Mass shifts and local space charge effects observed in the quadrupole ion trap at higher resolution

Cox, Kathleen; Cleven, Curtis D.; Cooks, R. Graham

doi:10.1016/0168-1176(95)04152-b

Cited by 107 publications

(101 citation statements)

References 30 publications

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“…As expected from published ion/ion rate models, increasing anion density reduces the required reaction duration (43). In practice, however, space charge effects limit the ion capacity of the trap (44). These data indicate that this threshold is reached at an anion AGC target value of ϳ200,000; no apparent reduction in reaction time was observed past this amount.…”

Section: H]supporting

confidence: 53%

Performance Characteristics of Electron Transfer Dissociation Mass Spectrometry

Good

Wirtala

McAlister

et al. 2007

Molecular & Cellular Proteomics

372

398

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We performed a large scale study of electron transfer dissociation (ETD) performance, as compared with ion trap collision-activated dissociation (CAD), for peptides ranging from ϳ1000 to 5000 Da (n ϳ 4000). These data indicate relatively little overlap in peptide identifications between the two methods (ϳ12%). ETD outperformed CAD for all charge states greater than 2; however, regardless of precursor charge a linear decrease in percent fragmentation, as a function of increasing precursor m/z, was observed with ETD fragmentation. We postulate that several precursor cation attributes, including peptide length, charge distribution, and total mass, could be relevant players. To examine these parameters unique ETDidentified peptides were sorted by length, and the ratio of amino acid residues per precursor charge (residues/ charge) was calculated. We observed excellent correlation between the ratio of residues/charge and percent fragmentation. For peptides of a given residue/charge ratio, there is no correlation between peptide mass and percent fragmentation; instead we conclude that the ratio of residues/charge is the main factor in determining a successful ETD outcome. As charge density decreases so does the probability of non-covalent interactions that can bind a newly formed c/z-type ion pair. Recently we have described a supplemental activation approach (ETcaD) to convert these non-dissociative electron transfer product ions to useful c-and z-type ions. Automated implementation of such methods should remove this apparent precursor m/z ceiling. Finally, we evaluated the role of ion density (both anionic and cationic) and reaction duration for an ETD experiment. These data indicate that the best performance is achieved when the ion trap is filled to its space charge limit with anionic reagents. In this largest scale study of ETD to date, ETD continues to show great promise to propel the field of proteomics and, for small-to medium-sized peptides, is highly complementary to ion trap CAD. Electron transfer dissociation (ETD), 1 a relatively new peptide/protein fragmentation method, holds great promise to advance the field of protein mass spectrometry (1-3). As compared with the conventional technique, collision-activated dissociation (CAD), ETD offers a more robust method to characterize post-translational modifications (PTMs) and to interrogate large peptides or even whole proteins (4 -7). Because of these attributes and the fact that it generates c-and z-type products, instead of b-and y-type, many propose that ETD is highly complementary to CAD. ETD reactions, of course, are generally conducted within the confines of ion trap mass spectrometers where sequential CAD and ETD experiments are easily performed. Most proteomics experiments, however, are coupled with on-line chromatographic separations, and analysis time, per peptide, is ideally minimized to increase dynamic range (8). Thus, to extract the most information from a given experiment, knowledge of how these two dissociation techniques complement one another ...

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Section: H]supporting

confidence: 53%

Performance Characteristics of Electron Transfer Dissociation Mass Spectrometry

Good

Wirtala

McAlister

et al. 2007

Molecular & Cellular Proteomics

372

398

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“…In addition, with gated ion injection the mass shift was less severe. Cooks reported variations in peak position in quadruple ion trap mass spectrometry based on the total number of ions inside the trap (27). This shift was explained by local space charge between ions of the same rrdz value and by ion-ion interaction between species separated by large mass difference.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, at this sampling position the tip of the initial radiation zone (IRZ) (25) is about 1-2 mm upstream from the sampling orifice. This is roughly the same sampling position that maximizes ion signal in ICP-MS (26)(27). Thus, ion lines in particular are enhanced at 1.11 rein-l.…”

