JP4806182B2 - Mass spectrometer - Google Patents

Description

  The present invention relates to a mass spectrometer and a mass spectrum measuring method.

  In the mass spectrum, background chemical noise can be particularly problematic. Background chemical noise observed in mass spectra is often periodic in nature, especially when the mass to charge ratio is less than 1000. As can be understood by those skilled in the art, all elements have a mass that is approximately an integer. Carbon-only graphite, by definition, has a mass of 12 that is exactly an integer. And for all other atoms with the same nominal mass, the exact mass will not be a perfectly exact integer value, but slightly higher than the mass of the corresponding carbon-only graphite Or only low.

  The majority of the excess mass ions formed from organic and biological molecules are saturated hydrocarbons, and the majority of the low mass ions formed from organic and biological molecules are Saturated carbon bromide. Saturated hydrocarbons have a mass excess of about 0.1%. Therefore, a saturated hydrocarbon with a nominal mass of 100 has an accurate mass of about 100.1, and similarly, a saturated hydrocarbon with a nominal mass of 200 has an accurate mass of about 200.2 . Saturated carbon bromide has a mass deficiency of about 0.1%. Therefore, a saturated carbon bromide with a nominal mass of 100 has an accurate mass of about 99.9, and similarly, a saturated carbon bromide with a nominal mass of 200 has an accurate mass of about 199.8. Have As a result, a charge number 1 ion with a nominal mass of 200 is expected to have its exact mass within a relatively narrow mass to charge ratio range of 199.8 to 200.2. Similarly, a charge number 1 ion with a nominal mass of 201 is expected to have its exact mass within a similarly narrow mass to charge ratio range of 200.8 to 201.2. Thus, it is recognized that no charge number 1 ions with an accurate mass in the range of 200.2 to 200.8 will be observed. Therefore, at relatively low mass-to-charge ratios, chemical background noise in the mass spectrum (mainly charge number 1) shows a distinct periodicity of approximately 1 atomic mass unit (amu) in a typical example. .

For ions with a charge number of 1 with a mass-to-charge ratio of 500 or more, the forbidden exact mass range is theoretically reduced to zero, and hence chemical background noise is approximately 1 atomic mass. It is expected that the unit will no longer exhibit periodicity. However, in practice, saturated hydrocarbons and saturated carbon bromides are rarely encountered when mass analyzing biochemical samples such as proteins and peptides. Therefore, chemical background noise in mass spectra for biochemistry or biomolecules generally exhibits a distinct periodicity of approximately 1 atomic mass unit when the mass-to-charge ratio exceeds 500.
In fact, mass spectra generally show a distinct periodicity of approximately one atomic mass unit up to a mass to charge ratio of 2000 or less, and periodic background noise can, under certain conditions, cause mass to charge. It can also be observed when the charge ratio exceeds 2000.

  Most non-halogenated organic molecules have a mass excess in the range of 0.0% to 0.1%. Therefore, assuming that no halogenated compound is present, it is expected that chemical background noise can still be expected to have a periodicity of approximately 1 atomic mass unit, up to a mass to charge ratio of 1000 or less. In fact, when an ion derived from a biomolecule having a mass-to-charge ratio of about 2000 or less is mass-analyzed, chemical background noise having a periodicity of about 1 atomic mass unit is generally observed. .

  Due to the presence of chemical background noise, the detection limits of many mass spectrometry techniques are limited or defective. The actual nature of background noise is often unknown, and the presence of undesirable chemical background noise is particularly important when the analyte signal is not completely analyzed depending on the chemical background noise. May adversely affect measurement accuracy.

  Chemical background noise can be due, for example, to impurities in the solvent, analyte or reagent. Impurities in the drying or atomizing gas can also cause chemical background noise. Contamination of the solution or analyte transport system, or contamination on or on the ionization chamber can be an additional source of chemical background noise.

  Atmospheric Pressure Ionisation ("API") ion source, eg Electrospray ("ESI"), Photo Ionisation ("APPI") or Atmospheric Chemical Ionisation ("APCI") ions At the source or the like, a chemical background can be created by clustering of solvent and analyte ions. In a chemical ionization (“CI”) ion source, the chemical background can be due to self-addition of reagent gas ions or contamination of the reagent gas. In a Matrix Assisted Laser Desorption Ionisation ("MALDI") ion source, the chemical background can be attributed to cluster ions in the matrix.

  In general, chemical background noise observed in mass spectra is complex in nature and can only be partially analyzed. Chemical background noise is charged with a charge number of 1 and tends to have a periodic nature of repeating units of about 1 atomic mass unit. Amino acids have a mass excess that varies from about 1.00009 to about 1.00074, with an average mass excess of about 1.00047. Therefore, biological samples generally exhibit a periodicity of about 1.005 atomic mass units (Dalton).

  A known way to reduce the effects of periodic background chemical noise in the mass spectrum is to convert the mass spectrum to the frequency domain and then filter out the noise component. Subsequently, the signal in the converted spectrum that is considered to represent noise is removed at the calculated specific frequency. Subsequently, an inverse transform is applied to the transformed spectrum in order to reproduce a mass spectrum that exhibits reduced periodic background noise.

  Non-sinusoidal periodic noise will appear as a series of sharp spikes and harmonics in the frequency domain or transformed spectrum. However, ion signals tend to be smeared over a relatively wide range of frequencies due to their relatively low degree of mass-to-charge ratio. Different characteristics of signal and noise in the frequency domain or transformed spectrum can theoretically be used at least to reduce the contribution of chemical background noise to the entire spectrum. However, one problem with frequency domain filtering is that the raw time-of-flight mass spectral data can include equally spaced intensity data in time, depending on the acquired electronics. Since the time of flight in a time-of-flight mass analyzer is proportional to the square root of the mass-to-charge ratio of ions, the intensity data can be spaced at uneven mass-to-charge ratios. Therefore, prior to filtering the data in the frequency domain or transformed spectrum, it is of primary importance to process the mass spectral data so that the mass data to charge ratio of the intensity data is more evenly spaced. is there. It is known to use an interpolation algorithm to process intensity data such that the mass to charge ratio of the data is equally spaced. Unfortunately, however, the use of an interpolation algorithm significantly increases the overall processing time.

  In addition to increasing the total processing time, a known method of reducing periodic noise in the mass spectrum by filtering data in the frequency domain is that a filter for removing noise components on the frequency domain data is actually applied. Has the disadvantage that it can cause the presence of additional noise and discontinuities in the mass spectrum after converting the data in the frequency domain back into the mass to charge ratio domain. As a result, artifacts or pseudo peaks that do not exist in the original mass spectrum data may appear in the final processed mass spectrum.

  Another problem with known frequency domain filtering methods is that the percentage of the desired analyte signal may have a frequency component that is similar or identical to the frequency component corresponding to the unwanted background noise. Therefore, removal of such components in the frequency domain leads to distortions in both analyte ion peak shape and analyte signal intensity in the final processed mass spectrum.

