Laboratory of Computational Proteomics
Proteomics Informatics Spring 2013
Center for Health Informatics and Bioinformatics
High Performance Computing Facility
NYU Langone Medical Center
Proteomics Informatics Spring 2013 (BMSC-GA 4437)

Course Director: David Fenyö, Associate Professor
Contact information:

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 (1/29/2013 at 4 pm in TRB 718) - 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 (2/5/2013 at 4 pm in TRB 718) - 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 (2/12/2013 at 4 pm in TRB 119) - 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 (2/19/2013 at 4 pm in TRB 718) - Slides: pdf, pptx

    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: search engines and protein sequence databases (3/5/2013 at 4 pm in TRB 718) - Slides: pdf, pptx

    Example data: E. coli (1, 2, 3), Yeast (1, 2, 3), Human (1, 2, 3)

    Reading list
  • Eng, J.K., McCormack, A.L. & Yates III, J.R. "An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database, Journal of the American Society for Mass Spectrometry 5, 976-989 (1994).
  • Craig, R. & Beavis, R.C. "TANDEM: matching proteins with tandem mass spectra, Bioinformatics 20, 1466-1467 (2004).
  • Craig, R., Cortens, J.C., Fenyo, D. & Beavis, R.C. "Using annotated peptide mass spectrum libraries for protein identification, J. Proteome Res 5, 1843-1849 (2006).

  • Week 6 Protein identification III: de novo sequencing (3/12/2013 at 4 pm in TRB 718) - Slides: pdf, pptx
    Instructor: Beatrix Ueberheide (

    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 7 Databases, data repositories and standardization (3/19/2013 at 4 pm in TRB 718) - Slides: pdf, pptx

    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 8 Protein quantitation I: Overview (4/2/2013 at 4 pm in TRB 718) - Slides: pdf, pptx

    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).
  • Cox, J. & Mann, M. "MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification", Nat Biotech 26, 1367-1372 (2008).

  • Week 9 Protein quantitation II: Multiple Reaction Monitoring (4/9/2013 at 4 pm in TRB 718) - Slides: pdf, pptx
    Instructor: Kelly Ruggles (

    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 10 Protein characterization: post-translational modifications, protein-protein interactions, cross-linking, top-down, non-covalent complexes (4/23/2013 at 4 pm in TRB 718) - Slides: pdf, pptx

    Reading list
  • Trost, M., Bridon, G., Desjardins, M. & Thibault, P. "Subcellular phosphoproteomics", Mass Spectrom. Rev. 29, 962-990 (2010).
  • 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 11 Molecular Signatures (4/30/2013 at 4 pm in TRB 718) - 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 12 Presentations of projects (5/7/2013 at 4 pm in TRB 718)

    Akgol Oksuz, Betul
    Henaff, Mikael
    Hiner, Rebecca
    Montenont, Emilie

    Week 13 Presentations of projects (5/14/2013 at 4 pm in TRB 718)

    Pelzek, Adam
    Prasad, Meera
    Roland, Zemla
    Tang, Zuojian
    Teubl, Jennifer
    Wu, Pamela

    Evaluation (This link only works from within NYU Medical Center)