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US 6,446,010 B1Granted
Method for assessing significance of protein identification
AssigneeThe Rockefeller University
InventorsJan Eriksson, David Feny{haeck over (o)}, Brian T. Chait
Life of this patent
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Abstract
A method of generating a frequency distribution of scores comprising: a) generating mass data for a biological molecule; b) generating mass data for a series of random hypothetical biological molecules; c) calculating a frequency distribution of high similarity scores between mass data of each molecule generated in steps a and b.
Claims67
A method of generating a frequency distribution of scores for a particular experimental condition, wherein the scores relate to random identifications of biological molecules, the method comprising:
- a) generating mass data for the particular experimental condition for biological molecules in a biological molecule database, wherein each biological molecule comprises a set of constituent parts;
- b) generating mass data of a hypothetical biological molecule for the experimental condition, wherein the hypothetical biological molecule comprises a set of constituent parts, and wherein the set of constituent parts of the hypothetical biological molecule is different from every set of constituent parts of each biological molecule of the database;
- c) comparing the data generated in step (b) with the data generated for each biological molecule in step (a);
- d) calculating a score for each comparison in step (c), wherein the score is a function of similarity between the data generated in step (a), which corresponds to a particular database biological molecule, and the data generated in step (b);
- e) selecting a score from the top twenty scores calculated in step (d), wherein the top twenty scores denote a high degree of similarity;
- f) repeating steps (b) through (e) with different hypothetical biological molecules until a sufficient quantity of scores are selected;
- and
- g) determining the frequency of selecting each score and generating therefrom a frequency distribution of scores.
5 more elements
A method of identifying an experimental biological molecule for a particular experimental condition and a particular significance level, wherein the statistical significance of the identification is assessed, the method comprising:
- a) selecting a significance level that represents a level of confidence in a biological molecule identification;
- b) cleaving the experimental biological molecule into constituent parts;
- c) generating mass data for these constituent parts;
- d) comparing the mass data generated in step (c) with mass data generated for the experimental condition from biological molecules of a biological molecule database;
- e) calculating scores for each comparison in step (d), wherein the scores are a function of similarity between mass data of the experimental biological molecule and mass data generated from the biological molecule database;
- f) selecting a score generated in step (e) wherein the score corresponds to a comparison which denotes a high degree of similarity and wherein the score corresponds to a particular biological molecule in the biological molecule database;
- g) comparing the score selected in step (f) with a frequency distribution of scores for the experimental condition, wherein the frequency distribution relates to random biological molecule identifications, wherein the frequency distribution has associated therewith a critical score which corresponds to the significance level, and wherein the distribution is generated by:
- i) generating mass data of a hypothetical biological molecule, wherein the hypothetical biological molecule comprises a set of constituent parts, and wherein the set of constituent parts of the hypothetical biological molecule is different from every set of constituent parts of each biological molecule of the database;
- ii) comparing mass data of the hypothetical biological molecule with mass data of biological molecules in the database;
- iii) calculating a score for each comparison, wherein the score is a function of similarity between the mass data of the hypothetical biological molecule and the mass data of the biological molecules in the database;
- iv) selecting a score from the top twenty scores, wherein the top twenty scores denote a high degree of similarity;
- v) repeating steps (i) to (iv) with different hypothetical biological molecules until a sufficient quantity of scores are selected;
- and determining the frequency of selecting each score and generating therefrom the frequency distribution of scores relating to random identifications;
- and
- h) determining whether the score selected in step (f) is equal to or larger than the critical score, wherein if the score selected in step (f) is equal to or larger than the critical score, the identification of the experimental biological molecule is statistically significant for the selected significance level.