  A further problem with known frequency domain filtering methods is the response to changes in background noise characteristics as a function of mass to charge ratio. Background noise observed in a mass spectrum often has different properties in different parts of the mass spectrum. That is, the background noise is often observed to change as a function of mass to charge ratio. If a filter therefore needs to change shape as a function of mass-to-charge ratio in response to changes in the nature of the background noise, the mass spectrum is firstly divided into several separate Each of which must subsequently be processed or filtered in a slightly different manner. However, if a complex mass spectrum is later reconstructed from separate parts of the data, discontinuities can now occur.

  It is therefore clear that the known frequency domain filtering methods have a number of problems as disadvantages.

  Accordingly, it would be desirable to provide an improved method for reducing the effects of background chemical noise in the mass spectrum and in particular reducing the effects of background chemical noise having periodic properties.

The present invention
Determining an intensity distribution from a plurality of different regions or portions of the mass spectral data or mass spectrum;
From the intensity distribution, evaluating a background intensity for the mass spectral data or one or more regions or portions of the mass spectrum; and
Adjusting the intensity of one or more regions or portions of the mass spectral data or the mass spectrum to remove or reduce the effect of the estimated background intensity;
A mass spectrometric method is provided.

  The plurality of regions or portions in the mass spectrum data or the mass spectrum are preferably separated discontinuous regions or portions. However, according to a less preferred embodiment, the mass spectrum data or the plurality of regions or portions in the mass spectrum may be substantially continuous regions or portions.

  (I) 0-0.1 amu; (ii) 0.1-0.2 amu; (iii) 0.2-0.3 amu; (iv) 0.3-0.4 amu; (v ) 0.4-0.5 amu; (vi) 0.5-0.6 amu; (vii) 0.6-0.7 amu; (viii) 0.7-0.8 amu; (ix) 0.8-0.9 amu; (x) 0.9-1.0 amu; (xi) 1.0 -1.1 amu; (xii) 1.1-1.2 amu; (xiii) 1.2-1.3 amu; (xiv) 1.3-1.4 amu; (xv) 1.4-1.5 amu; (xvi) 1.5-1.6 amu; (xvii) 1.6-1.7 (xviii) 1.7-1.8 amu; (xix) 1.8-1.9 amu; (xx) 1.9-2.0 amu; and (xxi)> 2.0 amu. According to a preferred embodiment, the mass spectral data or regions or portions of the mass spectrum are: (i) 0.4995-0.4996 amu; (ii) 0.4996-0.4997 amu; (iii) 0.4997-0.4998 amu; (iv) 0.4998-0.4999 amu; (v) 0.4999-0.5000 amu; (vi) 0.5000-0.5001 amu; (vii) 0.5001-0.5002 amu; (viii) 0.5002-0.5003 amu; (ix) 0.5003-0.5004 amu; (x) 0.5004- 0.5005 amu; (xi) 0.9990-0.9991 amu; (xii) 0.9991-0.9992 amu; (xiii) 0.9992-0.9993 amu; (xiv) 0.9993-0.9994 amu; (xv) 0.9994-0.9995 amu; (xvi) 0.9995-0.9996 amu (xvii) 0.9996-0.9997 amu; (xviii) 0.9997-0.9998 amu; (xix) 0.9998-0.9999 amu; (xx) 0.9999-1.0000 amu; (xxi) 1.0000-1.0001 amu; (xxii) 1.0001-1.0002 amu; ( (xxiii) 1.0002-1.0003 amu; (xxiv) 1.0003-1.0004 amu; (xxv) 1.0004-1.0005 amu; (xxvi) 1.0005-1.0006 amu; (xxvii) 1.0006-1.0007 amu; (xxviii) 1.0007-1.0008 amu; (xxix) 1.0008-1.0009 amu; (xxx) 1.0009-1.0010 amu; (xxxi) 0.5 amu; (xxxii) 1.0 amu; and (xxxiii) 1.0005 amu It may have a periodicity that is. The unit amu represents atomic mass unit (Dalton). Periodicity in the range of 0.9990-1.0010 amu may be observed for ions with a charge number of 1, and periodicity in the range of 0.4995-0.5005 amu may be observed for ions with a number of charges of 2.

  (I) 0-0.01 amu; (ii) 0.01-0.02 amu; (iii) 0.02-0.03 amu; (iv) 0.03 -0.04 amu; (v) 0.04-0.05 amu; (vi) 0.05-0.06 amu; (vii) 0.06-0.07 amu; (viii) 0.07-0.08 amu; (ix) 0.08-0.09 amu; (x) 0.09-0.10 (xi) 0.10-0.11 amu; (xii) 0.11-0.12 amu; (xiii) 0.12-0.13 amu; (xiv) 0.13-0.14 amu; (xv) 0.14-0.15 amu; (xvi) 0.15-0.16 amu; (xvii) 0.16-0.17 amu; (xviii) 0.17-0.18 amu; (xix) 0.18-0.19 amu; (xx) 0.19-0.20 amu; and (xxi)> 0.20 amu Is preferred.

  It is preferable to apply an overall mass window to the mass spectrum data or the mass spectrum. The overall mass window preferably includes m nominal mass windows, and m is preferably an integer. According to one embodiment, m may be an even number, for example, m is (i) 2; (ii) 4; (iii) 6; (iv) 8; (v) 10; (vi) 12 ; (vii) 14; (viii) 16; (ix) 18; (x) 20; (xi) 22; (xii) 24; (xiii) 26; (xiv) 28; (xv) 30; (xvi) 32 ; (xvii) 34; (xviii) 36; (xix) 38; (xx) 40; (xxi) 42; (xxii) 44; (xxiii) 46; (xxiv) 48; (xxv) 50; and (xxvi) It may be selected from the group consisting of ≧ 52. According to another more preferred embodiment, m is preferably an odd number. For example, m is (i) 1; (ii) 3; (iii) 5; (iv) 7; (v) 9; (vi) 11; (vii) 13; (viii) 15; (ix) 17; (x) 19; (xi) 21; (xii) 23; (xiii) 25; (xiv) 27; (xv) 29; (xvi) 31; (xvii) 33; (xviii) 35; (xix) 37; (xxi) 39; (xxi) 41; (xxii) 43; (xxiii) 45; (xxiv) 47; (xxv) 49; and (xxvi) ≧ 51.

  According to a less preferred embodiment, m may include a fraction.

  The nominal mass window preferably includes a substantially continuous region or part of the mass spectrum data or the entire mass spectrum. Although less preferred, the nominal mass window may include separate or discontinuous regions or portions in the mass spectral data or the mass spectrum. One or more of the nominal mass windows is (i) 0-0.1 amu; (ii) 0.1-0.2 amu; (iii) 0.2-0.3 amu; (iv) 0.3-0.4 amu; (v) 0.4-0.5 (vi) 0.5-0.6 amu; (vii) 0.6-0.7 amu; (viii) 0.7-0.8 amu; (ix) 0.8-0.9 amu; (x) 0.9-1.0 amu; (xi) 1.0-1.1 amu; (xii) 1.1-1.2 amu; (xiii) 1.2-1.3 amu; (xiv) 1.3-1.4 amu; (xv) 1.4-1.5 amu; (xvi) 1.5-1.6 amu; (xvii) 1.6-1.7 amu; (xviii (Xix) 1.8-1.9 amu; (xx) 1.9-2.0 amu; and (xxi)> 2 amu.

