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)
Typical Protein Yields, from the Paulovich lab at the Hutch
Useful Numbers for Cell Culture, information for various sizes of cell culture dishes and flasks
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
Reddit thread on helpful Mass Spec Videos and Tutorials
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
NIH BioArt, 2,000+ free, high-quality vectors, icons, and brushes for science and medical art visuals
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
Compound Interest by Andy Brunning using easy-to-understand graphics to take a closer look at common chemical compounds
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. 17 - 19, 2025
ASMS Winter Conference, Sante Fe, NM, Jan. 23 - 26, 2025
PITTCON, Boston, MA, March 1-5, 2025
US HUPO, Philadelphia, PA, February 22 - 26, 2025
Americal Chemical Society Spring Meeting, San Diego, CA, March 23 - 27
AUS-Omics, Cairns, Queensland, Australia, May 18 - 21, 2025
Single-Cell Proteomics, Boston, MA, May 27 - 28, 2025
ASMS Annual Meeting, 73rd Conference, Baltimore, MD, June 1 - 5, 2025
Advancing Molecular Structure (AMS), Atlanta, Georgia, July 20 - 23, 2025
NCQBCS Mass Spec Summer School, Madison, WI, July 21-24, 2025
International symposium on proteomics in the life sciences, Broad Institute, Cambridge, MA, August 17 - 21, 2025
Americal Chemical Society Fall Meeting, Washington, DC, August 17 - 21
Dagstuhl Seminar on Computational Proteomics, Saarbrucken, Germany, August 24 - 29, 2025
ASMS Asilomar Conference, 2025 TBD
ASMS Fall Workshop, 2025 TBD (keep early November on your radar!) (Nick is co-organizer)
HUPO World Congress, Toronto, Canada, November 9 - 13, 2025
UPPCON, 2026 (?), TBD
International Mass Spectrometry Conference (IMSC), Lyon, France, August 22 - 28, 2026
Glyco
GlycoBioTec2025, Berlin, Germany, February 10 - 12, 2025
Glycobiology Gordon Research Seminar (and associated GRC), Tuscany, Italy, March 22 - 23, 2025 (Nick is co-organizer)
Glycobiology Gordon Research Conference (and associated GRS), Tuscany, Italy, March 23 - 27, 2025
AUS-Omics, Cairns, Queensland, Australia, May 18 - 21, 2025
Glyco27, Edmonton, Canada, May 25-30, 2025 (joint with 8th Canadian Glycomics Symposium)
16th Jenner Glycobiology and Medicine Symposium, Maynooth University, Ireland, June 11 - 13, 2025
Carbohydrates Gordon Research Seminar (and associated GRC), Holderness, NH, June 14 - 15, 2025
Carbohydrates Gordon Research Conference (and associated GRS), Holderness, NH, June 15 - 20, 2025
Beilstein Glyco-Bioinformatics Symposium 2025, Limburg, Germany, July 1 - 3, 2025 (Nick is co-organizer)
Carbohydrate Active Enzymes for Glycan Conversions GRS (and associated GRC), Andover, NH, July 19 - 20, 2025
Carbohydrate Active Enzymes for Glycan Conversions GRC (and associated GRS), Andover, NH, July 20 - 25, 2025
Society for Glycobiology (SFG) Annual Meeting, San Diego, CA, November 9 - 12, 2025
Chemical Biology, Cancer, and More
Volcano Conference on Chemical Biology, Eatonville, WA, Feb. 21 - 23, 2025
ASBMB Annual Conference, Chicago, IL, April 12 - 15, 2025
AACR Annual Conference, Chicago, IL, April 25 - 30, 2025
Bioorganic Chemistry Gordon Research Seminar (and associated GRC), Andover, NH, June 14 - 15, 2025
Bioorganic Chemistry Gordon Research Conference (and associated GRS), Andover, NH, June 15 - 20, 2025
SITC Annual Conference, National Harbor, MD, Nov. 5 - 9, 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 Systems (Cell Sys)
Molecular Cell (Mol Cell)
Cell Chemical Biology (Cell Chem Bio)
Nature Methods (Nat Methods)
Nature Chemical Biology (Nat Chem Bio)
Nature Communications (Nat Comms)
Science Advances (Sci Adv)
Science Translational Medicine (STM)
Molecular Omics (Mol Omics)
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
A safe and welcoming place for all, a message from President Ana Mari Cauce.
