Non-contiguous regions processing
View Patent ↗Non-contiguous regions of interest as well as contiguous regions of interest are similarly processed. After an isotope peak detector has identified isotope peaks on LC/MS images, a microaligner microaligns bounding areas of identified isotope peaks and redefines the bounding areas to help subsequent scoring process. Forms of isotope peaks influence formation of a peak association matrix and a mass/charge association map which creates association in the mass/charge dimension. A correlation scorer produces reproducibility scores as well as quality scores to help aid scientists to discover biological features of interest.
1. A method comprising:
in a computer, computing a reproducibility score based on a peak association matrix and a mass/charge association map to test whether an isotope cluster, a label set, or a charge group is reproducible, wherein the computing of the reproducibility score comprises generating a three-dimensional array from the peak association matrix and the mass/charge association map, averaging rows of the peak association matrix to generate a first matrix of average vectors, calculating a first matrix of assimilated vectors from intensity values of the peak association matrix, and computing a first correlation coefficient using at least the first matrix of average vectors and the first matrix of assimilated vectors; and
computing a quality score by scoring a transposed peak association matrix together with the mass/charge association map to test whether the isotope cluster, the label set, or the charge group is well formed, wherein the computing of the quality score comprises transposing the peak association matrix to generate the transposed peak association matrix, averaging rows of the transposed peak association matrix to generate a second matrix of average vectors, calculating a second matrix of assimilated vectors from the transposed peak association matrix, and computing a second correlation coefficient using at least the second matrix of average vectors and the second matrix of assimilated vectors.
2. The method of claim 1 , further comprising evaluating whether the reproducibility score indicates that the isotope cluster, the label set, or the charge group is reproducible, and if not reproducible, to caution scientific conclusion based on the isotope cluster, the label set, or the charge group.
3. The method of claim 2 , further comprising reorganizing member isotope peaks of the isotope cluster, the label set, or the charge group to form a different isotope cluster, label set, or charge group, so that the reproducibility score is improved.
4. The method of claim 1 , further comprising evaluating whether the quality score indicates that the isotope cluster, the label set, or the charge group is well formed, and if not well formed, to caution scientific conclusion based on the isotope cluster, the label set, or the charge group.
5. The method of claim 4 , further comprising reorganizing member isotope peaks of the isotope cluster, the label set, or the charge group to form a different isotope cluster, label set, or charge group, so that the quality score is improved.
6. The method of claim 1 , further comprising creating a peak association matrix, each column of the peak association matrix containing one isotope cluster from the label set or charge group if isotope clusters are from a single label set or a single charge group on one LC/MS image.
7. The method of claim 1 , further comprising creating a peak association matrix, each cell of the peak association matrix containing an isotope peak, each column of the peak association matrix containing isotope peaks from one LC/MS image if isotope clusters are from more than one LC/MS image.
8. The method of claim 1 , further comprising creating a mass/charge association map based on the peak association matrix, isotope peaks that have different mass/charge values being associated with each other if the different mass/charge values share the same mapping number.
9. A computer-readable medium not consisting of a signal having computer-executable instructions stored thereon for performing a method, comprising:
computing a reproducibility score based on a peak association matrix and a mass/charge association map to test whether an isotope cluster, a label set, or a charge group is reproducible, wherein the computing of the reproducibility score comprises generating a three-dimensional array from the peak association matrix and the mass/charge association map, averaging rows of the peak association matrix to generate a first matrix of average vectors, calculating a first matrix of assimilated vectors from intensity values of the peak association matrix, and computing a first correlation coefficient using at least the first matrix of average vectors and the first matrix of assimilated vectors; and
computing a quality score by scoring a transposed peak association matrix together with the mass/charge association map to test whether the isotope cluster, the label set, or the charge group is well formed, wherein the computing of the quality score comprises transposing the peak association matrix to generate the transposed peak association matrix, averaging rows of the transposed peak association matrix to generate a second matrix of average vectors, calculating a second matrix of assimilated vectors from the transposed peak association matrix, and computing a second correlation coefficient using at least the second matrix of average vectors and the second matrix of assimilated vectors.
10. The computer-readable medium of claim 9 , further comprising evaluating whether the reproducibility score indicates that the isotope cluster, the label set, or the charge group is reproducible, and if not reproducible, to caution scientific conclusion based on the isotope cluster, the label set, or the charge group.
11. The computer-readable medium of claim 10 , further comprising reorganizing member isotope peaks of the isotope cluster, the label set, or the charge group to form a different isotope cluster, label set, or charge group, so that the reproducibility score is improved.
12. The computer-readable medium of claim 9 , further comprising evaluating whether the quality score indicates that the isotope cluster, the label set, or the charge group is well formed, and if not well formed, to caution scientific conclusion based on the isotope cluster, the label set, or the charge group.
13. The computer-readable medium of claim 12 , further comprising reorganizing member isotope peaks of the isotope cluster, the label set, or the charge group to form a different isotope cluster, label set, or charge group, so that the quality score is improved.
14. The computer-readable medium of claim 9 , further comprising creating a peak association matrix, each column of the peak association matrix containing one isotope cluster from the label set or charge group if isotope clusters are from a single label set or a single charge group on one LC/MS image.
15. The computer-readable medium of claim 9 , further comprising creating a peak association matrix, each cell of the peak association matrix containing an isotope peak, each column of the peak association matrix containing isotope peaks from one LC/MS image if isotope clusters are from more than one LC/MS image.
16. The computer-readable medium of claim 9 , further comprising creating the peak association matrix.
17. The method of claim 1 , further comprising creating the peak association matrix.