  The nominal mass windows are respectively (i) 0.4995-0.4996 amu; (ii) 0.4996-0.4997 amu; (iii) 0.4997-0.4998 amu; (iv) 0.4998-0.4999 amu; (v) 0.4999-0.5000 amu; (vi ) 0.5000-0.5001 amu; (vii) 0.5001-0.5002 amu; (viii) 0.5002-0.5003 amu; (ix) 0.5003-0.5004 amu; (x) 0.5004-0.5005 amu; (xi) 0.9990-0.9991 amu; (xii) 0.9991 -0.9992 amu; (xiii) 0.9992-0.9993 amu; (xiv) 0.9993-0.9994 amu; (xv) 0.9994-0.9995 amu; (xvi) 0.9995-0.9996 amu; (xvii) 0.9996-0.9997 amu; (xviii) 0.9997-0.9998 amu; (xix) 0.9998-0.9999 amu; (xx) 0.9999-1.0000 amu; (xxi) 1.0000-1.0001 amu; (xxii) 1.0001-1.0002 amu; (xxiii) 1.0002-1.0003 amu; (xxiv) 1.0003-1.0004 amu; (xxv) 1.0004-1.0005 amu; (xxvi) 1.0005-1.0006 amu; (xxvii) 1.0006-1.0007 amu; (xxviii) 1.0007-1.0008 amu; (xxix) 1.0008-1.0009 amu; (xxx) 1.0009-1.0010 amu; (xxxi ) 0.5 amu; (xxxii) 1.0 amu; and (xxxiii) 1.0005 amu.

  It is preferred that some or all of the nominal mass windows are each divided into y channels, where y is preferably (i) 1; (ii) 2; (iii) 3; (iv) 4; (v) 5; (vi) 6; (vii) 7; (viii) 8; (ix) 9; (x) 10; (xi) 11; (xii) 12; (xiii) 13; (xiv) 14; (xv) 15; (xvi) 16; (xvii) 17; (xviii) 18; (xix) 19; (xx) 20; (xxi) 21; (xxii) 22; (xxiii) 23; (xxiv) 24; (xxv) 25; (xxvi) 26; (xxvii) 27; (xxviii) 28; (xxix) 29; (xxx) 30; (xxxi) 31; (xxxii) 32; (xxxiii) 33; (xxxiv) 34; (xxxv) 35; (xxxvi) 36; (xxxvii) 37; (xxxviii) 38; (xxxix) 39; (xl) 40; (xli) 41; (xlii) 42; (xliii) 43; (xliv) 44; (xlv) 45; (xlvi) 46; (xlvii) 47; (xlviii) 48; (xlix) 49; (l) 50; and (li)> 50.

  The step of determining an intensity distribution from a plurality of different regions or portions in the mass spectrum data or mass spectrum preferably comprises the frequency of various intensities in the mass spectrum data or the mass spectrum as one or more of the nominal mass windows. Including determining in one or more of the nth channels above. Preferably n varies from 1 to y.

  From the intensity distribution, the step of evaluating background intensity for one or more regions or portions in the mass spectrum data set or mass spectrum preferably comprises determining x% intensity quantiles from the intensity distribution. Including.

  Preferably, x is (i) 0-5; (ii) 5-10; (iii) 10-15; (iv) 15-20; (v) 20-25; (vi) 25-30; (vii ) 30-35; (viii) 35-40; (ix) 40-45; (x) 45-50; (xi) 50-55; (xii) 55-60; (xiii) 60-65; (xiv) 65-70; (xv) 70-75; (xvi) 75-80; (xvii) 80-85; (xix) 85-90; (xx) 90-95; and (xxi) 95-100 Selected.

  The estimated background intensity preferably includes the x% intensity quantile or a factor thereof.

  The step of adjusting the intensity of one or more regions or portions in the mass spectral data set or mass spectrum to remove or reduce the effect of the estimated background intensity is preferably the mass spectral data. Or subtracting (subtracting) the estimated background intensity or fraction thereof from the one or more regions or portions of the mass spectrum. If the intensity of one or more regions or portions in the mass spectral data set or mass spectrum has one or more negative numbers after subtracting the estimated background intensity or fraction thereof, then The intensity of one or more regions or portions in the mass spectral data set or mass spectrum is adjusted or set to zero or near zero.

  The estimated background intensity or fraction thereof is preferably subtracted from z% of the mass spectral data set or mass spectrum, z is preferably (i) 0-10; (ii) 10-20; iii) 20-30; (iv) 30-40; (v) 40-50; (vi) 50-60; (vii) 60-70; (viii) 70-80; (ix) 80-90; and ( x) Selected from the group consisting of 90-100. The estimated background intensity or fraction thereof is preferably subtracted from the mass spectral data or one or more regions or parts of the mass spectrum.

  The overall mass window is preferably advanced one or more times (or less preferably, but recovered or reprocessed). For example, the overall mass window may be at least 1-10, 10-50, 50-100, 100-150, 150-200, 200-250, 250-300, 300-350, 350-400, 400-450, 450. -500, 500-600, 600-700, 700-800, 800-900, 900-1000, 100-1250, 1250-1500, 1500-1750, 1750-2000, 2000-2250, 2250-2500, 2500-2750 , 2750-3000 or more than 3000 times may be processed forward or collected. According to a preferred embodiment, the overall mass window may be stepped forward or reprocessed in steps of 0.5, 1.0, or 1.0005 atomic mass units (Daltons) or some other amount each time. The overall mass window is (i) 0.4995-0.4996 amu; (ii) 0.4996-0.4997 amu; (iii) 0.4997-0.4998 amu; (iv) 0.4998-0.4999 amu; (v) 0.4999-0.5000 amu; (vi ) 0.5000-0.5001 amu; (vii) 0.5001-0.5002 amu; (viii) 0.5002-0.5003 amu; (ix) 0.5003-0.5004 amu; (x) 0.5004-0.5005 amu; (xi) 0.9990-0.9991 amu; (xii) 0.9991 -0.9992 amu; (xiii) 0.9992-0.9993 amu; (xiv) 0.9993-0.9994 amu; (xv) 0.9994-0.9995 amu; (xvi) 0.9995-0.9996 amu; (xvii) 0.9996-0.9997 amu; (xviii) 0.9997-0.9998 amu; (xix) 0.9998-0.9999 amu; (xx) 0.9999-1.0000 amu; (xxi) 1.0000-1.0001 amu; (xxii) 1.0001-1.0002 amu; (xxiii) 1.0002-1.0003 amu; (xxiv) 1.0003-1.0004 amu; (xxv) 1.0004-1.0005 amu; (xxvi) 1.0005-1.0006 amu; (xxvii) 1.0006-1.0007 amu; (xxviii) 1.0007-1.0008 amu; (xxix) 1.0008-1.0009 amu; (xxx) 1.0009-1.0010 amu; (xxxi It is anticipated that it may be advanced or reprocessed in increments selected from the group consisting of: 0.5 amu; (xxxii) 1.0 amu; and (xxxiii) 1.0005 amu. According to another embodiment, the overall mass window comprises: (i) 0-0.1 amu; (ii) 0.1-0.2 amu; (iii) 0.2-0.3 amu; (iv) 0.3-0.4 amu; (v) 0.4-0.5 amu; (vi) 0.5-0.6 amu; (vii) 0.6-0.7 amu; (viii) 0.7-0.8 amu; (ix) 0.8-0.9 amu; (x) 0.9-1.0 amu; (xi) 1.0- 1.1 amu; (xii) 1.1-1.2 amu; (xiii) 1.2-1.3 amu; (xiv) 1.3-1.4 amu; (xv) 1.4-1.5 amu; (xvi) 1.5-1.6 amu; (xvii) 1.6-1.7 amu (xviii) 1.7-1.8 amu; (xix) 1.8-1.9 amu; (xx) 1.9-2.0 amu; and (xxi)> 2 amu in advance, recovery or translation (preferably It is expected that it may be repeated). According to other embodiments, the overall mass window may be forwarded or retrieved in regular, irregular or random steps or increments.

