Short Courses


Short courses are offered immediately preceding the conference. All courses are also located at the Westin Seattle (conference venue). Short Course enrollment is open to all, conference registration is not required. To register for a course, use the Conference > Registration pages. 


Half-day courses on Sunday, March 8

Tuition for each half-day course: Member $150; Non-member $200; Student or Post-doc Member $125; Student or Post-doc Non-member $150


Two-day course on Saturday and Sunday, March 7 & 8

Tuition: Member $350; Non-member $450; Student or Post-doc Member $250; Student or Post-doc Non-member $350


Short Course Descriptions

Cross-Linking Mass Spectrometry: Practical Uses in Studying Protein Interactions and Structures

Sunday morning, 9:00 am - 12:00 pm
Instructors: Lan Huang (University of California, Irvine) and Robert Chalkley (University of California, San Francisco)

Protein-protein interactions are fundamental to the assembly, structure and function of protein complexes. Aberrant protein interactions can have drastic impacts on cellular functions and thus lead to various human diseases. Mapping protein interactions and their binding interfaces in living cells is critical not only for understanding protein function, but also for therapeutic interventions. Cross-linking mass spectrometry represents a powerful and emergent technology which possesses unparalleled capabilities for studying protein interactions. The identification of cross-linked peptides by mass spectrometry provides direct molecular evidence describing the physical contacts between and within proteins. This information can be used for generating experimentally derived protein interaction network topology maps and for computational modeling to establish architectures of large protein complexes. This course will cover basic principles and practical uses of various cross-linking mass spectrometry approaches for studying protein interactions and structures. Specially, we will discuss about 1) sample preparation; 2) experimental workflows with conventional and MS-cleavable cross-linking reagents; 3) data analysis for identifying cross-linked peptides; 4) result interpretation, validation and usage. Register for this course, go to Conference > Registration.



Design and Analysis of Quantitative Proteomic Experiments: Introduction to Statistical Methods and Practical Examples using Skyline, R and MS Stats

Two-day Course, Saturday and Sunday, 9am-4pm each day
Instructors: Meena Choi (Northeastern University), Brendan MacLean (University of Washington), Birgit Schilling (Buck Institute for Research on Aging), and Olga Vitek (Northeastern University)

This 2-day course will discuss details of statistical experimental design of quantitative mass spectrometry-based proteomic experiments, and the analysis of the acquired data with Skyline and MSstats. It is designed for experimentalists looking to enhance their statistical and data analysis skills, and will contain both lectures and practical hands-on exercises.

First, the course will discuss the fundamental concepts of statistical experimental design, that are key for designing reproducible investigations. Second, the course will introduce the open-source software Skyline. In particular, we will demonstrate the use of Skyline for proteome-wide profiling of samples with label-free shotgun data-dependent spectral acquisition (DDA), and the process of building libraries from DDA spectra to analyze profiling experiments with data-independent acquisition (DIA). The participants will practice these analysis steps using example datasets. Finally, we will discuss the principles of statistical inference, including summarization of protein abundances from multiple spectral features, derivation of confidence intervals for fold changes, and testing proteins for differential abundance. The participants will perform hands-on analyses of the example datasets with open-source software R and MSstats.

The participants should bring their own laptop computers. Instructions regarding downloading and installing the software will be provided prior to the course. Register for this course, go to Conference > Registration.


Precision Medicine: From Biomarker Discovery to FDA

Sunday morning, 9:00 am - 12:00 pm
Instructors: Andy Hoofnagle (University of Washington), Michael MacCoss (University of Washington), Jennifer Van Eyk (Cedars-Sinai Medical Center), and John Yates (The Scripps Research Center)

Overview: In this half day course, we will explore the path from discovery of potential protein biomarkers to their clinical implementation.

Background: Over the last decades the technical processes and experimental requirements to discover high value candidate protein biomarkers has matured. This includes the recognition that exploiting fundamental protein characteristics (e.g. disease-induced-conformational or post-translational modification differences) may increase disease specificity. At the same time, higher throughput workflows are being used in broad based protein quantitation of large number of individual patent’s biofluid samples (e.g. plasma and CSF) to maximize an understanding of biological and pathological diversity in the initial discovery steps.  These high-content, high-throughput approaches also have a key role to play in population and epidemiology studies that provide the large data sets required for precision medicine.

Simultaneously, the analytics required for incorporating mass spectrometry-based protein assays into the clinical chemistry laboratory are being addressed.  This is being driven, in part, by examples in clinical chemistry of analytical improvements of some routinely measured analytes by moving them from currently used immunoassay to mass spectrometry-based protein assay.  Although possible it is still challenging to develop a single or small protein biomarker panel as a laboratory developed test or a regulatory FDA cleared assay in the clinic. Yet, complex protein assays (e.g. large protein/proteoform multiplexes) that may reflect broader pathological diversity are often proposed as part of precision medicine. The path from discovery of potential protein biomarkers to their clinical implementation and the impact on precision medicine is still evolving. Mass spectrometry has a role to play each step along the way.

Course structure: We have brought together four investigators to highlight the progress in clinical proteomics. As well, we will provide a forum for conversation about solutions to increase the number of established biomarker assays into the clinical arena and implementation of precision medicine.  Conference > Registration

  • John Yates, III: Novel approaches for conformational protein diagnostics.
  • Mike MacCoss: High throughput plasma discovery for maximizing success.
  • Andy Hoofnagle: The reality of mass spectrometry targeted proteins assays clinical chemistry.
  • Jenny Van Eyk: Moving from discovery of protein assays into FDA-clinical approved trials.
  • Panel discussion.

Stable and Transient Protein-Protein Interactions: Discovery, Quantification and Validation

Sunday afternoon, 1:00 - 4:00 pm
Instructors: Ileana Cristea (Princeton University) and Alexey Nesvizhskii (University of Michigan)

Dynamic protein interactions carry out the majority of the processes within a cell, including cellular responses to environmental stimuli and pathogens. Isolation of protein complexes and characterization of protein-protein interactions provide critical insights into their biological functions. An ideal isolation would maintain the protein-protein interaction or the protein assembly as close as possible to the original state in the cell. Therefore, proteomic-based methodologies that can access stable and transient interactions are invaluable for diverse studies, such as those of cell cycle or pathogen infection that require characterization of temporal and spatial protein interactions. This course will cover fundamental and practical aspects of studying protein interactions. Topics discussed will include:

  • protein function considerations for workflow design,
  • cell lysis methods for efficient protein extraction,
  • critical choices for optimizing an immunoaffinity purification experiment, including resin type and speed of isolation,
  • denaturing and non-denaturing methods of eluting captured protein complexes,
  • assessing the specificity of interactions using bioinformatics approaches, metabolic labeling with stable isotopes, or peptide labeling with isobaric tags,
  • challenges for assessing direct or indirect interactions,
  • aspects of data analysis and generation of interaction networks.

As we will gradually cover fundamental and more advanced topics concerning protein interactions, the course will be appropriate for both beginner- and advanced-level participants. Detailed protocols will be provided, and enough time will be set aside for discussing these topics from either a mass spectrometry or biology perspective. Register for this course, go to Conference > Registration.


New Course Ideas for 2021?