Proteomics: Everything you always wanted to know but were afraid to ask

The videos and slides below, from the 2012 Proteomics Workshop, provide a working knowledge of what proteomics is and how it can accelerate biologists’ and clinicians’ research. The focus of the workshop is on the most important technologies and experimental approaches used in modern mass spectrometry (MS)-based proteomics.

Videos from day one cover: 1) the essentials of the technology; 2) the most important classes of proteomics experiments and the specific sample requirements for each; 3) the software for proteomic data analysis and its proper use; 4) quantitative MS approaches applicable to global proteome and post-translational modification (PTM) analyses, including metabolic labeling methods, chemical labeling approaches, and label-free methods; and 5) the basics of targeted, hypothesis-driven MS using multiple reaction monitoring MS.

Day two of the workshop used case studies to focus on the data produced by each of the key classes of proteomics experiments described on day one (i.e., global proteomics, global PTM analysis, affinity proteomics, and targeted, hypothesis-driven proteomics). Data analysis approaches and statistical methods key to confident assignment of true differential proteins/peptides were presented. Finally, a primer on useful tools for annotation of the MS results and how to use these tools to extract knowledge, organize into pathways, etc., was given.

Day 1: Technology, samples, and experiments

   12/10/12 Fundamentals of peptide and protein mass spectrometry Steve Carr PDF Video
   12/10/12 Interpretation and automated analysis of proteomic data Karl Clauser PDF Video
   12/10/12 Sample prep for proteomics Monica Schenone PDF Video
   12/10/12 Quantitative methods in proteomics Jake Jaffe PDF Video
   12/10/12 Essentials of targeted hypothesis-driven MS Hasmik Keshishian PDF Video

Day 2: From lists to biological knowledge

   12/11/12 Applications of affinity proteomics and quantitative, global proteomics Namrata Udeshi PDF Video
   12/11/12 Global posttranslational modification analysis Philipp Mertins PDF Video
   12/11/12 Statistical methods of data analysis DR Mani PDF Video
   12/11/12 Applications of targeted MS in biology and medicine Susan Abbatiello PDF Video
   12/11/12 Use of Web-based annotation tools for bioinformatic analysis of proteomics data Kaspar Lage PDF Video