According to another aspect of the invention,
Means for determining an intensity distribution from a plurality of regions or portions in a mass spectral data set or mass spectrum, in use;
Means for evaluating a background intensity for one or more regions or portions in the mass spectral data set or mass spectrum from the intensity distribution in use; and
Means for adjusting the intensity of one or more regions or portions in the mass spectral data set or mass spectrum to remove or reduce the effect of the estimated background intensity in use;
A mass spectrometer is provided.

  The mass spectrometer preferably comprises: (i) an Electrospray ("ESI") ion source; (ii) an atmospheric pressure chemical ionization ("APCI") ion source; (iii) atmospheric pressure light Ionization (Atmospheric Pressure Photo Ionisation, “APPI”) ion source; (iv) Laser Desorption Ionisation, “LDI” ion source; (v) Inductively Coupled Plasma (“ICP”) ion source; (vi) Electron Impact (“EI”) ion source; (vii) Chemical Ionisation (“CI”) ion source; (viii) Field Ionisation (“FI”) ion source; (ix ) Fast Atom Bombardment (“FAB”) ion source; (x) Liquid Secondary Ion Mass Spectrometry (“LSIMS”) ion source; (xi) Atmospheric Pressure Ionisation , "API") ion source; (xii) Field Desorption, "FD") ion (xiii) Matrix Assisted Laser Desorption Ionisation ("MALDI") ion source; (xiv) Desorption / Ionisation on Silicon ("DIOS") ion source; and (xv) Desorption Desorption Electrospray Ionisation ("DESI") further includes an ion source selected from the group consisting of ion sources.

  The ion source may include a continuous ion source or a pulsed ion source.

  The mass spectrometer preferably further comprises an arranged mass analyzer, preferably the mass analyzer is preferably (i) an orthogonal acceleration time-of-flight mass analyzer; (ii) an axial acceleration time-of-flight mass spectrometer. (Iii) Quadrupole mass analyzer; (iv) Penning mass analyzer; (v) Fourier Transform Ion Cyclotron Resonance ("FTICR") mass analyzer; (vi) 2D or linear A quadrupole ion trap; (vii) a pawl or 3D quadrupole ion trap; and (viii) a magnetic sector mass analyzer.

  The preferred embodiment relates to an adaptive background subtraction method that reduces the effects of periodic chemical background noise in the mass spectrum.

  The preferred method tests the intensity distribution in the local area of the mass spectrum and evaluates the portion of the signal that depends on background noise by statistical analysis. Subsequently, preferably further areas of the mass spectrum are analyzed and the process is preferably repeated. According to the preferred embodiment, the estimated background noise in a particular part or region in the mass spectrum is subtracted from the raw or experimentally obtained mass spectrum data, and the background noise is significantly reduced. Generate a processed mass spectrum. The preferred embodiment is particularly effective in suppressing background noise with periodic properties and background noise that varies with mass to charge ratio.

According to the preferred embodiment, the mass spectral data intensity within the channel range in the central nominal mass window is modified by subtracting an intensity value from the mass spectral data within the specific channel range.
The intensity value to be subtracted is preferably the intensity quantile (eg 45% or 50%) of the intensity recorded in the mass spectral data within the channel corresponding to a plurality of adjacent or adjacent nominal mass windows. is there. A preferred intensity quantile is preferably 45% or 50%, but according to other embodiments, the intensity quantile may be in the range of 10-90%.

  The preferred method is particularly suitable for reducing the effects of background signals having periodic intensity displacements. The preferred embodiment also reduces the effects of the undesired background noise when the background noise exhibits a gradual continuous displacement in intensity compared to the intensity displacement associated with the analyte signal. It is effective. The preferred method also allows automated background subtraction to be performed, and allows mass spectra with significantly improved signal to noise ratios to be generated.

  According to one embodiment of the present invention, the mass spectrum may be divided into a plurality of nominal mass windows, preferably divided into a plurality, for example 1.005 atomic mass units (Daltons). The overall mass window size is preferably chosen to preferably include an odd integer nominal mass window. The overall mass window size is preferably relatively large compared to typical isotope clusters, and is also preferably relatively small compared to low frequency noise wavelengths. According to a particularly preferred embodiment, an overall mass window including 21 nominal mass windows may be used, and the overall mass window width may be 21.0105 Da. Each nominal mass window is preferably 1.0005 Da wide.

  The background noise is preferably evaluated and subsequently subtracted from the mass spectral data in one nominal mass window. Each nominal mass window is preferably divided into y separate channels. The width of each separated channel y is preferably relatively small compared to the width of the noise peak and also preferably relatively large compared to the spacing of the mass spectral data. According to the preferred embodiment, each nominal mass window may be divided into 10 to 20 channels.

  The data in the various nominal mass windows forming the overall mass window can be considered to be folded into y separate channels for each nominal mass window. The intensity quantile Q of data across all the same corresponding channels (ie across all the first, second or nth channels of the nominal mass window) is preferably determined by the fraction x%. The intensity value Q is preferably such that x% of the data in each nth channel of the various nominal mass windows is below the intensity value Q. The intensity quantile is preferably chosen to reject most signals while at the same time allowing most noise. The intensity quantile Q is therefore chosen to represent the noise in the corresponding channel in the central nominal mass window. This background noise is then preferably subtracted from the input or raw mass spectral data for the corresponding channel in the central nominal mass window. This process is then repeated for the other channels in the central nominal mass window. The overall mass window is then preferably advanced, for example to about 1 atomic mass unit, and the process is preferably repeated and preferably repeated multiple times.

