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Introduction to the Proteomics Bioinformatics Course 2016

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Presentation given during the Wellcome Trust Proteomics Bioinformatics Course 2016. It includes a little bit of history and curiosities

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Introduction to the Proteomics Bioinformatics Course 2016

  1. 1. Proteomics: History and introduction to the course Dr. Juan Antonio Vizcaíno Proteomics Team Leader EMBL-EBI Hinxton, Cambridge, UK
  2. 2. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Data resources at EMBL-EBI Genes, genomes & variation ArrayExpress Expression Atlas PRIDE InterPro Pfam UniProt ChEMBL ChEBI Molecular structures Protein Data Bank in Europe Electron Microscopy Data Bank European Nucleotide Archive European Variation Archive European Genome-phenome Archive Gene & protein expression Protein sequences, families & motifs Chemical biology Reactions, interactions & pathways IntAct Reactome MetaboLights Systems BioModels Enzyme Portal BioSamples Ensembl Ensembl Genomes GWAS Catalog Metagenomics portal Europe PubMed Central Gene Ontology Experimental Factor Ontology Literature & ontologies
  3. 3. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 • Useful definitions and concepts to start • A little bit of history… and curiosities • Importance of bioinformatics Overview
  4. 4. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Proteomics is the large-scale study of proteins, particularly their structures and functions The proteome is the entire complement of proteins including the modifications made to a particular set of proteins, produced by an organism or system. This will vary with time and distinct requirements, or stresses, that a cell or organism undergoes proteome = ‘protein’ + ‘genome’ (M. Wilkins, 1994) Definitions
  5. 5. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Genomics Transcriptomics Proteomics From the genome to the proteome
  6. 6. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Genome vs. proteome •Genome • Essentially static over time • Non location specific • Human genome mapped (initially on 2000) • ~20,000 genes • PCR is available to amplify DNA •Proteome • Dynamic over time • Location specific • Human proteome non- mapped: • How many??? • No equivalent of PCR for proteins
  7. 7. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 • Large increase in protein diversity due to: • Alternative splicing of pre-mRNA (introns and exons) • Post-translational modifications of proteins • Cell age and health/disease state Genome -> Proteome
  8. 8. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 20 naturally occurring amino acids Chirality L-aa Amino acids
  9. 9. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 From: Molecular Biology of the Cell (4th Ed) http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=mboc4&part=A388&rendertype=figure&id=A3 91 Individual amino acids polypeptide Peptide bond Protein backbone
  10. 10. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 • Useful definitions and concepts to start • A little bit of history… and curiosities • Importance of bioinformatics Overview
  11. 11. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Sanger's principal conclusion was that the two polypeptide chains of the protein insulin had precise amino acid sequences and, by extension, that every protein had a unique sequence. Nobel Prize in Chemistry in 1958 F. Sanger Protein sequencing: the pioneers
  12. 12. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 F. Sanger By 1975, he had developed the “dideoxy” method for sequencing DNA molecules, also known as the Sanger method. He sequenced the first organism: Phague F- x-174 Nobel Prize in Chemistry in 1980 Not only protein sequencing…
  13. 13. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 MS is an analytical technique that measures the mass-to-charge (m/z) ratio of charged particles. It is used for determining masses of particles, for the determination of the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and other chemical compounds. Many applications… one of them is proteomics Mass spectrometry (MS)
  14. 14. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 P. V. Edman By 1950, he first developed the Edman degradation method. A major drawback of this technique is that the peptides being sequenced cannot be longer than around 30 residues Protein sequencing: the pioneers
  15. 15. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Wolfgang Paul / Hans G. Dehmelt developed the ion trap technique (1950s and 1960s). Nobel Prize in Physics (1989) A commercial quadrupole ion trap (Finnigan MAT) was introduced in 1983. The ion trap quickly became the primary instrument for conducting proteomics because of its ability to conduct tandem MS (MS/ MS) analysis of complex mixtures of peptides, generated by enzymatic digestion of proteome samples such as cell lysates. History of Mass spectrometry
