fig1 shows a simplified mass spectrometry system 100 in block diagram form . components such as vacuum subsystems , power supplies , and the like are not shown . in operation , sample 110 is introduced into ionizer 120 , producing a group of ions . these ions are fed into analyzer 130 , and then to detector 140 . analyzer 130 may be a device such as a quadrupole analyzer , a time - of - flight analyzer , an ion cyclotron resonance device , or other mass analyzer as is known in the art . detector 140 is typically some form of electron multiplier connected to an analog to digital converter ( adc ) to make its output suitable for use in digital data processing . techniques such as oversampling and low pass filtering may be used in detector 140 to reduce noise . the output of the mass spectrograph detector 140 is a time series of m / z values and abundance values . the task of the analysis portion 200 of the instrument is to take this detector data , extract peak data and assign that data to ions , and match the ions to isotope and charge series , finally producing molecular weights for the uncharged analytes in the sample . this analysis may be performed on the data from a single spectrum , or the data from a number of spectra may be combined . using the data from a number of spectra has the advantage of possibly averaging out errors , while introducing the difficulty of broadening or smearing detail . the data analysis portion 200 comprises a digital computer system in which central bus 210 connects central processing unit ( cpu ) 220 with memory subsystem 230 , display 240 , and additional input / output devices 250 . while fig1 shows the analysis portion 200 of the instrument as part of the overall mass spectrometry system 100 , the analysis portion may be a separate stand alone unit , connected to detector 140 through input / output interfaces known to the art . the instrument deals with the abundance of ion samples in the m / z space . fig2 shows the typical output of detector 140 , with the x axis representing m / z , and the y axis abundance . operating in the m / z space has the practical effect of folding the higher charge state members of a species of ions to lower values in the m / z space . for example , a particular molecule of mass 840 daltons will have its singly charged species at m / z = 841 , the + 2 charged species at m / z = 842 / 2 = 421 , and the + 3 charged species , if present , at m / z = 843 / 3 = 281 . an instrument with high resolving power would be able to resolve the isotope cluster of each ion at any charge state . at the + 1 charge state , isotopes are separated 1 atomic mass units ( amu ) apart . at the + 2 charge state , because the instrument deals with m / z measurements , isotopes are 1 / 2 amu apart in m / z space . for + 3 charge states , isotope spacing is 1 / 3 amu , and so on . this is important as the finite resolving power of the instrument quickly loses the ability to resolve individual isotope peaks at higher charge states . this has the effect of &# 34 ; lumping &# 34 ; the isotopes together , producing a broadened peak . the effects of resolution are shown in fig3 through 5 . a device with high resolution is capable of resolving individual isotope peaks 310 and 330 , where a device with lower resolution may only be capable of resolving the overall envelope 320 . a measurement typically used in the art is peak width at half height ( pwhh ), some times just referred to as peak width . as implied by the name it is the width of an ion at an abundance value half the peak height . for isotope peak 310 of fig3 shows the peak width . for lower resolution peak 320 , the peak width is shown as 350 . the effects of resolution in resolving isotope spacing in multiple charge states are shown in fig6 through 8 . the + 3 charge state of ion in fig6 is resolved into isotopes spaced 1 / 3 amu apart , with the lower resolution instrument only showing the broader envelope 610 . the + 2 charge state of the ion of fig7 may show isotope spacing of 1 / 2 amu in a high resolution instrument , or may just show the overall envelope 710 . fig8 shows this same effect with an ion of charge state + 4 , the lower resolution instrument showing only the broader envelope rather than the individual isotope patterns space 1 / 4 amu apart . while examining isotope spacing is known to the art , this test alone is not sufficient to correctly assign charge state . in mixtures it is possible for ions of different components to mimic the isotopic spacing of a singly charged ion . additional testing , such as the width test or ratio test will detect that these are not isotopes . the first step in the data analysis as shown in fig9 through 12 is to extract peak information from the detector output as shown in fig2 and assign that information to ions . typically , the data is examined in increasing m / z sequence . abundance or intensity values below some noise threshold are discarded . a sequence of data points above the noise threshold are grouped together to form an ion . the data stored with the ion in the preferred embodiment of the invention includes the beginning and ending m / z values for the ion , and an assigned m / z value for the ion . this may be the m / z value with the highest abundance in the ion , or may be a calculated value such as the centroid . extraction of ion sets proceeds based on the list of ions . in the preferred embodiment , each pass of the process begins with the most abundant ion not already belonging to an ion series . one pass will process the entire list of remaining ions before proceeding to the next pass . there are up to three passes done on the list of