  The calculated background distribution may include, for example, data distributed over 20 channels per mass unit, although raw mass spectral data may include more data points per mass unit. good. In the case of time-of-flight data, the number of data points per mass unit will change. The estimated background noise intensity subtracted at a given data point in the original mass spectral data forms the estimated background distribution over one nominal mass window having a width of about 1 atomic mass unit. It may be calculated by interpolation between the 20 data points.

  The preferred method has particular advantages over known frequency domain filtering methods in that the preferred method avoids the generation of artifacts or extra noise spikes in the processed mass spectral data. Such artifacts or extra noise spikes can be particularly problematic when using known frequency domain filtering methods.

  Various embodiments of the invention will now be described with reference to the accompanying drawings, which are merely exemplary.

  FIG. 1A shows a portion of the mass spectrum showing repetitive chemical noise with an overall mass window. The overall mass window includes 9 nominal mass windows, each of which is divided into 10 channels that are superimposed on the portion of the mass spectrum. FIG. 1B shows the intensity distribution of all intensity data taken from all the first channels in the nine nominal mass window shown in FIG. 1A.

  FIG. 2 shows in more detail the central nominal mass window M5 and the immediately adjacent nominal mass windows M4, M6 shown in FIG. 1A, together with the background noise calculated for the majority of the central nominal mass window M5. The inset then shows in more detail an analyte peak having a mass to charge ratio of about 647.6 after background noise removal according to the preferred embodiment.

  FIG. 3A shows a portion of the mass spectrum showing periodic background noise. And FIG. 3B shows the same part of the mass spectrum after the periodic background noise removal according to the preferred embodiment.

  FIG. 4A shows a part of the mass spectrum shown in FIG. 3A in more detail. FIG. 4B shows the same part of the mass spectrum after the periodic background noise removal according to the preferred embodiment. FIG. 4C shows the evaluated periodic background noise subtracted from the raw mass spectrum shown in FIG. 4A.

  FIG. 5A shows a portion of the mass spectrum showing periodic background noise. And FIG. 5B shows the same part of the mass spectrum after the periodic background noise removal according to the preferred embodiment.

  FIG. 6A shows a portion of the mass spectrum showing a slowly continuous periodic background noise. And FIG. 6B shows the same part of the mass spectrum after the gently continuous periodic background noise removal according to the preferred embodiment.

  FIG. 7A shows a part of the mass spectrum shown in FIG. 6A in more detail. And FIG. 7B shows the same portion of the mass spectrum after the gently continuous periodic background noise removal according to the preferred embodiment.

  Hereinafter, an embodiment of the present invention will be described with reference to FIGS. 1A, 1B and 2. However, the embodiments shown and described with reference to FIGS. 1A, 1B and 2 are simplified for the sake of illustration. According to a particularly preferred embodiment, one overall mass window comprising 21 nominal mass windows having a width of 21.0105 atomic mass units (Dalton) and each width being 1.005 atomic mass units (Dalton), Applies to mass spectra. Each nominal mass window is preferably divided into 20 separate channels. However, for illustrative brevity, the embodiments shown and described with reference to FIGS. 1A, 1B and 2 are only 9 atomic mass units wide and each is exactly 1 atomic mass unit (Dalton) wide Relates to the use of smaller overall mass windows, including only 9 nominal mass windows having Again, for illustrative simplicity, each nominal mass window is shown divided into 10 separate channels.

  FIG. 1A shows a portion of the mass spectrum over a mass to charge ratio of 643-652 showing repetitive or periodic chemical background noise. The mass spectrum was obtained using an electrospray ion source and a time-of-flight mass analyzer. An overall mass window having a 9 atomic mass unit width is shown overlaid on the portion of the mass spectrum. The overall mass window includes nine nominal mass windows M1-M9. The nominal mass windows M1-M9 are centered around a central nominal mass window M5 corresponding to a mass-to-charge ratio of 647-648 and surround the periphery. Each of the nine nominal mass windows M1-M9 is further subdivided as ten equal width separated channels aj. In the particular example shown in FIG. 1A, each separate channel covers or includes approximately 15 mass intensity pairs or data points. The mass intensity pair or data point per channel depends on the digitization rate of the acquired electronics and the time of flight of the analyzed ions.

  According to the preferred embodiment, the background signal is evaluated and subsequently subtracted from the raw intensity data corresponding to the first channel M5a in the central nominal mass window M5. The background signal evaluated for the first channel M5a in the central nominal mass window M5 is in the first channel M1a-M9a in all nine nominal mass windows M1-M9 forming the overall mass window or in the first channel M1a. -Calculate by first determining the intensity distribution of the intensity data across all of M9a. The first channels M1a to M9a in the nominal mass windows M1 to M9 are shown as shaded areas in FIG. 1A.

  FIG. 1B is the resulting intensity distribution corresponding to intensity data taken from all of the first channels M1a-M9a in the nine nominal mass windows M1-M9 shown in FIG. 1A, or The representative ones are shown. Overall, the first channel M1a-M9a is formed from, covers or includes about 134 data points or separate intensity measurements. The dotted line indicates the 50% intensity quantile in the indicated intensity distribution. In the particular example shown in FIG. 1B, the 50% intensity quantile is 19. The 50% intensity quantile represents an intensity value in which 50% of the recorded intensity is located below the 50% quantile and 50% of the recorded intensity is located above the 50% quantile. Therefore, 50% of the intensity data in the first channel M1a-M9a in the 9 nominal mass windows M1-M9 shown in FIG. 1A has an intensity value of 19 units or less, and 50% of the intensity data in the entire first channel M1a-M9a in the nominal mass window M1-M9 has an intensity value of 19 units or more. Other embodiments using intensity quantiles other than 50% are also contemplated. For example, an intensity quantile of 45% can be used, with 45% of the intensity data having an intensity that is less than or equal to the 45% intensity quantile. In the particular example shown in FIG. 1B, the 45% intensity quantile will have a value of 18.

  In the particular example shown and described with reference to FIGS. 1A, 1B and 2, the 50% intensity quantile value 19 represents the average intensity of the background signal in the first channel M5a in the central nominal mass window M5. it is conceivable that. The 50% intensity quantile value 19 is therefore preferably subtracted from the intensity values of all raw intensity data that form or fall within the first channel M5a in the central nominal mass window M5. .

  According to one embodiment, if the intensity or intensity value takes a negative or negative value after subtracting the intensity quantile, then preferably the intensity or intensity value is set to zero or more Set or adjust to a value near zero but not preferred.

Once the expected intensity for the background signal in the first channel M5a in the central nominal mass window M5 has been determined, this step is then preferably repeated for the second channel M5b in the central nominal mass window M5. In the same manner, preferably, the 50% intensity quantile is determined for the intensity distribution for the entire intensity data taken from all of the second channels M1b-M9b in the nine nominal mass windows M1-M9. This intensity value is then preferably taken to represent the average intensity in the background signal in the second channel M5b in the central nominal mass window M5.
This new 50% intensity quantile value is then preferably subtracted from the intensity values of all raw intensity data that form or fall within the second channel M5b in the central nominal mass window M5. .

