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
Timeline
| Day 1 | Day 2 | Day 3 | |
|---|---|---|---|
| 9:00 AM-10:00 AM | Introduction to Proteomics and Protein Mass Spectroscopy (Lecture) | Introduction to Proteomics Data processing/Spectronaut (Lecture) | Data Analysis - Participant Samples (Lecture/Hands-On) (con’t) |
| 10:00 AM-11:00 AM | Tissue/Cell sample lysis and preparation for digestion (hands on) | Lecture continued, Proteomics Data Processing practice data sets (Lecture/hands on) | Data Analysis - Participant Samples (Lecture/Hands-On) (con’t) |
| 11:00 AM-12:00 PM | Tissue/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 PM | Break | Break | Closing Group Lunch |
| 1:00 PM-2:00 PM | Instrument Preparation, pressure digestion 2 (hands on) | Figure preparation for data presentation from (hands on) | |
| 2:00 PM-3:00 PM | Post digestion sample purification | Spectronaut processing of Participant Samples (hands on) | |
| 3:00 PM-4:00 PM | Sample running on Mass spec. (hands on) | Data Processing/Analysis Open discussion |