Husky Health and Well-being: all of UW-Seattle's health services in one place.
Office of Minority Affairs & Diversity works to increase and support diversity on our campus.
Disability Resources for Students ensures access and inclusion for students with disabilities.
Student Veteran Life, a group for student veterans, run by student veterans.
Leadership Without Borders works with and for undocumented students at UW.
Q Center, a resource center for "anyone with or without a gender or sexuality".
International Student Services advises UW students from other countries.
The Schmitz Hall Counseling Center offers a range of free services to UW students, including stress management workshops, individual and group counseling, and more! More at this page on Mental Health.
Student Legal Services offers confidential consultations for enrolled UW-Seattle and UW-Bothell students.
To report bias at UW, go to https://report.bias.washington.edu/submit ("reporter's name" not required).
SafeCampus is the University of Washington’s violence-prevention and response program that supports students, staff, faculty and community members in preventing violence.
Useful information to understand research funding
UNDERSTANDING INDIRECT COSTS AND FEDERAL RESEARCH FUNDING
Facilities & Administrative (F&A) Costs, AAMC (Association of American Medical Colleges)
Facilities & Administrative (F&A) Infographic, AAMC
Facilities & Administrative (F&A) Summary Document, AAMC
Indirect Costs 101, NIH Grants YouTube Channel
Great thread on the accounting and math of indirect costs, Jeremy Berg (former NIGMS director), Bluesky
Understanding the Real Costs of Research, AAMCtoday YouTube Channel, AAMC
Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates, Feb. 7, 2025, from Office of NIH Director (Memoli)
Indirect Costs at NIH, Stuart Buck, The Good Science Project
Perspective on IDC change from Sarah Tishkoff, PhD on Bluesky
Perspective on IDC change from Carl T. Bergstrom, PhD on Bluesky
Legislative Action Center, Federation of American Societies for Experimental Biology
Document from a legal team about NIH F&A measures, Ropes&Gray
Thoughts on the challenges of NIH block grants, Jeremy Berg (former NIGMS director), Bluesky
NIH in Your State, Impact of NIH funding across the USA, United for Medical Research
REPERCUSSIONS OF FEDERAL FUNDING AND ADMINISTRATIVE DECISIONS ON RESEARCH AND SCIENCE
Revised and Extended: What's Happening Inside the NIH and NSF, Derek Low, Science
The Continuing NIH/NSF Crisis, Part II, Derek Low, Science
The Continuing NIH/NSF Crisis, Part III: Indirect Costs, Derek Low, Science
AAMC Statement on Drastic Cuts to NIH-Funded Research, AAMC President/CEO David Skorton, MD, and CSO, Elena Fuentes-Afflick, MD
New NIH ‘Indirect Costs’ Funding Cuts Threaten Universities, Science, Bruce Y. Lee, Forbes
NIH Tosses Some Grant Applications from Minority Researchers, Maddie Khaw and Megan Zahneis, The Chronicle of High Education
Thoughts on the multiple federal actions by the executive branch with respect to science, research, and beyond, ButtonDown Blog
The NIH 6 months ago vs the NIH now, thread from Bridget McGann on Bluesky
Comments on actions surrounding F31-D fellowship applications, Bluesky
Thoughts on NIH F31 graduate student fellowships, DrugMonkey blog
Thread about cuts to NIH programs to increase diversity in the biomedical workforce, Jeremy Berg (former NIGMS director), Bluesky
Pages on Science and Policy and Current Administration, Science
Thread on impacts and damage to NIH from mass firings on February 14, Jeremy Berg (former NIGMS director), Bluesky (Feb 15, 2025)
THINGS YOU CAN DO AND OTHER RELATED RESOURCES
‘Despair is not an option’ — how scientists can help protect federal research, Gretchen T. Goldman, Nature
How basic research leads to biomedical discovery, article about Gila monsters and Ozempic, Katie Dangerfield, Global News
How to protect democracy, protectdemocracy.org
Save NIH and NSF Research Funding with 5calls
Stand Up And Be Counted, Derek Low, Science
Scientific institutions have a long history of anticipatory obedience, Philip Ball, Chemistry World
A Letter From a Brazilian Postdoc Who Survived the Bolsonaro Years, Reddit
Surviving Academia in 2025 and Beyond: A Must-Read Guide for Early Career Researchers, Ruopeng An, LinkedIn
Banner photo credit: Nick Riley