  This step is then repeated again for the third, fourth, fifth, sixth, seventh, eighth and ninth channels M5c-M5j in the central nominal mass window M5, preferably in a similar manner. . As a result, background noise is preferably evaluated over the entire width of the central nominal mass window M5, and the estimated background noise is then preferably, of course, preferably the central nominal mass window M5. Is subtracted from the raw intensity data in all 10 channels M5a-j. According to one embodiment, if the intensity data after subtracting the estimated background noise takes or has a negative value, then preferably the intensity data is set to zero or more. Adjust or set to near zero but not preferred.

  After calculating and preferably subsequently removing the estimated background noise from the raw intensity data for the central nominal mass window M5 for ions having a mass to charge ratio in the range of 647-648, the overall mass window Is then preferably further advanced by about 1 mass unit (or undesirably, but canceled back about 1 mass unit), at which time the overall mass window preferably has a mass of 648-649 Try to center on the range of charge to charge. The above procedure for determining background noise over the previous central nominal mass window and mass-to-charge ratio 647-648 is preferably followed by the new central nominal mass window and the background over mass-to-charge ratio 648-649. Repeat to evaluate ground noise next. The evaluated background noise is then preferably removed from the raw intensity data corresponding to the new central nominal mass window covering a mass to charge ratio in the range of 648-649. The overall mass window is then preferably further advanced by about 1 mass unit (or less preferred, but canceled back about 1 mass unit), and background noise is evaluated, and the evaluation The process of subtracting the background noise that has been performed from the new central nominal mass window is then preferably repeated.

  The steps of determining background noise and subtracting the background noise from a central nominal mass window and then moving forward processing, recovery, translation, or otherwise moving the overall mass window are preferably followed Repeat until the background noise is removed from the region, part or whole of the important mass spectrum. According to one embodiment, the overall mass window is at least 10, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500, 3000, 3500, 4000, May be processed, retrieved or translated 4500 or 5000 times. The overall mass window width preferably maintains the same width, but according to other embodiments, the overall mass window width is increased, decreased, or otherwise stepped, linear, It may be changed randomly or by other methods.

  FIG. 2 shows in more detail the central nominal mass window M5 and the immediately adjacent nominal mass windows M4, M6 shown in FIG. 1A. The background noise calculated for the majority of the central nominal mass window M5 is shown superimposed on the original or raw intensity or mass spectral data. The inset shows in more detail after subtracting the calculated or evaluated background noise from the intensity data for a portion of the central nominal mass window M5. An analyte mass peak with a mass to charge ratio of about 647.6 can be seen more clearly and the signal to noise ratio of the processed mass spectrum is significantly improved.

  FIG. 3A shows a portion of a mass spectrum showing periodic background noise with a periodicity of about 1 atomic mass unit. The mass spectrum was obtained using an electrospray ion source and a time-of-flight mass analyzer. Although an intense analyte peak can be identified, it is difficult to distinguish a relatively weak analyte peak from the periodic background noise. FIG. 3B shows after evaluating the periodic background noise for the same portion of the mass spectrum and subtracting from the intensity data according to the preferred embodiment. In this particular example, the overall mass window applied to the mass spectral data includes 21 nominal mass windows each having a width of 1.005 atomic mass units (Dalton). Each nominal mass window was divided into 20 channels and a 45% intensity quantile was used to distinguish between signal and background noise.

  FIG. 4A shows in more detail a portion of the mass spectrum shown in FIG. 3A over a mass to charge ratio range of 934-956. As can be seen, the intensity of some analyte mass peaks is not significantly greater compared to some peaks derived from periodic background noise. For example, it should be noted that peak recognition software supported analyte peaks with mass-to-charge ratios of 944.7, 953.7 and 955.7 as analyte peaks. However, in reality, those peaks are considered to be peaks derived from background noise. FIG. 4B shows the corresponding mass spectrum after evaluating the periodic background noise and subtracting from the intensity data shown in FIG. 4A. At this time, analyte peaks having mass to charge ratios of 937.5, 938.5, 947.7 and 948.7 can be more clearly recognized as analyte peaks. Further, at this time, among the peaks observed in FIG. 4A, those determined to have mass-to-charge ratios of 944.7, 953.7, and 955.7 are substantially suppressed as background noise. FIG. 4C shows the intensity of periodic background noise calculated or evaluated according to the preferred embodiment for the intensity data shown in FIG. 4A. The background noise shown in FIG. 4C is removed from or otherwise subtracted from the raw mass spectrum data shown in FIG. 4A to produce the improved processed mass spectrum shown in FIG. 4B. I let you.

  FIG. 5A shows a portion of another mass spectrum showing periodic background noise with a periodicity of about 1 atomic mass unit. This mass spectrum was obtained using an electrospray ion source and a time-of-flight mass analyzer. FIG. 5B shows the resulting mass spectrum after calculating or evaluating the periodic background noise and subtracting from the intensity data according to the preferred embodiment. To this mass spectral data, an overall mass window including 21 nominal mass windows each having a width of 1.005 atomic mass units (Dalton) was applied. Each nominal mass window was divided into 20 channels and a 45% intensity quantile was used to distinguish signal and background. As can be seen in FIG. 5B, the periodic background noise is strongly suppressed, and the signal-to-noise ratio is significantly increased or improved.

  FIG. 6A shows a mass spectrum of tryptic protein digestion products ionized with a matrix assisted laser desorption ionization ion source and mass analyzed with an axial time-of-flight mass analyzer. This mass spectrum shows both slowly changing background noise and periodic background noise (as can be seen more clearly in FIG. 7A). FIG. 6B shows the resulting mass spectrum after calculating or evaluating the slowly changing background noise and the periodic background noise and subtracting from the intensity data according to the preferred embodiment. . To this mass spectral data, an overall mass window including 21 nominal mass windows each having a width of 1.005 atomic mass units (Dalton) was applied. Each nominal mass window was divided into 20 channels and a 45% intensity quantile was used to distinguish signal and background.

  FIG. 7A shows in more detail a portion of the mass spectrum shown in FIG. 6A, over a range of mass to charge ratios 1754-1789. FIG. 7B shows the resulting mass spectrum after evaluating the slowly changing background noise and the periodic background noise and subtracting from the intensity data, according to the preferred embodiment. As can be seen in FIG. 7B, the background noise is strongly suppressed and the signal to noise ratio is significantly improved.

  The preferred embodiment is particularly useful for reducing the undesirable effects of chemical background noise having a periodicity of about 1 atomic mass unit, typically observed in mass spectra at a mass to charge ratio of less than 2000. It is effective. Other embodiments also have different widths, particularly if the background noise in the mass spectrum exhibits a periodicity other than about 1 atomic mass unit, and / or if the background noise exhibits more complex properties. It is contemplated that a nominal mass window and / or a nominal mass window with a different number of channels per channel can be used.

