Ch08_MassSpec

Ch08_MassSpec - www.bioalgorithms.info An Introduction to...

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Unformatted text preview: www.bioalgorithms.info An Introduction to Bioinformatics Algorithms Protein Sequencing and Identification by Mass Spectrometry An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Outline • Tandem Mass Spectrometry • De Novo Peptide Sequencing • Spectrum Graph • Protein Identification via Database Search • Identifying Post Translationally Modified Peptides • Spectral Convolution • Spectral Alignment An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Masses of Amino Acid Residues An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Protein Backbone H...-HN-CH-CO-NH-CH-CO-NH-CH-CO-…OH R i-1 R i R i+1 AA residue i-1 AA residue i AA residue i+1 N-terminus C-terminus An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Peptide Fragmentation • Peptides tend to fragment along the backbone. • Fragments can also loose neutral chemical groups like NH 3 and H 2 O. H...-HN-CH-CO . . . NH-CH-CO-NH-CH-CO-…OH R i-1 R i R i+1 H + Prefix Fragment Suffix Fragment Collision Induced Dissociation An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Breaking Protein into Peptides and Peptides into Fragment Ions • Proteases, e.g. trypsin, break protein into peptides . • A Tandem Mass Spectrometer further breaks the peptides down into fragment ions and measures the mass of each piece. • Mass Spectrometer accelerates the fragmented ions; heavier ions accelerate slower than lighter ones. • Mass Spectrometer measure mass/charge ratio of an ion. An Introduction to Bioinformatics Algorithms www.bioalgorithms.info N- and C-terminal Peptides N- t e r m i n a l p e p t i d e s C- t e r m i n a l p e p t i d e s An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Terminal peptides and ion types Peptide Mass (D) 57 + 97 + 147 + 114 = 415 Peptide Mass (D) 57 + 97 + 147 + 114 – 18 = 397 without An Introduction to Bioinformatics Algorithms www.bioalgorithms.info N- and C-terminal Peptides N- t e r m i n a l p e p t i d e s C- t e r m i n a l p e p t i d e s 415 486 301 154 57 71 185 332 429 An Introduction to Bioinformatics Algorithms www.bioalgorithms.info N- and C-terminal Peptides N- t e r m i n a l p e p t i d e s C- t e r m i n a l p e p t i d e s 415 486 301 154 57 71 185 332 429 An Introduction to Bioinformatics Algorithms www.bioalgorithms.info N- and C-terminal Peptides 415 486 301 154 57 71 185 332 429 An Introduction to Bioinformatics Algorithms www.bioalgorithms.info N- and C-terminal Peptides 415 486 301 154 57 71 185 332 429 Reconstruct peptide from the set of masses of fragment ions ( mass-spectrum ) An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Peptide Fragmentation y 3 b 2 y 2 y 1 b 3 a 2 a 3 HO NH 3 + | | R 1 O R 2 O R 3 O R 4 | || | || | || | H -- N --- C --- C --- N --- C --- C --- N --- C --- C --- N --- C -- COOH | | | | | | | H H H H H H H b 2- H 2 O y 3- H 2 O b 3- NH 3 y 2- NH 3 An Introduction to Bioinformatics Algorithms...
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This note was uploaded on 02/10/2012 for the course CSE 5615 taught by Professor Mitra during the Fall '11 term at FIT.

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Ch08_MassSpec - www.bioalgorithms.info An Introduction to...

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