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Proteomics Informatics Spring 2014 (BMSC-GA 4437)
Course Director: David Fenyö, Associate Professor
Contact information: David@FenyoLab.org
Instructors:
David Fenyö (David@FenyoLab.org)
Himanshu Grover (Himanshu.Grover@nyumc.org) - Python Lab
Kelly Ruggles (Kelly.Ruggles@nyumc.org) - Week 7 Protein quantitation II: Multiple Reaction Monitoring and Week 9 Proteogenomics
Beatrix Ueberheide (Beatrix.Ueberheide@nyumc.org) - Week 5 de novo sequencing
This course will give an introduction of proteomics and mass spectrometry workflows, experimental design, and data analysis with a focus on algorithms for extracting information from experimental data. The following subjects will be covered in: (1) Protein identification (peptide mass fingerprinting, tandem mass spectrometry, database searching, spectrum library searching, de novo sequencing, significance testing); (2) Protein characterization (protein coverage, top-down proteomics, post-translational modifications, protein processing and degradation, protein complexes); (3) Protein quantitation (metabolic labeling - SILAC, chemical labeling, label-free quantitation, spectrum counting, stoichiometry, biomarker discovery and verification). Examples will be provided throughout the course on how the different approaches can be applied to investigate biological systems. The class will be structured to include hands-on practical techniques for analyzing relevant proteomics datasets.
Week 1 Overview of proteomics (1/28/2014 at 4 pm in TRB 718)
- Lecture Slides: pdf, pptx, Python Slides: pdf, pptx
Reading list
M.A. Gillette, S.A. Carr, "Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry", Nature Methods 10 (2013) 28–34.
A. Bensimon, A.J.R. Heck R. Aebersold, "Mass Spectrometry–Based Proteomics and Network Biology", Annual Review of Biochemistry 81 (2012) 379-405.
Week 2 Overview of mass spectrometry (2/4/2014 at 4 pm in TRB 718)
- Lecture Slides: pdf, pptx
Example data (Slice video)
Reading list
Beavis, R.C. & Chait, B.T. "Matrix-assisted laser desorption ionization mass-spectrometry of proteins" Meth. Enzymol 270, 519-551 (1996).
Banks, J.F. & Whitehouse, C.M. "Electrospray ionization mass spectrometry" Meth. Enzymol 270, 486-519 (1996).
Chalkley, R. "Instrumentation for LC-MS/MS in proteomics" Methods Mol. Biol 658, 47-60 (2010).
Week 3 Analysis of mass spectra: signal processing, peak finding, and isotope clusters (2/11/2014 at 4 pm in TRB 717)
- Lecture Slides: pdf, pptx, Python Slides: pdf, pptx
Reading list
Zhang, J., Gonzalez, E., Hestilow, T., Haskins, W. & Huang, Y. "Review of peak detection algorithms in liquid-chromatography-mass spectrometry" Curr. Genomics 10, 388-401 (2009).
Yang, C., He, Z. & Yu, W. "Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis" BMC Bioinformatics 10, 4 (2009).
Week 4 Protein identification I: searching protein sequence collections and significance testing (2/18/2014 at 4 pm in TRB 718)
- Lecture Slides: pdf, pptx, Python Slides: pdf, pptx
Example code: Ex1.py, computeMz.py
Example data:
E. coli (1, 2, 3),
Yeast (1, 2, 3),
Human (1, 2, 3)
Reading list
Eriksson, J., Chait, B.T. & Fenyö, D. "A statistical basis for testing the significance of mass spectrometric protein identification results" Anal. Chem 72, 999-1005 (2000).
Fenyö, D. & Beavis, R.C. "A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes" Anal. Chem 75, 768-774 (2003).
Elias, J.E. & Gygi, S.P. "Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry" Nat. Methods 4, 207-214 (2007).
Week 5 Protein identification II: de novo sequencing (2/25/2014 at 4 pm in TRB 718)
- Lecture Slides: pdf, pptx, Python Slides: pdf, pptx
Instructor: Beatrix Ueberheide (Beatrix.Ueberheide@nyumc.org)
Example code: peptideFragmentation.py
Example data:
Cheat sheet,
Example 1: CAD Spectrum,
Example 1: HCD Spectrum,
Example 2: CAD Spectrum,
Example 3: ETD Spectrum,
Example 4: ETD Spectrum.
Reading list
Seidler J, Zinn N, Boehm ME, Lehmann WD, "De novo sequencing of peptides by MS/MS, Proteomics 10 (2010) 634-49.
Standing KG, "Peptide and protein de novo sequencing by mass spectrometry, Curr Opin Struct Biol. 13 (2003) 595-601.
