Methods for deriving a cumulative ranking

• US 8,352,193 B2
• Filed: 05/30/2006
• Issued: 01/08/2013
• Est. Priority Date: 10/19/2000
• Status: Expired due to Fees

• Current Assignee: Target Discovery Incorporated
• Original Assignee: Target Discovery Incorporated
• Inventors: Schneider, Luke V., Hall, Michael P., Petesch, Robert
• Primary Examiner(s): Riggs, II, Larry D
• Application Number:
  US11/444,215
• Publication Number:
  US 20070154900A1
• Time in Patent Office: 2,415 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/6872 involving mass spectrometry
• CPC Class Codes: G01N 33/6848 Methods of protein analysis involving mass spectrometry
• CPC Class Codes: H01J 49/0045 characterised by the fragmentation or other specific reaction
• CPC Class Codes: Y10T 436/105831 Protein or peptide standard or control [e.g., hemoglobin, etc.]
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]
• CPC Class Codes: Y10T 436/24 Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry
• CPC Class Codes: Y10T 436/25125 Digestion or removing interfering materials

Abstract

Methods and apparatuses for deriving the sequence of an oligomer. In one exemplary method for deriving the sequence of a polypeptide, a predetermined set of mass/charge values for amino acid sequences is stored. An abundance value from mass spectrum data for each mass/charge value in the predetermined set is determined to produce a plurality of abundance values. A first ranking, based on the plurality of abundance values, is calculated for each sequence of a set of amino acid sequences having a first number of amino acids. A second ranking, based on the plurality of abundance values, for each sequence of a set of amino acid sequences having a second number of amino acids is calculated. A cumulative ranking, based on the first ranking and the second ranking, is calculated for each sequence of a set of amino acid sequences having at least the second number of amino acids.

Claims

1. A computer implemented method for deriving probability distributions for a plurality of subject peptide sequences useful in calculating a cumulative ranking for peptide sequences of a protein or protein fragment, said method comprising the steps of:

(i) generating a mass spectrum data of a protein or protein fragment;

(ii) calculating a first set of m/z values for a first peptide sequence of a length and storing said first set of m/z values in a memory system of said computer;

(iii) determining a first abundance value for said first peptide sequence using said first set of m/z values and said mass spectrum data, and erasing said first set of m/z values in said memory system;

(iv) calculating a second set of m/z values for a second peptide sequence of the length and storing said second set of m/z values in said memory system;

(v) determining a second abundance value for said second peptide sequence using the second set of m/z values and said mass spectrum data;

(vi) mathematically combining the first abundance value and the second abundance value thereby forming an abundance combination for said first and second peptide sequences, and erasing said second set of m/z values in said memory system;

(vii) iterating steps (iv) to (vi) for additional peptide sequences of the length thereby accumulating an abundance combination for a plurality of peptide sequences of the length;

(viii) calculating a subject set of m/z values for each of a plurality of subject peptide sequences of the length and storing said subject sets of m/z values in said memory system;

(ix) determining a subject abundance value for each of said plurality of subject peptide sequences of the length using the corresponding subject set of m/z values and said mass spectrum data; and

(x) deriving a probability distribution for each of said plurality of subject peptide sequences by autoscaling said corresponding subject abundance value based on said abundance combination for said plurality of peptide sequences of the length, and erasing said subject sets of m/z values in said memory system,

wherein at least one of each of said plurality of probability distributions is retrievable for calculating a cumulative ranking for peptide sequences for said protein or protein fragment.

2. The method of claim 1 wherein

(a) said mathematically combining in step (vi) consists of summing the first abundance value and the second abundance value thereby accumulating a sum for the first and second peptide sequences, and summing the square of said first abundance value and the square of said second abundance value thereby accumulating a sum squared for said first and second peptide sequences;

(b) said abundance combination in step (vii) consists of a sum for said plurality of peptide sequences of length and a sum squared for said plurality peptide sequences of the length;

(c) said autoscaling in step (x) consists of calculating a mean abundance and standard deviation for said plurality of peptide sequences of the length using said sum and said squared sum.

3. The method of claim 1, wherein the length is greater than 1.

4. The method of claim 1, wherein at least one of each of said plurality of probability distributions is a Gaussian distribution.

5. The method of claim 1, wherein at least one of each of said plurality of probability distributions is a Poisson distribution.

6. The method of claim 1, wherein the length is 7 or less.

7. The method of claim 1, wherein a label is attached to the terminus of said protein or protein fragment.

8. The method of claim 7, wherein said label is covalently bonded to said protein prior to generating said mass spectrum data.

9. The method of claim 7, wherein said protein is fragmented by collision-induced dissociation to generate fragments, which are then accelerated toward a detector to generate said mass spectrum data.

10. The method of claim 7, wherein said protein is isolated from other proteins extracted from a sample and wherein said computer which implements said method comprises a digital processing system which executes computer programming instructions.

11. The method of claim 1, wherein said method is performed for each protein in a set of proteins extracted from a biological material and wherein said set of proteins is more than 100 different proteins.

12. The method of claim 1, wherein said mass spectrum is digitally filtered to minimize spectral noise prior to said determining said first abundance value.

13. The method of claim 1, wherein said protein is labeled prior to being fragmented.

14. The method of claim 1, wherein said protein is fragmented and the resulting fragments are labeled.

15. A method as in claim 1, wherein said protein is labeled with a labeling moiety comprising at least one mass defect element having an atomic number from 17 to 77.

16. The method of claim 1, wherein prior to calculating said first set of mass/charge (m/z) values, said method comprises the steps of:

(a) discriminating between a mass spectrum peak associated with the labeled protein and a mass spectrum peak associated with an unlabeled protein, wherein said discriminating is based on the nuclear binding energy of the labeling moiety; and

(b) deconvolving the mass spectrum peak associated with the labeled protein from the mass spectrum peak associated with the unlabeled protein.

17. The method of claim 1, wherein said protein is labeled with a labeling moiety comprising at least one isotope element.

18. The method of claim 17, wherein the first abundance value and the second abundance value are determined using an isotope ranking factor.

19. The method of claim 1, wherein said protein is labeled with a labeling moiety comprising at least one isotope element and at least one mass defect element having an atomic number from 17 to 77, wherein

(a) prior to calculating said first set of mass/charge (m/z) values, said method comprises the steps of:

(1) discriminating between a mass spectrum peak associated with the labeled protein and a mass spectrum peak associated with an unlabeled protein, wherein said discriminating is based on the nuclear binding energy of the labeling moiety; and

(2) deconvolving the mass spectrum peak associated with the labeled protein from the mass spectrum peak associated with the unlabeled protein;

(b) wherein the first abundance value and the second abundance value are determined using an isotope ranking factor.