1 / 27

Proteomics Informatics (BMSC-GA 4437)

Proteomics Informatics (BMSC-GA 4437). Instructor David Fenyö Contact information David@FenyoLab.org http://fenyolab.org/presentations/Proteomics_Informatics_2013/. Proteomics Informatics – Learning Objectives.

avak
Download Presentation

Proteomics Informatics (BMSC-GA 4437)

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Proteomics Informatics (BMSC-GA 4437) Instructor David Fenyö Contact information David@FenyoLab.org http://fenyolab.org/presentations/Proteomics_Informatics_2013/

  2. Proteomics Informatics – Learning Objectives Be able analyze a proteomics data set and understand the limitations of the results.

  3. Proteomics Informatics – Overview of Proteomics (Week 1) • Why proteomics? • Bioinformatics • Overview of the course

  4. Motivating Example: Protein Regulation Geiger et al., “Proteomic changes resulting from gene copy number variations in cancer cells”, PLoS Genet. 2010 Sep 2;6(9). pii: e1001090.

  5. Motivating Example: Protein Complexes Alber et al., Nature 2007

  6. Motivating Example: Signaling Choudhary & Mann, Nature Reviews Molecular Cell Biology 2010

  7. Bioinformatics Biological System Experimental Design Samples Measurements Raw Data Data Analysis Information

  8. Mass Spectrometry Based Proteomics Lysis Fractionation Digestion Mass spectrometry Peak Finding Charge determination De-isotoping Integrating Peaks Searching MS Identified and Quantified Proteins

  9. Proteomics Informatics – Overview of Mass spectrometry (Week 2) Ion Source Mass Analyzer Detector intensity mass/charge

  10. Proteomics Informatics – Overview of Mass spectrometry (Week 2) Ion Source Mass Analyzer 1 Frag-mentation Mass Analyzer 2 Detector y b

  11. Proteomics Informatics – Overview of Mass spectrometry (Week 2) LC Ion Source Mass Analyzer 1 Frag-mentation Mass Analyzer 2 Detector intensity intensity intensity intensity intensity intensity intensity intensity intensity intensity intensity intensity intensity intensity intensity mass/charge mass/charge mass/charge mass/charge mass/charge mass/charge mass/charge mass/charge mass/charge mass/charge mass/charge mass/charge mass/charge mass/charge mass/charge Time

  12. Proteomics Informatics – Analysis of mass spectra: signal processing, peak finding, and isotope clusters (Week 3) Intensity m/z

  13. Proteomics Informatics – Protein identification I: searching protein sequence collections and significance testing (Week 4)

  14. Proteomics Informatics – Protein identification II: search engines and protein sequence databases (Week 5)

  15. Proteomics Informatics – Protein identification III: de novo sequencing (Week 6) Amino acid masses 762 100 875 [M+2H]2+ % Relative Abundance 633 292 405 534 1022 260 389 504 907 1020 663 778 1080 0 250 500 750 1000 m/z Mass Differences Sequences consistent with spectrum

  16. Proteomics Informatics – Protein identification IV: spectrum library searching  (Week 7) Spectrum Library Lysis Fractionation Digestion LC-MS/MS Pick Spectrum Repeat for all spectra MS/MS Compare, Score, Test Significance Identified Proteins

  17. Proteomics Informatics – Protein quantitation I: metabolic labeling (SILAC), chemical labeling, label-free quantitation, spectrum counting  (Week 8)

  18. Proteomics Informatics – Protein quantitation I: metabolic labeling (SILAC), chemical labeling, label-free quantitation, spectrum counting  (Week 8)

  19. Proteomics Informatics – Protein quantitation II: software  (Week 9) Skyline MaxQuant

  20. Proteomics Informatics – Protein characterization I: post-translational modifications (Week 10) Peptide with two possible modification sites Matching MS/MS spectrum Intensity m/z Which assignmentdoes the data support? 1,1or2, or 1and2?

  21. Proteomics Informatics – Protein Characterization II: protein-protein interactions, cross-linking, top-down, non-covalent complexes (Week 11) A D A C B Protein identification

  22. Proteomics Informatics – Molecular Signatures (Week 12)

  23. Proteomics Informatics – Molecular Signatures (Week 12)

  24. Proteomics Informatics – Presentations of projects (Week 13) Select a published data set that has been made public and reanalyze it. Highlighted data sets: http://www.thegpm.org/ 10 min presentations

  25. Proteomics Informatics (BMSC-GA 4437) Instructor David Fenyö Contact information David@FenyoLab.org http://fenyolab.org/presentations/Proteomics_Informatics_2013/

More Related