9

Graphs: peptide identification

instructor: Ross A. Lippert

http://www-math.mit.edu/~lippert/18.417/

Announcements:

finish ch. 8
problem set to hand back
problem set due friday

Masses of Amino Acids

Glycine	Gly	G	57.02147
Alanine	Ala	A	71.03712
Serine	Ser	S	87.03203
Proline	Pro	P	97.05277
Valine	Val	V	99.06842
Threonine	Thr	T	101.04768
Cysteine	Cys	C	103.00919
Isoleucine	Ile	I	113.08407
Leucine	Leu	L	113.08407
Asparagine	Asn	N	114.04293
Aspartic acid	Asp	D	115.02695
Glutamine	Gln	Q	128.05858
Lysine	Lys	K	128.09497
Glutamic acid	Glu	E	129.0426
Methionine	Met	M	131.04049
Histidine	His	H	137.05891
Phenylalanine	Phe	F	147.06842
Arginine	Arg	R	156.10112
Tyrosine	Tyr	Y	163.06333
Tryptophan	Trp	W	186.07932

A nice link to a referrence on mass spec

Amino Acids are differentiated by their side-chains

Much like the nucleotides

Proteins are chains of amino acids

Amine carboxyl chain - peptide bond

MALDI-TOF cartoon

Fragment types

The most common one's are b and y ions

Peptides are cleaved into small fragments

N-terminal, b-ions, prefixes

C-terminal, y-ions, suffixes

Modifications when little bits fall off (or attach)

An ideal spectrum

Prefix-suffix masses are modified by ion type: GPFNA

Sequence graph

Problems remaining:

Telling C-terminal ions from N-terminal ions
Dealing with multiple paths
Incomplete spectra
Noise

Spectral comparison: shared peak counts and convolutions

Post-translational modification

Need a more tolerant scoring scheme

Spectral Alignment

Spectral Alignment "Grid"