12 more elements
A method of determining statistical significance of a biological molecule identification score, the method comprising:
- a) selecting a significance level that represents a level of confidence in a biological molecule identification;
- b) calculating a score associated with an experimental biological molecule, wherein the score is a function of similarity between mass data of the experimental biological molecule and mass data generated for biological molecules of a biological molecule database;
- c) comparing the score with a score frequency distribution, wherein the distribution relates to random biological molecule identifications, wherein the frequency distribution has associated therewith a critical score which corresponds to the significance level, and wherein the distribution is generated by:
- i) generating mass data of a hypothetical biological molecule, wherein the hypothetical biological molecule comprises a set of constituent parts, and wherein the set of constituent parts of the hypothetical biological molecule is different from every set of constituent parts of each biological molecule of the database;
- ii) comparing mass data of the hypothetical biological molecule with mass data of biological molecules in the database;
- iii) calculating a score for each comparison, wherein the score is a function of similarity between the mass data of the hypothetical biological molecule and the mass data of the biological molecules in the database;
- iv) selecting a score from the top twenty scores, wherein the top twenty scores denote a high degree of similarity;
- v) repeating steps (i) to (iv) with different hypothetical biological molecules until a sufficient quantity of scores are selected;
- and determining the frequency of selecting each score and generating therefrom the frequency distribution of scores relating to random identifications;
- and
- d) determining whether the score associated with the experimental biological molecule identification is equal to or larger than the critical score corresponding with the significance level, wherein if the score is equal to or larger than the critical score, the identification of the experimental biological molecule is statistically significant for the selected significance level.
8 more elements
A means for generating a frequency distribution of scores for a particular experimental condition, wherein the scores relate to random identifications of biological molecules, comprising:
- a) a means for generating mass data for the particular experimental condition for biological molecules in a biological molecule database;
- b) a means for generating mass data of a hypothetical biological molecule for the experimental condition, wherein the hypothetical biological molecule comprises a set of constituent parts, and wherein the set of constituent parts of the hypothetical biological molecule is different from every set of constituent parts of each biological molecule of the database;
- c) a means for comparing the data generated in step (b) with the data generated for each biological molecule in step (a);
- d) a means for calculating a score for each comparison in step (c), wherein the score is a function of similarity between the data generated in step (a) which corresponds to a particular biological molecule and the data generated in step (b);
- e) a means for selecting a score from the top twenty scores calculated in step (d), wherein the selected score corresponds to the comparison which denotes a high degree of similarity between the data generated in step (a) and the data generated in step (b);
- f) a means for repeating steps (b) through (e) with different hypothetical biological molecules until a sufficient quantity of scores are selected;
- and
- g) a means for determining the frequency of selecting each score and generating therefrom a frequency distribution of scores.
5 more elements
A means for identifying an experimental biological molecule for a particular experimental condition and a particular significance level comprising:
- a) a means for selecting a significance level that represents a level of confidence in a biological molecule identification;
- b) a means for cleaving the experimental biological molecule into constituent parts by a method that produces constituent parts;
- c) a means for generating mass data for these constituent parts;
- d) a means for comparing the mass data generated in step (c) with mass data generated for the experimental condition from biological molecules of a biological molecule database;
- e) a means for calculating scores for each comparison in step (d), wherein the scores are a function of similarity between mass data of the experimental biological molecule and mass data generated from the biological molecule database;
- f) a means for selecting a score generated in step (e) wherein the score corresponds to a comparison which denotes a high degree of similarity and wherein the score corresponds to a particular biological molecule in the biological molecule database;
- g) a means for comparing the score selected in step (f) with a frequency distribution of scores for the experimental condition, wherein the frequency distribution relates to random biological molecule identifications, wherein the frequency distribution has associated therewith a critical score which corresponds to the significance level, and wherein the distribution is generated by:
- i) generating mass data of a hypothetical biological molecule, wherein the hypothetical biological molecule comprises a set of constituent parts, and wherein the set of constituent parts of the hypothetical biological molecule is different from every set of constituent parts of each biological molecule of the database;
- ii) comparing mass data of the hypothetical biological molecule with mass data of biological molecules in the database;
- iii) calculating a score for each comparison, wherein the score is a function of similarity between the mass data of the hypothetical biological molecule and the mass data of the biological molecules in the database;
- iv) selecting a score from the top twenty scores, wherein the top twenty scores denote a high degree of similarity;
- v) repeating steps (i) to (iv) with different hypothetical biological molecules until a sufficient quantity of scores are selected;
- and determining the frequency of selecting each score and generating therefrom the frequency distribution of scores relating to random identifications;
- and
- h) a means for determining whether the score selected in step (f) is equal to or larger than the critical score, wherein if the score selected in step (f) is equal to or larger than the critical score, the identification of the experimental biological molecule is statistically significant for the selected significance level.
