Apparatus for identifying peptides and proteins by mass spectrometry
AssigneeMicromass UK Limited
InventorJohn Skilling
Life of this patent
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Abstract
An apparatus for identifying a protein, polypeptide or peptide by means of mass spectrometry and especially by tandem mass spectrometry is disclosed. The apparatus preferably functions to model the fragmentation of a peptide or protein in a tandem mass spectrometer to facilitate comparison with an experimentally determined spectrum. A fragmentation model is used which takes account of all possible fragmentation pathways which a particular sequence of amino acids may undergo. A peptide or protein may be identified by comparing an experimentally determined mass spectrum with spectra predicted using such a fragmentation model from a library of known peptides or proteins.
Claims4
Apparatus for identifying a most probable sequence of amino acids in an unknown peptide, said apparatus comprising a mass spectrometer for generating a mass spectrum of said unknown peptide and data processing means programmed to:
- (a) process data generated by said mass spectrometer to produce a processable mass spectrum;
- and
- (b) calculate the likelihood that any given trial amino-acid sequence would account for said processable mass spectrum using a fragmentation model which sums probabilistically over a plurality of fragmentation routes which together represent possible ways that said trial sequence might fragment in accordance with a set of predefined rules, each said fragmentation route being assigned a prior probability based on the chemical process involved, wherein a likelihood factor of the processable mass spectrum, given a particular trial sequence, is established according to:
- P
-
- (
- D
-
-
- GIVEN
-
-
- S
- )
- =
- ∑
- f
-
- P
-
- (
- D
-
-
- GIVEN
-
-
- f
- )
-
-
- P
-
- (
- f
-
-
- GIVEN
-
-
- S
- )
- where
- ∑
- f
- represents the sum over all permitted fragmentation pattems ƒ, P(D GIVEN ƒ) is the probability of the processable mass spectrum assuming a particular fragmentation pattern ƒ, and P(ƒGIVEN S) is the probability of having a fragmentation pattern ƒ from the trail sequence S.
Dependencies are inferred from the claim text.