Week 6 Protein quantitation I: Overview (3/4/2014 at 4 pm in TRB 718)
- Lecture Slides: pdf, pptx, Python Slides: pdf, pptx
Example code: peptideFragmentation_withFunctions.py
Reading list
Domon, B. & Aebersold, R. "Options and considerations when selecting a quantitative proteomics strategy", Nat. Biotechnol 28, 710-721 (2010).
Zhang, G. et al. "Protein quantitation using mass spectrometry" Methods Mol. Biol 673, 211-222 (2010).
Week 7 Protein quantitation II: Multiple Reaction Monitoring (3/11/2014 at 4 pm in TRB 718)
- Lecture Slides: pdf, pptx, Python Slides: pdf, pptx
Instructor: Kelly Ruggles (Kelly.Ruggles@nyumc.org)
Reading list
D.R. Mani, S.E. Abbatiello, S.A. Carr, "Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics", BMC Bioinformatics 13 (2012) S9.
A. Maiolica, M.A. Jünger, I. Ezkurdi, R. Aebersold, "Targeted proteome investigation via selected reaction monitoring mass spectrometry", Journal of Proteomics 75 (2012) 3495-3513.
MacLean, B. et al. "Skyline: an open source document editor for creating and analyzing targeted proteomics experiments", Bioinformatics 26, 966-968 (2010).
Week 8 Databases, data repositories and standardization (3/18/2014 at 4 pm in TRB 718)
- Lecture Slides: pdf, pptx, Python Slides: pdf, pptx
Example code: Pandas_GE_tTest.py
Example data: leukemia.tab
Reading list
Craig R, Cortens JP, Beavis RC, "Open source system for analyzing, validating, and storing protein identification data", J Proteome Res. 3 (2004) 1234-42.
D. Fenyö, J. Eriksson, R. Beavis, "Mass spectrometric protein identification using the global proteome machine", Methods Mol Biol 673 (2010) 189-202.
CF Taylor, NW Paton, KS Lilley, P-A Binz, RK Julian Jr, AR Jones, W Zhu, R Apweiler, R Aebersold, EW Deutsch, MJ Dunn, AJR Heck, A Leitner, M Macht, M Mann, L Martens, TA Neubert, SD Patterson, P Ping, SL Seymour, P Souda, A Tsugita, J Vandekerckhove, TM Vondriska, JP Whitelegge, MR Wilkins, I Xenarios, JR Yates III, H Hermjakob, "The minimum information about a proteomics experiment (MIAPE)", Nat Biotechnol. 25 (2007) 887-93.
Week 9 Proteogenomics (3/25/2014 at 4 pm in TRB 718)
- Lecture Slides: pdf, pptx, Python Slides: pdf, pptx, docx
Instructor: Kelly Ruggles (Kelly.Ruggles@nyumc.org)
Reading list
Week 10 Protein characterization I: post-translational modifications (4/1/2014 at 4 pm in TRB 718)
- Lecture Slides: pdf, pptx, docx
Example code: Pandas_GE_standardization_tTest.py
Example data: leukemia.tab
Reading list
Trost, M., Bridon, G., Desjardins, M. & Thibault, P. "Subcellular phosphoproteomics", Mass Spectrom. Rev. 29, 962-990 (2010).
Week 11 Protein characterization II: Protein interactions (4/11/2014 at 3:30 pm in TRB 718)
- Lecture Slides: pdf, pptx, Python Slides: pdf, pptx, docx
Reading list
A Leitner, R Reischl, T Walzthoeni, F Herzog, S Bohn, F Förster, and R Aebersold, "Expanding the Chemical Cross-Linking Toolbox by the Use of Multiple Proteases and Enrichment by Size Exclusion Chromatography", Mol Cell Proteomics 11 (2012)
Week 12 Molecular Signatures (4/22/2014 at 4 pm in TRB 718)
- Lecture Slides: pdf, pptx, Python Slides: pdf, pptx
Reading list
EF Petricoin III, AM Ardekani, BA Hitt, PJ Levine, VA Fusaro, SM Steinberg, GB Mills, C Simone, DA Fishman, EC Kohn, LA Liotta, "Use of proteomic patterns in serum to identify ovarian cancer", Lancet 359 (2002) 572–77
DF Ransohoff, "Bias as a threat to the validity of cancer molecular-marker research", Nat Rev Cancer 5 (2005) 142-9.
TA Addona, X Shi, H Keshishian, DR Mani, M Burgess, MA Gillette, KR Clauser, D Shen, GD Lewis, LA Farrell, MA Fifer, MS Sabatine, RE Gerszten & SA Carr, "A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease", Nature Biotechnology 29 (2011) 635
Week 13 Presentations of projects (4/29/2014 at 4 pm in TRB 718)
Evaluation (This link only works from within NYU Medical Center)
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