Lorne, Victoria, Australia, Jan. 31 - Feb. 1, 2024
PITTCON, San Diego, CA, Feb. 24 - 28, 2024
US HUPO, 2024: Bridging ‘Omics to Function, Portland, OR, March 9 - 13, 2024
Single-Cell Proteomics, Boston, MA, May 28 - 29, 2024
ASMS Annual Meeting, 72nd Conference, Anaheim, CA, June 2 - 6, 2024
NCQBCS Mass Spec Summer School, Madison, WI, July 8 - 11, 2024
UPPCON, 2024 Darmstadt, Germany, TBD
International Mass Spectrometry Conference (IMSC), Melbourne, Australia, August 17 - 23, 2024
ASMS Asilomar Conference, 2024 TBD
ASMS Fall Workshop, 2024 TBD
HUPO World Congress, Dresden, Germany, Oct. 20 - 24, 2024
Advancing Molecular Structure (AMS), 2025 (?) TBD
International symposium on proteomics in the life sciences, Broad Institute, Cambridge, MA, August 17 - 21, 2025
Glyco
Canadian Glycomics Symposium (associated with Warraen Workshop), Edmonton, Canada, May 27 - 29, 2024
Warren Workshop in GlycoBioinformatics (associated with CGS), Edmonton, Canada, May 27 - 29, 2024
Mucins in Health & Disease, Gothenburg, Sweden, June 17 - 20, 2024
Australasian Glycoscience Symposium, Wellington, New Zealand, August 27 - 30, 2024
Society for Glycobiology Annual Meeting, Amelia Island, FL, Nov 10 - 13, 2024
Glycobiology Gordon Research Seminar (and associated GRC), Tuscany, Italy, March 22 - 23, 2025
Glycobiology Gordon Research Conference (and associated GRS), Tuscany, Italy, March 23 - 27, 2025
Chemical Biology, Cancer, and More
Volcano Conference on Chemical Biology, Eatonville, WA, Feb. 23 - 25, 2024
ASBMB Annual Conference, San Antonio, TX, March 23 - 26, 2024
AACR Annual Conference, San Diego, CA, April 5 - 10, 2024
SITC Annual Conference, Houston, TX, Nov. 6 - 10, 2024
Journals we frequent
This is not a comprehensive list, but where we find ourselves doing a lot of reading (and our shorthand for them in the group):
Journal of Proteome Research (JPR)
Journal of the American Society for Mass Spectrometry (JASMS)
ACS Chemical Biology (ACS Chem Bio)
Molecular & Cellular Proteomics (MCP)
Journal of Biological Chemistry (JBC)
Proceedings of the National Academy of Sciences (PNAS)
Cell Chemical Biology (Cell Chem Bio)
Nature Chemical Biology (Nat Chem Bio)
Nature Communications (Nat Comms)
UW related links
UW Department of Genome Sciences
Biological Physics, Structure, and Design Program (BPSD) at UW
Molecular and Cellular Biology (MCB) Program (UW, Fred Hutch)
Molecular Engineering & Sciences Institute (MolES) at UW
Cancer Consortium (UW, Fred Hutch, Seattle Children's)
The Chemistry Graduate Club at UW
Other UW Resources
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