Suffix tree approach to the interpretation of MS

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Suffix tree approach to the interpretation of MS

• A suffix tree approach to the interpretation of
  tandem mass spectra applications to peptides of
  non-specific digestion and post-translational
  modifications
• Bioinformatics 2003
• Bingwen Lu and Ting Chen

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Interpretation of mass spectra
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Ion type

• B ion positive charge remains on the N-terminal
  side
• Y ion positive charge remains on the C-terminal
  side

R
O

N
C
C

C
C
N
O
R
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Construction of suffix tree
1 2 3 4 5 6 7 8

• i.e. string PRRQKQL

root
8
L
Q

K
L

P
R
Q
6
7
L
K
R

Q
Q
R
R
K
L
5
Q
Q

Q
K
K
L
4
Q
Q

L
L
3


2
1
5
Generalized suffix tree
String RQPKL and RQPKG gt RQPKL_at_RQPKG

Root
12
G

_at_
R
Q
L
_at_
P
R
R
11
K
Q
Q
P
K
G
Q
P
G
K

G

P
P
K

L
K
6
K
G
_at_
5
10
L
L
R

_at_
Q
_at_
G
L
G
P
R
R

_at_
K

Q
Q
G
R
P
P

9
7
Q
K
K
G
P
G
8
K
P
4


G
1
3

2
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Construction of spectrum graph

• NC-spectrum graph
• Peptide q has molecular weight W and k fragmented
  ions I1Ik, let m 2k 1
• Nodes mass of some ions
• Z0, mass 0
• Zm, mass W-18 (H2018)

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Construction of spectrum graph

• For Ij
• Ij is a b-ion, node zj ,mass wj-1
• Ij is a y-ion, node zm-j ,mass W-(wj-2)
• Edge mass difference of two node zi and zw if
  the difference total sum of some amino acids
• Direct acyclic graph

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Example
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Algorithm

• ST node r (root), u, v
• NC node x, w
• Map path of the suffix tree to the spectrum graph
• Start traversal beginning from root r of the
  suffix tree and the Z0 of NC.
• (u, v) path from u to the letter v

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Algorithm

• N0 to w has been mapped by the (r, u)
• current path is (u, v)
• Case 1 (u, v) can be mapped to (w, z)
• Case 2 (u, v) cannot be mapped to (w, z)

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Case 1

• If z is the ending node, report path (r, v)
• If z is not the ending node
• let u lt- v, w lt- z
• Continue the traversal

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Case 2

• If v is an internal node, expand (u, v) one more
  letter to one of vs children.
• If v is a leaf, stop extension and backtrack on
  the suffix tree.
• If v is neither a leaf nor a internal node, let
  v be the next letter of the current edge.

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String RQPKL_at_RQPKG
Weight of amino acid residue Arg 174.000 R
156 Gln 146.000 Q 128 Leu 131.000 L 113 Lys
146.000 K 128 Pro 115.000 P 97 Gly 75.000
G 57
Z00
Z2 284
Z5 114
Z1 156
Z8 467
Z4 509
Z9 622
Z3 356
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Modification