Useful Links

Mass Spec and Proteomics

• University of Washington's Proteomics Resource (UWPR)

• 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

• Symbol Nomenclature for Glycans (SNFG) (with update)

• 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

• National Center for Functional Glycomics

• 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

• Carbohydrate-Active enZYmes Database (CAZy)

• 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)

• O-GlcNAc Database

• N-GlycositeAtlas

• NetOGlyc4.0 and related resources

• GlycoDomainViewer

• Complex Carbohydrate Research Center (CCRC) at UGA

• Glycomics Institute of Alberta Educational Resources

• Glycoinformatics videos on Swiss Institute of Bioinformatics YouTube channel

• Institute for Glycomics at Griffith University

• IonSource Glyco-Protein Navigation Page

• NIST Glyco Mass Calculator

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

• Open Researcher and Contributor ID (ORCID)

• 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

• How to Pick a Graduate Advisor by Dr. Ben Barres

• 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

• NIH Standard Due Dates

• Blog about NIH paylines

• 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

American Society for Mass Spectrometry (ASMS)

American Society for Biochemistry and Molecular Biology (ASBMB)

Human Proteome Organization (HUPO)

US 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 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

This is not a comprehensive list, but where we find ourselves doing a lot of reading (and our shorthand for them in the group):

Analytical Chemistry (AC)

Journal of Proteome Research (JPR)

Journal of the American Society for Mass Spectrometry (JASMS)

ACS Central Science

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 Biotechnology (NBT)

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)

Glycobiology

eLife

bioRxiv pre-print server

ChemRxiv pre-print server

UW Department of Chemistry

UW Department of Biochemistry

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

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