Section: Methodsmentioning

confidence: 95%

“…Resolution and peak shapes are affected by the mechanical accuracy with which the rods are constructed and mounted (26). In a given quadruple, the resolution is proportional to the square of the number of RF cycles the ions spend inside the rods (27). Thus the resolution can be improved greatly by allowing the ions to stay inside the rods for more cycles.…”

Section: Mass Analyzersmentioning

confidence: 99%

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Development and evaluation of high resolution quadrupole mass analyzer and an inductively coupled plasma-Mach disk

Amad¹

1999

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“…Linear and 3-D ion traps also experience detrimental effects from excessive space charge. These space charge effects lead to shifts in secular frequencies, changes in optimal excitation amplitude, and plasma effects, which can be addressed by controlling the number of ions injected into the ion trap [15][16][17][18][19]. The importance of mass accuracy is apparent in proteomics where, for example, the number of proteolytic fragments needed for a correct identification from a protein database is inversely related to the mass measurement accuracy (MMA) [20].…”

mentioning

confidence: 99%

Automatic gain control in mass spectrometry using a jet disrupter electrode in an electrodynamic ion funnel

Page

Bogdanov

Vilkov

et al. 2005

J. Am. Soc. Mass Spectrom.

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We report on the use of a jet disrupter electrode in an electrodynamic ion funnel as an electronic valve to regulate the intensity of the ion beam transmitted through the interface of a mass spectrometer in order to perform automatic gain control (AGC). The ion flux is determined by either directly detecting the ion current on the conductance limiting orifice of the ion funnel or using a short mass spectrometry acquisition. Based upon the ion flux intensity, the voltage of the jet disrupter is adjusted to alter the transmission efficiency of the ion funnel to provide a desired ion population to the mass analyzer. Ion beam regulation by an ion funnel is shown to provide control to within a few percent of a targeted ion intensity or abundance. The utility of ion funnel AGC was evaluated using a protein tryptic digest analyzed with liquid chromatography Fourier transform ion cyclotron resonance (LC-FTICR) mass spectrometry. The ion population in the ICR cell was accurately controlled to selected levels, which improved data quality and provided better mass measurement accuracy. M ass spectrometry (MS) has become a vital tool in biological research. This information-rich detection method can produce sensitive, qualitative, and quantitative measurements, and provides the basis for characterizing proteins, identifying novel biomarkers, and studying protein interactions within biological networks and pathways. Many challenges in protein analysis stem from sample complexity, e.g., a typical mammalian cell can have protein abundances ranging from less than a few hundred to tens of millions of copies [1]. A focus in MS research continues to be the development of techniques to better handle the broad range of relative abundances from a single sample. Developments have included chemical methods [2][3][4], coupling MS to separation techniques [5,6], and improvements in instrumentation [7][8][9]. An example of the latter is automatic gain control (AGC) [8 -11], first developed by the Finnigan Corporation (now Thermo Electron Corporation) [9]. AGC provides automated regulation to a dynamic ion flux transmitted from the source of the instrument (common in liquid chromatography {LC} coupled MS experiments), resulting in a more constant ion population in the mass analyzer. AGC accomplishes this regulation by monitoring the ion production from the ion source (typically with a pre-scan) and providing on-the-fly adjustments of the ion accumulation time of an ion trap.The regulation or control of the ion population is important to the operation of most mass spectrometers, and particularly those based upon ion trapping where performance is degraded by excessive space charge. For example, a key source of mass error in Fourier transform ion cyclotron resonance (FTICR) MS comes from the effect of excessive space charge [12][13][14]. Linear and 3-D ion traps also experience detrimental effects from excessive space charge. These space charge effects lead to shifts in secular frequencies, changes in optimal excitation amplitude, and plasma e...

show abstract

Mass shifts and local space charge effects observed in the quadrupole ion trap at higher resolution

Cited by 107 publications

References 30 publications

Performance Characteristics of Electron Transfer Dissociation Mass Spectrometry

Performance Characteristics of Electron Transfer Dissociation Mass Spectrometry

Development and evaluation of high resolution quadrupole mass analyzer and an inductively coupled plasma-Mach disk

Automatic gain control in mass spectrometry using a jet disrupter electrode in an electrodynamic ion funnel

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