Short Courses

***This short course requires pre-registration and an additional fee. Click here for more details.*** Machine learning - and correspondingly, artificial intelligence - has become a dominant technology for data-intensive discovery in nearly all scientific domains. Today, almost all biomedical research employs machine learning techniques to derive new knowledge from complex biological data. This course will introduce the fundamentals of machine learning with a specific focus on the analysis of proteomics data, through a series of lectures and hands-on labs.

***This short course requires pre-registration and an additional fee. Click here for more details.*** Metabolites encompass molecular classes such as small bioactive molecules and lipids, and these molecules are directly linked to cellular processes, response to injury, progression to disease, and can serve as guiding markers of cell types and disease state. Notably, metabolomics measurements can provide direction insights into the function of genes and proteins, as well as cell states. Mass spectrometry imaging (MSI) is a dynamic and thriving arena of research that works to uncover the spatial biology of health and disease. The MSI field has advanced greatly over more than 25 years with diverse applications, and MSI is becoming an extremely popular method for performing spatial metabolomics (down to single-cell resolution). This course will be a combination of education on state-of-the-art MSI and discussion with MSI experts on state-of-the-art imaging studies. Lectures will include examples of sample preparation, instrumentation, and practical application of topics. First, sample preparation methods will be discussed, which include on-tissue chemical derivatization approaches. Next, state-of-the-art instrumentation will be presented followed by imaging study applications integrating spatial metabolomics data with (spatial) proteomics and (single cell) transcriptomics data from the same sample. Next, we will discuss workflows to increase biological information and interpretation by multimodal imaging strategies utilizing immunohistochemistry, optical, and microspectroscopies. These topics will be covered within a broad array of tissue microenvironments, species, and cells. Educational sessions on topics will be 50 minutes long followed by 20 minutes of class discussion. An electronic handbook of resources and items used in mass spectrometry imaging studies will be available to attendees. A goal is to educate and disseminate information on MSI to users familiar with 'Omics by other mass spectrometry methodology.

***This short course requires pre-registration and an additional fee. Click here for more details.*** This course will cover both theory and practice for analyzing quantitative proteomics data. The course will be a mixture of both "lecture" and "lab" portions. The "lectures" will discuss best practices, considerations, and pitfalls for interpreting label-free and labeled measurements, including those produced by DDA, DIA, PRM, TMT/iTRAQ, and SILAC methods. The "labs" will give students a chance to explore and analyze raw data from different instrument platforms with Skyline and other open source tools using Windows laptops that they either bring with them or have remote access to. While participants are highly recommended to bring their own computers to get the full experience, participants without Windows laptops will be able to join up as teams to analyze datasets. The goal of this course is to give students a foundation for how data analysis tools work and to build an intuition for what data analysis challenges lurk in their datasets. A portion of the class will be devoted to "office hours" where students will get a chance to discuss their specific quantitative proteomics challenges. Audience: proteomics researchers at all levels that want to learn what common proteomics data analysis tools/methods are doing, how they work, and where they break down.

***This short course requires pre-registration and an additional fee. Click here for more details.*** Chemoproteomics = chemical biology + proteomics. If that doesn't clear things up, this course is for you! Chemoproteomics leverages mass spectrometry-based proteomics to study the action of chemical probes (typically, small molecules) in biological systems, with the aim of identifying and developing chemical tools to explore biology and expand the "druggable proteome". This course will provide an introductory overview of chemoproteomics, exploring its methodologies, applications, and challenges. Participants will learn about the use of chemoproteomics in drug discovery, proteome-wide target identification, and emerging techniques for mass spectrometry-based phenotypic assays. By the end of the course, participants will have a solid understanding of the principles and applications of chemoproteomics.

***This short course requires pre-registration and an additional fee. Click here for more details.*** In our grant proposals, most of us think we need to dive right in explaining the details of how we are going to do very specific things and get really deep into the weeds of our projects way too soon. But to make sure our audience-the grant reviewers-will care about those details, we need to first paint the picture of WHY our project is so interesting and impactful, and teach them the layout of how to think about the experiments we've planned in the context of that potential impact. In this workshop, we will spend time thinking about and practicing strategies for crafting the WHY message and getting reviewers excited about our research questions. We will go over the importance of visuals to illustrate both the scientific questions/ideas, and the conceptual and practical organization of our experimental design. We will learn about current tools for scientific illustration that make creation of informative illustrations more accessible to all. Participants should come away from this workshop with ideas for crafting a grant proposal as a science communication piece, blending messaging about impact with targeted attention to details that maintain the links between why→what→how in a way that should help your reviewers understand and get excited about your proposal. Audience: Scientists who are newer to grant writing (e.g. grad or postdoctoral trainees, new principal investigators), or who have been feeling stuck in a rut with their grant strategy and want to take a fresh perspective on how they craft their proposals.

***This short course requires pre-registration and an additional fee. Click here for more details.*** This will be an interactive short course that dives into the broader reaches of proteomics technologies beyond academic research environments. The goal of this course is to build your scientific communication skills so that you can converse more effectively with colleagues, clients, regulators, and scientists who are not proteomicists. We will learn to identify key relationships, common value propositions, and common calls to action in these types of interactions. We will share experiences communicating with various proteomics-adjacent professionals, from venture capitalists to Congressmen. Finally, we will build a common vocabulary or language to use when describing proteomics, and a playbook for how to communicate the significance of proteomics to non-science professionals including those in finance, legal, government, regulatory affairs, and tech transfer. Audience: proteomics researchers looking to transition careers away from the bench or expand their networks