In addition, embodiments are contemplated that intend to filter out background noise having two or more characteristic repetition periods.
According to such an embodiment, the overall mass window format applied to the mass spectrum is such that, for example, only the mass spectral data in the odd, even or all nth nominal mass windows determines the background noise. Modifications may be made or changed so that they are sampled. Further contemplated are embodiments in which the width of each nominal mass window may have a value other than 1, for example 0.5 atomic mass units, or some other numerical value.

  According to another embodiment, in order to speed up processing time, intensities within one or more channels in a nominal mass window may be averaged prior to calculating the desired intensity quantile.

  As described above, the intensity data after subtracting the intensity quantile can be determined as having a negative numerical value. In such an environment, the intensity data is then preferably set or adjusted to zero or near zero.

  Although the invention has been described with reference to preferred embodiments, those skilled in the art will recognize that various changes in form and detail may be made without departing from the scope of the invention as set forth in the appended claims. It is.

A portion of the mass spectrum showing repetitive chemical noise is shown with an overall mass window. It shows the intensity distribution of all intensity data taken from all the first channels in the nine nominal mass window shown in FIG. 1A. The nominal mass windows M4, M5, M6 shown in FIG. 1A are shown in more detail. A portion of the mass spectrum showing periodic background noise is shown. Figure 2 shows the same part of the mass spectrum after periodic background noise removal. A part of the mass spectrum shown in FIG. 3A is shown in more detail. Figure 2 shows the same part of the mass spectrum after periodic background noise removal. 4B shows periodic background noise subtracted from the mass spectrum shown in FIG. 4A. A portion of the mass spectrum showing periodic background noise is shown. Figure 2 shows the same part of the mass spectrum after periodic background noise removal. A portion of the mass spectrum showing a slowly continuous periodic background noise is shown. Figure 2 shows the same part of the mass spectrum after periodic background noise removal. Part of the mass spectrum shown in FIG. 6A is shown in more detail. Figure 2 shows the same part of the mass spectrum after periodic background noise removal.

Claims (23)