12 more elements
A means for determining statistical significance of a biological molecule identification score, comprising:
- a) a means for selecting a significance level that represents a level confidence in a biological molecule identification;
- b) a means for calculating a score associated with the experimental biological molecule, wherein the score is a function of similarity between mass data of the experimental biological molecule and mass data generated from a biological molecule database;
- c) a means for comparing the score with a score frequency distribution, wherein the distribution relates to random biological molecule identifications, wherein the frequency distribution has associated therewith a critical score which corresponds to the significance level, and wherein the distribution is generated by:
- i) generating mass data of a hypothetical biological molecule, wherein the hypothetical biological molecule comprises a set of constituent parts, and wherein the set of constituent parts of the hypothetical biological molecule is different from every set of constituent parts of each biological molecule of the database;
- ii) comparing mass data of the hypothetical biological molecule with mass data of biological molecules in the database;
- iii) calculating a score for each comparison, wherein the score is a function of similarity between the mass data of the hypothetical biological molecule and the mass data of the biological molecules in the database;
- iv) selecting a score from the top twenty scores, wherein the top twenty scores denote a high degree of similarity;
- v) repeating steps (i) to (iv) with different hypothetical biological molecules until a sufficient quantity of scores are selected;
- and determining the frequency of selecting each score and generating therefrom the frequency distribution of scores relating to random identifications;
- and
- d) a means for determining whether the score associated with the experimental biological molecule identification is equal to or larger than the critical score corresponding with the significance level, wherein if the score is equal to or larger than the critical score, the identification of the experimental biological molecule is statistically significant for the selected significance level.
8 more elements
A computer program product comprising:
- a computer usable medium having computer readable program code means embodied in said medium for generating a frequency distribution of scores, wherein the scores relate to random identifications of biological molecules, said computer program product including:
- computer readable program code means for causing a computer to generate mass data for biological molecules in a biological molecule database for a particular experimental condition;
- computer readable program code means for causing the computer to generate mass data of a hypothetical biological molecule for the experimental condition, wherein the hypothetical biological molecule comprises a set of constituent parts, and wherein the set of constituent parts of the hypothetical biological molecule is different from every set of constituent parts of each biological molecule of the database;
- computer readable program code means for causing the computer to compare the mass data of the hypothetical biological molecule with the mass data generated for em biological molecules in the biological molecule database for the particular experimental condition;
- computer readable program code means for causing the computer to calculate a score for each mass data comparison, wherein the score is a function of similarity between the mass data corresponding to a particular database biological molecule and the mass data corresponding to the hypothetical biological molecule;
- computer readable program code means for causing the computer to select a score from the top twenty calculated scores, wherein the selected score corresponds to the comparison which denotes a high degree of similarity between the mass data corresponding to the particular database biological molecule and the mass data corresponding to the hypothetical biological molecule;
- computer readable program code means for causing the computer to repeatedly generate mass data of different hypothetical biological molecules, compare the mass data of the hypothetical molecules with the mass data generated for biological molecules in the biological molecule database, calculate a score for each of the mass data comparisons and select a score from the calculated scores until a sufficient quantity of scores are selected;
- and
- computer readable program code means for causing the computer to determine the frequency of selecting each score and to generate therefrom a frequency distribution of scores.
