What is claimed as new and desired to be secured by Letters Patent of United States is:
1. A method for mining mass spectra, comprising:
specifying spectral characteristics of said mass spectra to mine;
specifying a relationship between said spectral characteristics;
searching said mass spectra for portions of said mass spectra which match said spectral characteristics based on said relationship; and
assigning scores to said portions of said mass spectra to indicate a degree of correlation between said portions of said mass spectra and said spectral characteristics.
2. The method of claim 1, wherein said mass spectra are obtained by any one of dissociation and full-scan.
3. The method of claim 1, wherein the step of specifying spectral characteristics includes specifying at least one of a product ion, a loss ion, and an ion series.
4. The method of claim 1, wherein said step of specifying a relationship includes:
identifying each of said spectral characteristics as being one of a primary and a secondary spectral characteristic, said secondary spectral characteristic being linked hierarchically with said primary spectral characteristic and detected only after said primary spectral characteristic is detected.
5. The method of claim 3, wherein said assigning step includes:
calculating a product ion score;
calculating a loss ion score;
calculating an ion series score;
adjusting said product ion, loss ion, or said ion series score if respective said product ion, loss ion, or ion series spectral characteristic is secondary; and
adding said product ion, loss ion, and ion series scores.
6. The method of claim 5, wherein the step of calculating a product ion score includes:
identifying a most abundant ion within a window around said product ion spectral characteristic; and
setting said product ion score as a percentage of total ion current of said identified ion.
7. The method of claim 5, wherein the step of calculating a loss ion score includes:
calculating a loss ion mass per unit charge based on an actual precursor ion mass per unit charge and said loss ion spectral characteristic;
identifying a most abundant ion within a window around said calculated loss ion mass per unit charge; and
setting said loss ion score as a percentage of total ion current of said identified ion.
8. The method of claim 5, wherein said step of calculating said ion series score includes:
specifying distances between ions in an ion series as the ion series spectral characteristic;
generating hypothetical ions separated by said specified distances;
aligning said mass spectra with said hypothetical ions;
identifying most abundant ions within respective windows around said aligned mass spectra at said specified distances; and
setting said ion series score as a geometric mean of a percentage of total ion current of said identified ions,
wherein said ion series score includes the following term,
N(I1I2I3 . . . In)1n
where N is a number of said identified ions that correspond to said hypothetical ions and I1In are respective percentages of said total ion current of said identified ions.
9. The method of claim 5, wherein said adjusting step includes:
setting said secondary spectral characteristic score as a geometric mean of a primary spectral characteristic score and said secondary spectral characteristic score,
wherein said secondary spectral characteristic score does not exceed said primary spectral characteristic score to which said secondary spectral characteristic score is linked.
10. The method of claim 1, further comprising:
preprocessing said mass spectra; and
displaying said scores from said assigning step.
11. The method of claim 10, wherein said preprocessing step includes:
subtracting nonfragment ions from said mass spectra;
estimating precursor charge of mass spectra resulting from said subtracting step; and
normalizing ion intensities of mass spectra from said estimating step as a percentage of a total ion current.
12. The method of claim 10, wherein the displaying step includes displaying said scores in one of tabular and graphical form.
13. The method of claim 1, wherein the step of specifying spectral characteristics includes automatically specifying said spectral characteristics based on said mass spectra, and
wherein the step of specifying a relationship includes automatically specifying said relationship based on said mass spectra.
14. The method of claim 1, further comprising:
adjusting control parameters of a device that produces said mass spectra based on said assigned scores.
15. A method for mining collision-induced dissociation (CID) spectra, comprising:
specifying spectral characteristics of said CID spectra to mine;
specifying a relationship between said spectral characteristics;
searching said CID spectra for portions of said CID spectra which match said spectral characteristics based on said relationship; and
assigning scores to said portions of said CID spectra to indicate a degree of correlation between said portions of said CID spectra and said spectral characteristics.
16. The method of claim 15, wherein the step of specifying spectral characteristics includes specifying at least one of a product ion, a loss ion, and an ion series.
17. The method of claim 15, wherein said step of specifying a relationship includes:
identifying each of said spectral characteristics as being one of a primary and a secondary spectral characteristic, said secondary spectral characteristic being linked hierarchically with said primary spectral characteristic and detected only after said primary spectral characteristic is detected.
18. The method of claim 16, wherein said assigning step includes:
calculating a product ion score;
calculating a loss ion score;
calculating an ion series score;
adjusting said product ion, loss ion, or said ion series score if respective said product ion, loss ion, or ion series spectral characteristic is secondary; and
adding said product ion, loss ion, and ion series scores.
19. The method of claim 18, wherein the step of calculating a product ion score includes:
identifying a most abundant ion within a window around said product ion spectral characteristic; and
setting said product ion score as a percentage of total ion current of said identified ion.
