RI-INBRE Workforce Development Training (WDT) Summer 2023 Syllabus

Module Title: Proteomics

Instructor: Joseph Schrader, PhD

Course Overview

This WDT Module aims to train students in proteomic analysis using the Sequential Acquisition of All Theoretical Mass-spectra (SWATH-MA) method. The module will include lectures on protein MS methods, hands-on laboratory experience with sample prep and analysis, and post-run data processing/presentation. The module is intended for students new to proteomics data generation and analysis and will provide sufficient background for students to pursue further training in these and related research areas. This module also complements the separate module on genomic data generation and sequencing. The module will be completed over 2.5
days and participants who complete the module will receive an RI-INBRE Certificate of Completion.

Learning Outcomes

  • Learn background on protein-MS methods sufficient to understand basic sequencing
    techniques and terminology.
  • Prepare animal tissue samples for proteomic analysis on a Thermo Fisher Exploris 240
    Orbitrap mass spectrometer
  • Learn basic operation of mass spectrometer.
  • Process LC-MS/MS data using hands-on learning modules, using both example data and
    (if time permits) data generated by the participants.
    o Total protein approach conversion
    o Disease model specific protein expression changes
  • Analyze proteomics data using established methods such as differential expression
    analysis and pathway analysis

Lab Report

Students will be expected to maintain detailed laboratory notes to include:

  • Sample preparation and digestion protocols
  • Data processing/analysis protocols (e.g., workflows, software used, etc.)
  • Results of bioinformatics analysis (differential expression, pathway analysis)

Resources Used in this Module:

  • Spectronaut Biognosys Manual
  • Standard Operating Procedure – Sample Preparation and MS operation
  • Lab Notebooks for Hands-On Analysis
  • Slide Decks for Lectures


 Day 1Day 2Day 3
9:00 AM-10:00 AMIntroduction to
Proteomics and
Protein Mass
Spectroscopy (Lecture)
Introduction to Proteomics
Data processing/Spectronaut
Data Analysis - Participant
Samples (Lecture/Hands-On)
10:00 AM-11:00 AMTissue/Cell sample
lysis and preparation
for digestion (hands
Lecture continued,
Proteomics Data Processing
practice data sets
(Lecture/hands on)
Data Analysis - Participant
Samples (Lecture/Hands-On)
11:00 AM-12:00 PMTissue/Cell sample
lysis and preparation
for digestion, pressure
digestion 1 (hands on)
Proteomics Data Processing
practice data sets
(hands on)
Frontiers in Bioinformatics
(Open Discussion)
12:00 - 1:00 PMBreakBreakClosing Group Lunch
1:00 PM-2:00 PMInstrument
Preparation, pressure
digestion 2 (hands on)
Figure preparation for data
presentation from (hands
2:00 PM-3:00 PMPost digestion sample
Spectronaut processing of
Participant Samples (hands
3:00 PM-4:00 PMSample running on
Mass spec. (hands on)
Data Processing/Analysis
Open discussion