ions . a pass is made to find all ion series with 1 or more charge states , where resolved isotopes are found for at least one of the charge states . then a pass is made to find all ion series with at least 4 charge states . isotopes are also found if they exist for all ions in each series . the final pass , if the user has specified a minimum of 3 peaks in a set , is to find all ion series with 3 charge states . also find isotopes if they exist for all ions in each series . the remaining residual ions in the list remain available for further analysis . once this processing has been completed , for each ion series , the molecular weight of the uncharged molecule is calculated using the equation m i =( m i - m a ) i for each charge state , where m i = m / z value of ion with charge state i and m a = m / z value of adduct ion . also , the average molecular weight m = 1σm i is calculated . finally , for each ion series , a mass spectrum of the uncharged molecule is reconstructed by transforming each data point in the isotope cluster of the ion at each charge state from the m / z space to the m , or mass , space , and summing the abundance values for each mass value m . from these summed abundance values , the molecular weight of the uncharged peak is calculated using curve fitting or centroids . if possible , ions with low charge states are assigned their charge states prior to deconvolution . in all passes , this is done by looking at the isotope spacing , then verifying that spacing is possible considering the resolution of the instrument and the proposed charge state . the ion width is examined to insure it is consistent with the instrument resolution . finally , the ratio of adjacent isotopes is examined to insure it is consistent with the proposed mass and the likely elemental composition ( the ratio of c , h , n , o , s for peptides , for example ) of the analyte . in all passes , isotopes are found as shown in fig1 by first calculating the isotope spacing for the predicted charge state . isotope spacing is the inverse of charge state ; at a charge state of + 1 , isotopes are spaced 1 amu apart ; at + 2 , 1 / 2 amu apart , at + 3 , 1 / 3 amu apart , and so on . if the instrument is capable of resolving ions at this charge level , a search is made for resolved isotopes , as shown in fig1 . the preferred embodiment searches for resolved isotopes if the instrument pwhh is less than or equal to 0 . 8 time the calculated isotope spacing . if the instrument is capable of resolving some isotope detail at the predicted charge state , a search is made for unresolved isotopes as shown in fig1 . the preferred embodiment searches for unresolved isotopes if the instrument pwhh is less than or equal to twice the calculated isotope spacing . in all passes , if a charge state is assigned to an ion , a search is made for corresponding ions at plus and minus one charge unit . this process is repeated until an ion series is exhausted . each proposed ion in the series is tested for peak width , isotope ratios , and isotope spacing to insure it is consistent with the proposed series . only if all the tested ions fit the series , passing the tests applied , are they considered to be part of a series . once an ion is designated as part of a series , it is removed from the list of ions available for starting a new set . peak width testing , where the peak width is calculated at half the maximum height of the ion is extremely valuable . peak width is used in two types of testing . first , for low charge states where isotopes may be resolved or partially resolved by the instrument , peak width is used to insure the isotope peak width is consistent with the ion peak width . for higher charge states where isotopes are not resolved by the instrument , the ion peak width decreases smoothly as the charge state goes from low to high . this peak width testing may be used to exclude ions that are not truly part of a series . for example , an analyte with a base molecular weight of 1320 would have a + 3 charge ion appearing at a m / z value of 441 , as shown in fig6 . unfortunately , a + 4 charge state of an ion with a base molecular weight of 1760 also has an m / z value of 441 . this is shown in fig8 . where the approach used by fenn would erroneously incorporate this + 4 charge state of the heavier analyte into the series , the difference in peak widths between the + 3 and + 4 charge state analytes , shown in fig6 and 8 , clearly identifies and excludes the + 4 charge state ion from being incorporated . by only marking those ions that pass all the above tests , fewer charge assignment errors are made . molecular weight can be assigned to samples having only one charge state . monomer / dimer pairs can be distinguished from + 1 and + 2 pairs . dimers can be formed in the ionization process when high concentrations of the sample are present ; two molecules of the analyte are non - covalently associated and acquire a proton . this dimer appears with an m / z of twice that of the monomer m / z . without applying these tests , in approaches such as fenn , the monomer is misassigned as a + 2 charge state of the dimer , which is assigned a + 1 . this deconvolves to give an erroneous mass of twice that of the true mass of the monomer . the disclosed invention reports the monomer and the dimer as both singly charged , reporting them as separate sets . the foregoing detailed description of the present invention is provided for the purpose of illustration and is not intended to be exhaustive or to limit the invention to the precise embodiments disclosed . accordingly the scope of the present invention is defined by the appended claims .