20. The method of claim 18, wherein the step of calculating a loss ion score includes:
calculating a loss ion mass per unit charge based on an actual precursor ion mass per unit charge and said loss ion spectral characteristic;
identifying a most abundant ion within a window around said calculated loss ion mass per unit charge; and
setting said loss ion score as a percentage of total ion current of said identified ion.
21. The method of claim 18, wherein said step of calculating said ion series score includes:
specifying distances between ions in an ion series as the ion series spectral characteristic;
generating hypothetical ions separated by said specified distances;
aligning said CID spectra with said hypothetical ions;
identifying most abundant ions within respective windows around said aligned CID spectra at said specified distances; and
setting said ion series score as a geometric mean of a percentage of total ion current of said identified ions,
wherein said ion series score includes the following term,
N(I1I2I3 . . . In)1n
where N is a number of said identified ions that correspond to said hypothetical ions and I1In are respective percentages of said total ion current of said identified ions.
22. The method of claim 18, wherein said adjusting step includes:
setting said secondary spectral characteristic score as a geometric mean of a primary spectral characteristic score and said secondary spectral characteristic score,
wherein said secondary spectral characteristic score does not exceed said primary spectral characteristic score to which said secondary spectral characteristic score is linked.
23. The method of claim 15, further comprising:
preprocessing said CID spectra; and
displaying said scores from said assigning step.
24. The method of claim 23, wherein said preprocessing step includes:
subtracting nonfragment ions from said CID spectra;
estimating precursor charge of CID spectra resulting from said subtracting step; and
normalizing ion intensities of CID spectra from said estimating step as a percentage of a total ion current.
25. The method of claim 23, wherein the displaying step includes displaying said scores in one of tabular and graphical form.
26. The method of claim 15, wherein the step of specifying spectral characteristics includes automatically specifying said spectral characteristics based on said CID spectra, and
wherein the step of specifying a relationship includes automatically specifying said relationship based on said CID spectra.
27. The method of claim 15, further comprising:
adjusting control parameters of a device that produces said CID spectra based on said assigned scores.
28. A system for mining mass spectra, comprising:
means for specifying spectral characteristics of said mass spectra to mine;
means for specifying a relationship between said spectral characteristics;
means for searching said mass spectra for portions of said mass spectra which match said spectral characteristics based on said relationship; and
means for assigning scores to said portions of said mass spectra to indicate a degree of correlation between said portions of said mass spectra and said spectral characteristics.
29. The system of claim 28, wherein said mass spectra are obtained by any one of dissociation and full-scan.
30. The system of claim 28, further comprising:
means for preprocessing said mass spectra; and
means for displaying said scores from said assigning means.
31. The system of claim 28, wherein the means for specifying spectral characteristics includes means for automatically specifying said spectral characteristics based on said mass spectra, and
wherein the means for specifying a relationship includes means for automatically specifying said relationship based on said mass spectra.
32. The system of claim 28, further comprising:
means for adjusting control parameters of a device that produces said mass spectra based on said assigned scores.
33. A system comprising:
a memory device having embodied therein mass spectra; and
a processor in communication with the memory device, the processor configured to
specify spectral characteristics of said mass spectra to identify,
specify a relationship between said spectral characteristics,
search said mass spectra for portions of said mass spectra which match said spectral characteristics based on said relationship, and
assign scores to said portions of said mass spectra to indicate a degree of correlation between said portions of said mass spectra and said spectral characteristics.
34. A computer program product including a computer readable medium for mining mass spectra, comprising:
a graphical user interface code configured to allow a user to input spectral characteristics to mine and specify a relationship between said spectral characteristics; and
a mining code configured to search said mass spectra for portions of said mass spectra matching said spectral characteristics based on said relationship and assign scores to said portions of said mass spectra to indicate a degree of correlation between said portions of said mass spectra and said spectral characteristics.
35. The computer program product of claim 34, wherein said mass spectra are obtained by any one of dissociation and full-scan.
36. The computer program product of claim 34, wherein the graphical user interface code is configured to accept at least one of a product ion, a loss ion, and an ion series as an input,
identify said spectral characteristics as being one of a primary and a secondary spectral characteristic, and
link said secondary spectral characteristic with said primary spectral characteristic such that said secondary spectral characteristic is detected only after said primary spectral characteristic is detected.
37. The computer program product of claim 34, wherein the graphical user interface code comprises:
a control window configured to input the spectral characteristics and the relationship between said spectral characteristics of said mass spectra; and
a results window configured to display said scores of said mass spectra.