Superimposing an overall mass window containing an integer number of nominal mass windows over a plurality of different regions or portions of experimentally obtained mass spectral data or mass spectra;
Dividing some or all of the m nominal mass windows into integer y channels;
The mass spectral data or the mass spectrum obtained experimentally in one or more of the nth channels of one or more of the nominal mass windows or over one or more of the nth channels. Determining the intensity distribution by determining the distribution of intensity data for
By selecting the intensity value Q representing the ratio of the intensity data due to background noise, from the determined intensity distribution, to assess background intensity for one or more of the n-th channel, and,
In order to eliminate or reduce the influence of the estimated background intensity, from the mass spectral data or an experimentally obtained intensity value of the mass spectrum in one or more of the n th channels, the evaluation A method of mass spectrometry comprising adjusting the intensity in one or more of the n th channel by subtracting the determined background intensity value Q or a fraction thereof . The method of claim 1 , wherein m is an even number. m is (i) 2; (ii) 4; (iii) 6; (iv) 8; (v) 10; (vi) 12; (vii) 14; (viii) 16; (ix) 18; (x ) 20; (xi) 22; (xii) 24; (xiii) 26; (xiv) 28; (xv) 30; (xvi) 32; (xvii) 34; (xviii) 36; (xix) 38; (xx ) 40; (xxi) 42; (xxii) 44; (xxiii) 46; (xxiv) 48; (xxv) 50; and (xxvi) are selected from the group consisting of ≧ 52, the method of claim 2. The method of claim 1 , wherein m is an odd number. m is (i) 1; (ii) 3; (iii) 5; (iv) 7; (v) 9; (vi) 11; (vii) 13; (viii) 15; (ix) 17; (x ) 19; (xi) 21; (xii) 23; (xiii) 25; (xiv) 27; (xv) 29; (xvi) 31; (xvii) 33; (xviii) 35; (xix) 37; (xx ) 39; (xxi) 41; (xxii) 43; (xxiii) 45; (xxiv) 47; (xxv) 49; and (xxvi) are selected from the group consisting of ≧ 51, the method of claim 4. The method according to claim 1 , wherein the nominal mass window includes the mass spectrum data or a continuous region or part of the mass spectrum. The nominal mass window includes the mass spectral data or separate or discrete areas or portions of the mass spectrum, the method according to any one of claims 1 to 5. One or more of the nominal mass windows is (i) 0-0.1 amu; (ii) 0.1-0.2 amu; (iii) 0.2-0.3 amu; (iv) 0.3-0.4 amu; (v) 0.4-0.5 (vi) 0.5-0.6 amu; (vii) 0.6-0.7 amu; (viii) 0.7-0.8 amu; (ix) 0.8-0.9 amu; (x) 0.9-1.0 amu; (xi) 1.0-1.1 amu; (xii) 1.1-1.2 amu; (xiii) 1.2-1.3 amu; (xiv) 1.3-1.4 amu; (xv) 1.4-1.5 amu; (xvi) 1.5-1.6 amu; (xvii) 1.6-1.7 amu; (xviii ) 1.7-1.8 amu; (xix) 1.8-1.9 amu; (xx) 1.9-2.0 amu; and (xxi)> has a width selected from the group consisting of 2 amu, according to any one of claims 1 to 7 the method of. The nominal mass windows are respectively (i) 0.4995-0.4996 amu; (ii) 0.4996-0.4997 amu; (iii) 0.4997-0.4998 amu; (iv) 0.4998-0.4999 amu; (v) 0.4999-0.5000 amu; (vi ) 0.5000-0.5001 amu; (vii) 0.5001-0.5002 amu; (viii) 0.5002-0.5003 amu; (ix) 0.5003-0.5004 amu; (x) 0.5004-0.5005 amu; (xi) 0.9990-0.9991 amu; (xii) 0.9991 -0.9992 amu; (xiii) 0.9992-0.9993 amu; (xiv) 0.9993-0.9994 amu; (xv) 0.9994-0.9995 amu; (xvi) 0.9995-0.9996 amu; (xvii) 0.9996-0.9997 amu; (xviii) 0.9997-0.9998 amu; (xix) 0.9998-0.9999 amu; (xx) 0.9999-1.0000 amu; (xxi) 1.0000-1.0001 amu; (xxii) 1.0001-1.0002 amu; (xxiii) 1.0002-1.0003 amu; (xxiv) 1.0003-1.0004 amu; (xxv) 1.0004-1.0005 amu; (xxvi) 1.0005-1.0006 amu; (xxvii) 1.0006-1.0007 amu; (xxviii) 1.0007-1.0008 amu; (xxix) 1.0008-1.0009 amu; (xxx) 1.0009-1.0010 amu; (xxxi 8. The method of any one of claims 1 to 7 , having a width selected from the group consisting of: 0.5 amu; (xxxii) 1.0 amu; and (xxxiii) 1.0005 amu. y is (i) 1; (ii) 2; (iii) 3; (iv) 4; (v) 5; (vi) 6; (vii) 7; (viii) 8; (ix) 9; (x ) 10; (xi) 11; (xii) 12; (xiii) 13; (xiv) 14; (xv) 15; (xvi) 16; (xvii) 17; (xviii) 18; (xix) 19; (xx ) 20; (xxi) 21; (xxii) 22; (xxiii) 23; (xxiv) 24; (xxv) 25; (xxvi) 26; (xxvii) 27; (xxviii) 28; (xxix) 29; (xxx ) 30; (xxxi) 31; (xxxii) 32; (xxxiii) 33; (xxxiv) 34; (xxxv) 35; (xxxvi) 36; (xxxvii) 37; (xxxviii) 38; (xxxix) 39; (xl ) 40; (xli) 41; (xlii) 42; (xliii) 43; (xliv) 44; (xlv) 45; (xlvi) 46; (xlvii) 47; (xlviii) 48; (xlix) 49; (l The method of claim 1 , selected from the group consisting of: 50) and (li)> 50. The method of claim 1 , wherein n varies from 1 to y. 12. A method according to any preceding claim , wherein the step of evaluating background intensity comprises determining a fraction x% of intensity data due to background noise from the intensity distribution . x is (i) 0-5; (ii) 5-10; (iii) 10-15; (iv) 15-20; (v) 20-25; (vi) 25-30; (vii) 30- 35; (viii) 35-40; (ix) 40-45; (x) 45-50; (xi) 50-55; (xii) 55-60; (xiii) 60-65; (xiv) 65-70 selected from the group consisting of: (xv) 70-75; (xvi) 75-80; (xvii) 80-85; (xix) 85-90; (xx) 90-95; and (xxi) 95-100 The method of claim 12 . If the intensity value of the mass spectral data set or mass spectrum in one or more of the n th channel has a negative numerical value after subtracting the estimated background intensity or fraction thereof, then the n The method of claim 1 , wherein an intensity value of the mass spectral data set or mass spectrum in one or more of the first channels is adjusted or set to zero or near zero. Subtracting the estimated background intensity value Q or fraction thereof from z% of the experimentally obtained intensity value of the mass spectrum data set or mass spectrum in one or more of the n th channels , wherein z is (i) 0-10; (ii) 10-20; (iii) 20-30; (iv) 30-40; (v) 40-50; (vi) 50-60; (vii) 60-70; ( 2. The method of claim 1 selected from the group consisting of viii) 70-80; (ix) 80-90; and (x) 90-100. The overall mass window, one or more times, to translate, further comprising superimposed over another a plurality of different areas or portions of the mass spectral data or the mass spectrum obtained experimentally, claim The method in any one of 1-15 . (I) 0.4995-0.4996 amu; (iii) 0.4997-0.4998 amu; (iv) 0.4998-0.4999 amu; (v) 0.4999-0.5000 amu; (vi ) 0.5000-0.5001 amu; (vii) 0.5001-0.5002 amu; (viii) 0.5002-0.5003 amu; (ix) 0.5003-0.5004 amu; (x) 0.5004-0.5005 amu; (xi) 0.9990-0.9991 amu; (xii) 0.9991 -0.9992 amu; (xiii) 0.9992-0.9993 amu; (xiv) 0.9993-0.9994 amu; (xv) 0.9994-0.9995 amu; (xvi) 0.9995-0.9996 amu; (xvii) 0.9996-0.9997 amu; (xviii) 0.9997-0.9998 amu; (xix) 0.9998-0.9999 amu; (xx) 0.9999-1.0000 amu; (xxi) 1.0000-1.0001 amu; (xxii) 1.0001-1.0002 amu; (xxiii) 1.0002-1.0003 amu; (xxiv) 1.0003-1.0004 amu; (xxv) 1.0004-1.0005 amu; (xxvi) 1.0005-1.0006 amu; (xxvii) 1.0006-1.0007 amu; (xxviii) 1.0007-1.0008 amu; (xxix) 1.0008-1.0009 amu; (xxx) 1.0009-1.0010 amu; (xxxi 17. The method of claim 16 , wherein the translation is with a numerical value selected from the group consisting of: 0.5 amu; (xxxii) 1.0 amu; and (xxxiii) 1.0005 amu. Means for superimposing an overall mass window comprising an integer number of nominal mass windows over a plurality of different regions or portions of experimentally obtained mass spectral data or mass spectrum , in use;
Means for dividing, in use, some or all of the m nominal mass windows into integer y channels;
In use , the experimentally obtained mass spectral data in one or more of the nth channels of one or more of the nominal mass windows, or over one or more of the nth channels, or Means for determining an intensity distribution by determining a distribution of intensity data of the mass spectrum ;
In use, by selecting the intensity value Q representing the ratio of the intensity data due to background noise, from the determined intensity distribution, means for evaluating the background intensity for one or more of the n-th channel ,and,
In use, in order to remove or reduce the effect of the estimated background intensity, from the mass spectral data or the experimentally obtained intensity values of the mass spectrum in one or more of the n th channel Means for adjusting the intensity in one or more of the n th channels by subtracting the estimated background intensity value Q or a fraction thereof ;
Including mass spectrometer. (i) Electrospray ("ESI") ion source; (ii) Atmospheric Pressure Chemical Ionisation ("APCI") ion source; (iii) Atmospheric Pressure Photo Ionisation, "APPI" ) Ion source; (iv) Laser Desorption Ionisation ("LDI") ion source; (v) Inductively Coupled Plasma ("ICP") ion source; (vi) Electron Impact, EI ") ion source; (vii) chemical ionization (" CI ") ion source; (viii) field ionization (" FI ") ion source; (ix) fast atom collision (Fast Atom Bombardment," (X) Liquid Secondary Ion Mass Spectrometry ("LSIMS") ion source; (xi) Atmospheric Pressure Ionisation ("API") ion source; (xii ) Field Desorption ("FD") ion source; (xiii) Matrix-assisted laser desorption ions (Matrix Assisted Laser Desorption Ionisation, "MALDI") ion source; (xiv) Desorption / Ionisation on Silicon, "DIOS" ion source; and (xv) Desorption Electrospray Ionisation, " The mass spectrometer of claim 18 , further comprising an ion source selected from the group consisting of DESI ") ion sources. 20. A mass spectrometer according to claim 18 or 19 , wherein the ion source comprises a continuous ion source. The mass spectrometer according to claim 18 or 19 , wherein the ion source includes a pulsed ion source. The mass spectrometer according to any one of claims 18 to 21 , further comprising a mass analyzer. The mass analyzer comprises: (i) an orthogonal acceleration time-of-flight mass analyzer; (ii) an axial acceleration time-of-flight mass analyzer; (iii) a quadrupole mass analyzer; (iv) a Penning mass analyzer; v) Fourier Transform Ion Cyclotron Resonance ("FTICR") mass spectrometer; (vi) 2D or linear quadrupole ion trap; (vii) Paul or 3D quadrupole ion trap; and ( 23. A mass spectrometer according to claim 22 selected from the group consisting of viii) magnetic sector mass analyzer.

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