Table 1. Description of the Proteomics Training Curriculum.

Lectures and labs were paired to prepare the students for carrying out experiments independently. Quizzes administered after Module 2 and Module 5 tested understanding using free response short essay questions. Lab reports for Module 2 and Modules 3–4 were designed to give experience in writing manuscripts for scientific journals. In Module 6, Protein quantification techniques have been used by each student in their research internship, so the quiz and lab report were not administered.

Curriculum Components
Module 1: Introduction
Concepts: Foundations of Proteomics
Lab Exercise: Tour of Proteomics Core and Labs
Skills: Understand Background
Module 2: Accurate Mass Measurement and Peptide Mass Fingerprinting
Concepts: Theory of MALDI-TOF-MS, Proteolytic Digestion, Protein Identification using Peptide Masses
Lab Exercises: Identification of Standard Proteins, Saliva Profiling
Skills: MALDI Instrument Operation, Protein Denaturation, Tryptic Digestion, Peptide Extraction, Database Searching
Module 3: Protein Identification using Liquid Chromatography-Tandem Mass Spectrometry Peptide Sequencing
Concepts: Affinity Purification, Liquid Chromatography, Tandem Mass Spectrometry, In-Gel Digestion, Peptide Sequencing, Database Searching
Lab Exercise: Analysis of a Protein Complex
Skills: MALDI MS/MS Instrument Operation, LC-MS/MS Sample Submission, Immunoprecipitation, SDS-PAGE, In-gel Digestion, Database Searching with Tandem Mass Spectra
Module 4: Proteome Cataloging
Concepts: Extension of Protein Identification, Proteome Fractionation by Gel-Based or Chromatography-Based Methods, Application to Biomarker Discovery
Lab Exercise: GeLC-MS/MS and MuDPIT E. coli Proteome Catalogs
Skills: LC Operation, Fraction Collection, Comparison of Analytical Methods, Quantification of Proteins by Spectral Counting, Summarization of Complex Proteomics Data
Module 5: Post-Translational Modification Analysis
Concepts: Molecular Changes by Modification, Separation Techniques for Enrichment, Phosphoproteomic Profiling, Utility in Assessing Drug Response
Lab Exercise: Analysis of STAT Phosphorylation in K562 Cells
Skills: Selection of Proteolytic Enzymes Based on Protein Sequence, Affinity Purification of Modified Proteins, Manual Verification of Modification Sites
Module 6: Protein Quantification
Concepts: Label-Free Quantification, Relative Quantification using Chemical Labeling (iTRAQ) or Biological Labeling (SILAC), Multiple Reaction Monitoring, Stable Isotope-Labeled Standard Peptides, Biomarker Evaluation
Lab Exercise: Develop Assays to Quantify Cancer-Related Proteins
Skills: Assay Development for LC-MRM, Data Analysis