38. The computer program product of claim 36, wherein the mining code is configured to
calculate a product ion score,
calculate a loss ion score,
calculate an ion series score,
adjust said product ion, loss ion, or said ion series score if respective said product ion, loss ion, or ion series spectral characteristic is secondary, wherein said secondary spectral characteristic score does not exceed said primary spectral characteristic score to which said secondary spectral characteristic score is linked, and
add said product ion, loss ion, and ion series scores.
39. The computer program product of claim 38, wherein said mining code is further configured to
calculate the product ion score by identifying a most abundant ion within a window around said product ion spectral characteristic and setting said product ion score as a percentage of total ion current of said identified ion,
calculate the loss ion score by calculating a loss ion mass per unit charge based on an actual precursor ion mass per unit charge and said loss ion spectral characteristic, identifying a most abundant ion within a window around said calculated loss ion mass per unit charge, and setting said loss ion score as a percentage of total ion current of said identified ion, and
calculate the ion series score by specifying distances between ions in an ion series as the ion series spectral characteristic, generating hypothetical ions separated by said specified distances, aligning said mass spectra with said hypothetical ions, identifying most abundant ions within respective windows around said aligned mass spectra at said specified distances, and setting said ion series score as a geometric mean of a percentage of total ion current of said identified ions,
wherein said ion series score includes the following term,
N(I1I2I3 . . . In)1n
where N is a number of said identified ions that correspond to said hypothetical ions and I1In are respective percentages of said total ion current of said identified ions.
40. The computer program product of claim 34, further comprising:
a preprocessing code configured to process said mass spectra prior to mining in order to remove spurious mass spectra.
41. The computer program product of claim 40, wherein the preprocessing code is configured to
subtract nonfragment ions from said mass spectra,
estimate precursor charge of mass spectra resulting from said subtracting step, and
normalize ion intensities of mass spectra from said estimating step as a percentage of a total ion current.
42. The computer program product of claim 37, wherein the graphical user interface code further comprises:
a product ion window configured to input said product ion spectral characteristic;
a loss ion window configured to input said loss ion spectral characteristic; and
an ion series window configured to input said ion series spectral characteristic,
wherein said product ion, loss ion, and ion series windows open when respective said spectral characteristics are selected in said control window.
43. The computer program product of claim 37, wherein said results window displays said scores in one of tabular and graphical form.
44. The computer program product of claim 34, wherein the graphical user interface code is configured to accept automatically specified said spectral characteristics and said relationship based on said mass spectra.
45. The computer program product of claim 34, further comprising:
a control code configured to adjust control parameters of a device which generates said mass spectra based on said assigned scores.
46. A computer readable medium containing program instructions for execution on a computer system, which when executed by the computer system, cause the computer system to perform the method recited in any one of claims 1 through 14.
47. A graphical user interface, comprising:
a control window configured to input spectral characteristics and a relationship between said spectral characteristics of mass spectra; and
a results window configured to display scores of said mass spectra indicating how well said mass spectra match said spectral characteristics.
48. The graphical user interface of claim 47, wherein said results window displays said scores in one of tabular and graphical form.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
1. A spread spectrum clock generator comprising:
a phase comparator configured to detect a phase difference between a reference input clock signal and a feedback signal and output a control voltage in line with the phase difference;
a voltage controlled oscillator configured to generate an output clock signal with a frequency in line with the control voltage;
a phase selector configured to equally divide one cycle of the output clock signal into a predetermined number of phases and select any of the phases, generate a phase shift clock signal having a rising edge at the selected phase, and transmit the phase shift clock signal to the phase comparator as the feedback signal;
a phase controller configured to
decide a phase of the rising edge of the phase shift clock signal so that the phase shift clock signal has a cycle different from the cycle of the output clock signal by a first phase shift amount and control the phase selector to select the decided phase, and
generate a second phase shift amount which cyclically varies in a predetermined range, decide the rising edge of the phase shift clock signal to add the second phase shift amount to the first phase shift amount and subject the output clock signal to spread spectrum modulation by the cyclically varying second phase shift amount.
2. A spread spectrum clock generator according to claim 1, wherein
the phase controller is configured to discretely change the second phase shift amount by repeatedly switching phase shift amounts before and after the change so that the changed phase shift amount is gradually increased.
3. A spread spectrum clock generator according to claim 1, wherein
the spread spectrum clock generator operates as a fractional PLL circuit by varying the cycle of the phase shift clock signal from that of the output clock signal by the first phase shift amount.
4. A spread spectrum clock generator according to claim 1, further comprising
a frequency divider configured to divide the phase shift clock signal to transmit the divided phase shift clock signal as the feedback signal to the phase comparator.
5. A spread spectrum clock generator according to claim 1, wherein
the phase controller is configured to decide the phase of the rising edge of the phase shift clock signal so that the phase shift clock signal has a cycle different by a predetermined phase shift amount from that of a predetermined number of clocks of the output clock signals.