  16. 16. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 John B. Fenn (Yale University) and co-workers use electrospray (ESI) to ionize biomolecules (high- molecular weight proteins). Koichi Tanaka (Shimadzu Corp) used the “ultra fine metal plus liquid matrix method” to ionize intact proteins (Soft Laser Desorption): “With the proper combination of laser wavelength and matrix, a protein can be ionized”. Fenn and Tanaka: Nobel Prize in Chemistry (2002) Ionization methods were too energetic to be used with biological molecules F. Hillenkamp & M. Karas developed the MALDI technique: use of organic matrices to obtain MS of large proteins Mass spectrometry: Soft ionization methods
  17. 17. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Patrick H. O’Farrell J. Klose 1D SDS gel MW MW pI 2D SDS gel 2D gel image from: http://www.fixingproteomics.org/ Gel electroforesis
  18. 18. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 The rapid development of genomics allowed the development of proteomics Shot-gun proteomics: Method of identifying proteins in complex mixture HPLC MS 100 300 500 700 900 1100 1300 1500 1700 1900 2100 m/z0 100 % 100 300 500 700 900 1100 1300 1500 1700 1900 2100 m/z0 100 % There are only 20 aminoacids. The physico-chemical properties of the peptides are more homogeneous and ‘manageable’ than the ones from the proteins From protein centric to peptide centric
  19. 19. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Mass Spectrometry (MS)-based proteomics • Many different workflows. • Discovery mode: • Bottom-up proteomics • Data dependent acquisition (DDA) • Data independent acquisition (DIA) • Top down proteomics (intact proteins) • Targeted mode: • SRM/ MRM (Selected Reaction Monitoring/ Multiple Reaction Monitoring)
  20. 20. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Not only identify, but also quantify the amount of each protein in the sample The current methods rely mainly on MS: Vaudel et al., Proteomics 2010 Feb;10(4):650-670 Proteomics becomes quantitative
  21. 21. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 The Yeast-two-hybrid method was developed by S. Fields in 1989. Many more methods developed since then: - Affinity electrophoresis - Co-inmunoprecipitation -Tandem affinity purification (TAP) Protein-protein interactions: yeast-two hybrid
  22. 22. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Proteomics in a clinical environment • Biomarker discovery is a very active field of research. • MS technology is slowly incorporating into the clinical world. • Used to identify microorganisms by MALDI MS profiling. • Approved in Europe. On August 2013 it become the first MS diagnostic tool approved in the US. J Rohn (2013) Nat Biotechnol, 31, 862
  23. 23. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 http://thehpp.org/ The Human Proteome Project (HPP)
  24. 24. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Draft Human proteome papers published in 2014 Wilhelm et al., Nature, 2014 Kim et al., Nature, 2014 •Two independent groups claimed to have produced the first complete draft of the human proteome by MS. • Some of their findings are controversial and need further validation… but generated a lot of discussion and put proteomics in the spotlight. •They used many different tissues. Nature cover 29 May 2014
  25. 25. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Proteomics for structural biology • Increased focus in recent years (a lot more to come). • MS/MS cross- linking approaches • HD-exchange mass spectrometry Lössl et al., EMBO J, 2016
  26. 26. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 • Useful definitions and concepts to start • A little bit of history… and curiosities • Importance of bioinformatics Overview
  27. 27. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Atlas what happens where Need for bioinformatics Biology is changing: • High-throughput • More data produced • New types of data • Emphasis on systems biology Bioinformatics enables new applications: • molecular medicine • agriculture • food • environmental sciences
  28. 28. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 On 21 July 1986, SWISS-PROT was created by A. Bairoch (it contained around 3,900 protein sequences) In 1979, the first software was developed for 2DE image analysis (ELSIE) Bioinformatics is very much needed in proteomics
  29. 29. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 On 21 July 1986, SWISS-PROT was created by A. Bairoch (it contained around 3,900 protein sequences) In 1979, the first software was developed for 2DE image analysis (ELSIE) Bioinformatics is very much needed in proteomics
  30. 30. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Mallick & Kuster, Nat. Biotechnol. 2010 Jul;28(7):695-709 Proteomics is a complex discipline
  31. 31. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 MS based proteomics Hein et al., Handbook of Systems Biology, 2012
  32. 32. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Genomics Transcriptomics Proteomics More multi-omics studies… Metabolomics
  33. 33. Juan A. Vizcaíno juan@ebi.ac.uk WT Proteomics Bioinformatics Course 2016 Hinxton, 4 December 2016 Questions?

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