Proteomics Informatics (BMSC-GA 4437)
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1 Proteomics Informatics (BMSC-GA 4437) Instructor David Fenyö Contact information htt://fenyolab.org/resentations/proteomics_informatics_2013/
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3 Learning Objectives Be able analyze a roteomics data set and understand the limitations of the results.
4 Overview of Proteomics (Week 1) Why roteomics? Bioinformatics Overview of the course
5 Motivating Examle: Protein Regulation Geiger et al., Proteomic changes resulting from gene coy number variations in cancer cells, PLoS Genet Se 2;6(9). ii: e
6 Motivating Examle: Protein Comlexes Alber et al., Nature 2007
7 Motivating Examle: Signaling Choudhary & Mann, Nature Reviews Molecular Cell Biology 2010
8 Bioinformatics Biological System Exerimental Design Samles Measurements Raw Data Data Analysis Information
9 Mass Sectrometry Based Proteomics Lysis Fractionation Digestion Mass sectrometry MS Peak Finding Charge determination De-isotoing Integrating Peaks Searching Identified and Quantified Proteins
10 Overview of Mass sectrometry (Week 2) Ion Source Mass Analyzer Detector mass/charge
11 Overview of Mass sectrometry (Week 2) Ion Source Mass Analyzer 1 Fragmentation Mass Analyzer 2 Detector b y
12 Proteomics Informatics Overview of Mass sectrometry (Week 2) Ion Source LC Mass Analyzer 1 Fragmentation Mass Analyzer 2 Detector 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
13 Analysis of mass sectra: signal rocessing, eak finding, and isotoe clusters (Week 3) Intensity m/z
14 Protein identification I: searching rotein sequence collections and significance testing (Week 4) Sequence DB Lysis Fractionation LC-MS MS/MS MS/MS Digestion Pick Protein Pick Petide All Fragment Masses Comare, Score, Test Significance Reeat for all etides Reeat for all roteins
15 Protein identification II: search engines and rotein sequence databases (Week 5)
16 % Relative Abundance Amino acid masses 1-letter 3-letter Chemical Monois Average code code formula otoic A Ala C 3 H 5 ON R Arg C 6 H 12 ON N Asn C 4 H 6 O 2 N D As C 4 H 5 O 3 N C Cys C 3 H 5 ONS E Glu C 5 H 7 O 3 N Q Gln C 5 H 8 O 2 N G Gly C 2 H 3 ON H His C 6 H 7 ON I Ile C 6 H 11 ON L Leu C 6 H 11 ON K Lys C 6 H 12 ON M Met C 5 H 9 ONS F Phe C 9 H 9 ON P Pro C 5 H 7 ON S Ser C 3 H 5 O 2 N T Thr C 4 H 7 O 2 N W Tr C 11 H 10 ON Y Tyr C 9 H 9 O 2 N V Val C 5 H 9 ON Proteomics Informatics Protein identification III: de novo sequencing (Week 6) [M+2H] m/z Sequences consistent with sectrum Mass Differences
17 Protein identification IV: sectrum library searching (Week 7) Identified Proteins Lysis Fractionation Digestion LC-MS/MS MS/MS Sectrum Library Pick Sectrum Reeat for all sectra Comare, Score, Test Significance
18 Protein quantitation I: metabolic labeling (SILAC), chemical labeling, label-free quantitation, sectrum counting (Week 8) C ij L ij D ijk LC ik I ij Pr Pe ik C Lysis Fractionation Digestion LC-MS ik k ij ij ij ijk j C k ij k L ij L Pr ij Pr I D ijk ik D Pe ik Pe ik LC ik MS ik I ik Samle i Protein j Petide k LC ik MS ik MS ik MS k
19 Protein quantitation I: metabolic labeling (SILAC), chemical labeling, label-free quantitation, sectrum counting (Week 8) Lysis Fractionation Digestion LC-MS Assumtion: k L ij Pr ij D ijk Pe ik LC constant for all samles C i j/ C j I j/ n m n i Samle i Protein j Petide k i ik I i m j MS ik MS MS
20 Protein quantitation II: software (Week 9) Skyline MaxQuant
21 Protein characterization I: ost-translational modifications (Week 10) Petide with two ossible modification sites Intensity Matching MS/MS sectrum m/z Which assignment does the data suort? 1, 1 or 2, or 1 and 2?
22 Protein Characterization II: rotein-rotein interactions, cross-linking, to-down, non-covalent comlexes (Week 11) A D A C B Protein identification
23 Molecular Signatures (Week 12)
24 Molecular Signatures (Week 12)
25 Presentations of rojects (Week 13) Select a ublished data set that has been made ublic and reanalyze it. Highlighted data sets: htt:// 10 min resentations
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27 Proteomics Informatics (BMSC-GA 4437) Instructor David Fenyö Contact information htt://fenyolab.org/resentations/proteomics_informatics_2013/
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