Systems and methods for reducing noise from mass spectra

1. A system for quantitatively or qualitatively analyzing a sample based on filtered mass spectrometry data, comprising:

a mass spectrometer that performs a plurality of scans of a sample, producing a plurality of mass spectra; and

a processor that

combines neighboring mass spectra of the plurality of mass spectra into a collection of mass spectra based on sample location, time, or mass,

calculates a background noise estimate for the collection of mass spectra,

filters the collection of mass spectra using the background noise estimate, producing a filtered collection of one or more mass spectra, and

performs quantitative or qualitative analysis using the filtered collection of one or more mass spectra.

2. The system of claim 1 , further comprising a separation device that separates one or more compounds of the sample, wherein the mass spectrometer performs a plurality of scans of the separating sample, producing a plurality of mass spectra scans at different times and wherein the processor combines neighboring mass spectra of the plurality of mass spectra into a collection of mass spectra based on time.

3. The system of claim 1 , wherein the processor combines neighboring mass spectra of the plurality of mass spectra into a collection of mass spectra based on sample location, time, or mass by

combining neighboring precursor ion spectra.

4. The system of claim 1 , wherein the processor combines neighboring mass spectra of the plurality of mass spectra into a collection of mass spectra based on sample location, time, or mass by

combining neighboring product ion spectra.

5. The system of claim 4 , wherein combining neighboring product ion spectra comprises

combining neighboring product ion spectra from a same precursor ion.

6. The system of claim 4 , wherein combining neighboring product ion spectra comprises

combining neighboring product ion spectra from at least two or more different precursor ions.

7. The system of claim 1 , wherein the processor calculates a background noise estimate for the collection of mass spectra using time-frequency analysis.

8. The system of claim 1 , wherein the processor calculates a background noise estimate for the collection of mass spectra by

dividing the collection of mass spectra into two or more windows of mass spectra,

for each window of the two or more windows, combining all spectra within each window producing a combined spectrum for each of the two or more windows, and

for each combined spectrum of the two or more windows

(a) estimating a noise spectrum corresponding to background noise in the each combined spectrum and

(b) repeating step (a) one or more additional times to generate a modified noise spectrum for the each combined spectrum.

9. The system of claim 8 , wherein the processor filters the collection of mass spectra using the background noise estimate by

subtracting each modified noise spectrum for the each combined spectrum from the each combined spectrum, generating a filtered spectrum for each of the two or more windows and

assembling the plurality of filtered spectra of the two or more windows into a single spectrum for the plurality of intervals.

10. The system of claim 8 , wherein the processor filters the collection of mass spectra using the background noise estimate by

subtracting each modified noise spectrum for the each combined spectrum from each spectrum of the combined spectrum, generating a collection of filtered spectra, wherein each filtered spectrum of the collection of filtered spectra corresponds to a spectrum of the collection of mass spectra.

11. The system of claim 8 , wherein the processor calculates a background noise estimate for the collection of mass spectra by

calculating an adjusted background noise estimate for each scan of the plurality of scans from a moving average of modified noise spectra from the two or more windows.

12. The system of claim 8 , wherein the processor calculates a background noise estimate for the collection of mass spectra by

calculating an adjusted background noise estimate for each scan of the plurality of scans from an interpolation of modified noise spectra from the two or more windows.

13. The system of claim 8 , wherein step (a) comprises the steps of:

A) affecting a transformation of the each combined spectrum into the frequency domain to obtain an original frequency spectrum;

B) identifying at least one dominant frequency in the original frequency spectrum;

C) generating a noise frequency spectrum by selectively filtering for said at least one dominant frequency; and

D) determining the modified noise spectrum by affecting a transformation of the noise frequency spectrum into the mass domain.

14. The system of claim 13 , wherein the each combined spectrum comprises a plurality of original intensity data points and wherein the modified noise spectrum comprises a plurality of noise intensity data points such that each noise intensity data point correlates to an original intensity data point, step (a) of the method further comprising the following step:

E) for each correlated pair of original and noise intensity data points: (i) determining the minimum value; and (ii) modifying the modified noise spectrum by making the noise intensity data point equal to the minimum value.

15. The system of claim 14 , step (a) further comprising the following steps:

F) affecting a transformation of the modified noise spectrum modified in step (E) into the frequency domain to obtain a noise frequency spectrum;

G) identifying at least one dominant frequency in the noise frequency spectrum;

H) modifying the noise frequency spectrum by selectively filtering for said at least one dominant frequency; and

I) determining the modified noise spectrum by affecting a transformation of the noise frequency spectrum into the mass domain.

16. The system of claim 15 , step (b) further comprising the following step:

J) repeating step (E) utilizing the modified noise spectrum determined in step (I).

17. The system of claim 16 , further comprising repeating steps (F) through (J) inclusively.

18. The system of claim 17 , further comprising the step of segmenting the each combined spectrum into a plurality of initial windows prior to step A, and separately affecting steps A through D inclusive for each initial window.

19. The system of claims claim 18 , further comprises the step of segmenting the modified noise spectrum into a plurality of subsequent windows prior to step F, and separately affecting steps F through I inclusive for each subsequent window.

20. The system of claim 19 , wherein the subsequent windows are configured such that no subsequent window is coextensive with any initial window.

21. The system of claim 20 , further comprising the step of subsequent to step J, for each repeat of steps G through J, segmenting the modified noise spectrum into a plurality of new windows prior to step G, and separately affecting steps G through J inclusive for each new window, and wherein the new windows are configured such that no new window is coextensive with any subsequent window.

22. A method for quantitatively or qualitatively analyzing a sample based on filtered mass spectrometry data, comprising:

performing a plurality of scans of a sample, producing a plurality of mass spectra using a mass spectrometer;

combining neighboring mass spectra of the plurality of mass spectra into a collection of mass spectra based on sample location, time, or mass using a processor;

calculating a background noise estimate for the collection of mass spectra using the processor;

filtering the collection of mass spectra using the background noise estimate, producing a filtered collection of one or more mass spectra using the processor, and

performing quantitative or qualitative analysis using the filtered collection of one or more mass spectra using the processor.

23. A computer program product, comprising a non-transitory and tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for quantitatively or qualitatively analyzing a sample based on filtered mass spectrometry data, the method comprising:

providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise a measurement module, a filtering module, and an analysis module;

receiving a plurality of mass spectra produced by a mass spectrometer that performs a plurality of scans of a sample using the measurement module;

calculating a background noise estimate for the collection of mass spectra using the filtering module;

filtering the collection of mass spectra using the background noise estimate, producing a filtered collection of one or more mass spectra using the filtering module, and

performing quantitative or qualitative analysis using the filtered collection of one or more mass spectra using the analysis module.