6 more elements
A computer program product comprising:
- a computer usable medium having computer readable program code means embodied in said medium for identifying an experimental biological molecule for a particular experimental condition and a particular significance level, said computer program product including:
- computer readable program code means for causing a computer to generate mass data of an experimental biological molecule, the experimental biological molecule having been cleaved into constituent parts by a method that produces constituent parts;
- computer readable program code means for causing the computer to compare the mass data of the experimental biological molecule with mass data generated for the experimental condition from biological molecules of a biological molecule database;
- computer readable program code means for causing the computer to calculate scores for each mass data comparison, wherein the scores are a function of similarity between mass data of the experimental biological molecule and mass data generated from the biological molecule database;
- computer readable program code means for causing the computer to select a score from the calculated scores, wherein the selected score corresponds to a particular biological molecule in the biological molecule database, and wherein the selected score corresponds to a comparison which denotes a high degree of similarity;
- computer readable program code means for causing the computer to compare the selected score with a frequency distribution of scores for the experimental condition, wherein the distribution relates to random biological molecule identifications, wherein the frequency distribution has associated therewith a critical score which corresponds to the significance level, and wherein the distribution is generated by:
- i) generating mass data of a hypothetical biological molecule, wherein the hypothetical biological molecule comprises a set of constituent parts, and wherein the set of constituent parts of the hypothetical biological molecule is different from every set of constituent parts of each biological molecule of the database;
- ii) comparing mass data of the hypothetical biological molecule with mass data of biological molecules in the database;
- iii) calculating a score for each comparison, wherein the score is a function of similarity between the mass data of the hypothetical biological molecule and the mass data of the biological molecules in the database;
- iv) selecting a score from the top twenty scores, wherein the top twenty scores denote a high degree of similarity;
- v) repeating steps (i) to (iv) with different hypothetical biological molecules until a sufficient quantity of scores are selected;
- and determining the frequency of selecting each score and generating therefrom the frequency distribution of scores relating to random identifications;
- and
- computer readable program code means for causing the computer to determine whether the selected score is equal to or larger than the critical score.
11 more elements
A computer program product comprising:
- a computer usable medium having computer readable program code means embodied in said medium for determining statistical significance of a biological molecule identification score, said computer program product including:
- computer readable program code means for selecting a significance level that represents a level confidence in a biological molecule identification, wherein the significance level has a corresponding critical score;
- computer readable program code means for causing a computer to calculate a score associated with an experimental biological molecule, wherein the score is a function of similarity between mass data of the experimental biological molecule and mass data generated from a biological molecule database;
- computer readable program code means for causing the computer to compare the score with a score frequency distribution, wherein the frequency distribution relates to random biological molecule identifications, wherein the frequency distribution has associated therewith a critical score which corresponds to the significance level, and wherein the distribution is generated by:
- i) generating mass data of a hypothetical biological molecule, wherein the hypothetical biological molecule comprises a set of constituent parts, and wherein the set of constituent parts of the hypothetical biological molecule is different from every set of constituent parts of each biological molecule of the database;
- ii) comparing mass data of the hypothetical biological molecule with mass data of biological molecules in the database;
- iii) calculating a score for each comparison, wherein the score is a function of similarity between the mass data of the hypothetical biological molecule and the mass data of the biological molecules in the database;
- iv) selecting a score from the top twenty scores, wherein the top twenty scores denote a high degree of similarity;
- v) repeating steps (i) to (iv) with different hypothetical biological molecules until a sufficient quantity of scores are selected;
- and determining the frequency of selecting each score and generating therefrom the frequency distribution of scores relating to random identifications;
- and
- computer readable program code means for causing the computer to determine whether the score associated with the experimental biological molecule identification is equal to or larger than the critical score associated with the significance level,
- wherein if the score is equal to or larger than the critical score, the identification of the experimental biological molecule is statistically significant for the selected significance level.
10 more elements
Dependencies are inferred from the claim text.